All Classes and Interfaces
Class
Description
Feature based on an amino acid identity.
An amino acid identity feature at a fixed position on the peptide sequence.
An amino acid identity feature at a position relative to the end of an ion on the peptide sequence.
Displays the mass of a series of amino acids.
This class gathers statistics on the occurrence of amino acids in a fasta
file.
Feature based on an amino acid property.
An amino acid property feature at a fixed position on the peptide sequence.
An amino acid property feature at a position relative to the end of an ion on the peptide sequence.
Feature based on the relationship between two amino acid features.
The different relationships implemented.
Feature based on the amino acid properties of a sequence.
The different functions implemented to compare the amino acid features.
This class represents a sequence for a protein or peptide.
Matrix of amino acid substitutions.
Table model to display the content of an amino acid substitution matrix.
This class serves as a base for the implementation of
IdentificationParametersCLI in specific tools.
Accession meta data.
The advocate of a hit can be a search engine, a sequencing algorithm, a
rescoring algorithm, etc.
The different types of advocates.
Alanine.
Interface for an algorithm settings dialog.
ListCellRenderer with alignment functionality.
TableCellRenderer with alignment functionality.
AlignmentBlock.
This class provides a simple extension on a JTable, allowing even and uneven rows to
have different colours.
Iterator going through the possible sequences of a sequence containing
combinations of amino acids.
Class representing amino acids.
Properties of the amino acids.
An amino acid pattern is a sequence of amino acids.
This dialog allows the design and test of amino acid patterns.
This class represents a series of amino acids with associated modifications.
Class representing an amino acid substitution.
This IdfileReader reads identifications from an Andromeda result file.
The Andromeda specific parameters.
The available decoy modes.
Dialog for the Andromeda specific settings.
This class contains the spectrum annotation parameters.
Enum of the types of intensity thresholds available.
A simple dialog for setting the spectrum annotation preferences.
This class writes spectrum files in Andromeda Peak List (APL) format.
Arginine.
Utility functions to work with arrays.
Asparagine.
Aspartic Acid.
Peptide Assumption filter.
Enum of the different items an assumption filter can filter on.
This interface contains information about atoms.
A chain of atoms.
AtomChainDialog.
Class for a specific atom.
Panel for selecting atoms.
Asn or Asp: Asx (Mascot).
Dialog for editing the background species.
Class that makes it possible to open a URL in the default browser.
Class used to perform basic mathematical functions.
Functions operating with BigDecimal objects.
Utils for the manipulation of big numbers.
Persistence independent object model implementation class:
Filters by binning.
Implementation of a binomial distribution.
Mapping of the species to BioMart dataset.
Class used to store entire objects in the database as a blob.
Convenience class allowing the boxing of an object.
A simple bug report dialog.
ByteArrayRenderer.
The cache element.
The calcium atom.
Carbon.
This class contains convenience methods for the handling of charges.
Objects used in CheckBoxCellRenderer.
Cell renderer for JComboBox supporting multiple selection.
JComobox supporting multiple selection.
The Chlorine atom.
This class provides a JPanel that can display a profileChromatogram.
Simple logger.
Iterator for a Compomics Mass Spectrometry (cms) file.
Reader for Compomics Mass Spectrometry (cms) files.
Utils to store ms files.
Writer for cms files.
Placeholder for the temp folder to use for cms files.
The Cobalt atom.
ColorAdapter required to avoid illegal reflective access warnings.
This class converts column types into Strings representing
corresponding Java types.
The Comet specific parameters.
The available output formats.
Dialog for the Comet specific settings.
Exception handler for command line processes.
This class provides a generic interface for the parsing of command-line
arguments, options and flags.
This class groups some convenience methods for the use of compomics tools in
command line.
Convenience methods for the validation of command line parameters.
Class for comparing tool version numbers.
Comparator for tool version numbers.
Feature based on the amino acid properties of the complementary ion.
Feature based on a property of the complementary ion.
This enum types all computational omics tools and libraries that make use of the utilities library.
A general wrapper for compomics tools.
This interface describes the behaviour for classes that can accept an
incoming DB connection.
This class implements a dialog to gather all information concerning a DB connection.
Convenience class listing constants used throughout the library.
This class will generate the code for a default and full constructor for a DBAccessor,
defined by the metadata passed in via the constructor.
An object for storing Contact details.
An object for storing ContactGroup details.
The copper atom.
This IdfileReader reads identifications from a COSS tsv result file.
A simple CvTerm object.
Cysteine.
DasAlignment.
DasAnnotationServerAlingmentReader.
DasAnnotationServerResultReader
DasFeature.
This class can be used to draw roc curves from experimental data.
Enum listing the possible ways of interpolating points on the ROC.
This class provides a simple date chooser.
File filter for *.dat files.
This class represents an accessor class' sourcecode as generated by the DBAccessorGenerator
class.
This class generates an Object that can be used for access to a
given table in a JDBC accessible RDBMS.
This interface indicates that the implementing class can be stored, manipulated and deleted in a
permanent storage (typically a RDBMS).
This class wraps the metadata retrieved from a table on the DB.
Placeholder for the db mutex.
This class wraps a DB resultset in an 'offline' object.
This class appends decoy sequences to the given FASTA file.
This class implements a default logger (for debugging purposes).
This class provides a default implementation of the SpectrumAnnotation interface.
Default style for Excel sheets.
This interface indicates that the implementing class can be deleted from permanent storage.
This class generates the code to make a DBAccessor class an implementation of the Deleteable interface.
Class representing an amino acid deletion.
This class groups the parameters for the digestion of proteins.
Enum for the different types of digestion.
Enum for the different types of enzyme specificity.
An identification file reader for Direct tag results.
The DirecTag specific parameters.
Dialog for editing the DirecTag advanced settings.
This class represents a statistical distribution model like a Gaussian
distribution.
This class can be used to draw roc curves from experimental data.
Implementation of a matrix for double objects.
Download the latest zip file from the repository.
File filter for *.dta files.
This class implements an enzyme with a dual specificity; the N-terminus of a
resultant peptide will have certain residue, the C-terminus will have another,
eg.
A simple class used to be able to show a JDialog without a parent frame in
the OS task bar.
Dummy parameters used to retrieve the parameters type and version.
Class used to measure duration of a process.
This class can be used to retrieve elementary elements like a neutron.
This class represents an elementary ion.
This class contains empty collections that can be used for empty results without creating new objects.
Mapping of the Ensembl species.
Enum of the different Ensembl divisions.
Class for the handling of Ensembl versions.
This class models an enzyme.
This class implements the functionality for an Enzyme.
This factory will load enzymes from a JSON file and provide them on demand as
a standard class.
Simple dialog for mapping a PRIDE enzyme to a utilities enzyme.
Command line to manage the enzymes.
This class parses the parameters from an EnzymeCLI.
Enum class specifying the EnzymesCLI parameters.
Dialog for the Enzymes.
ExportWriter for the export to Excel files.
Interface for the general handling of exceptions.
This abstract class provides customization facilities.
Includes export to figure formats for Components and JFreeCharts.
An export factory manages and generates reports.
This interface represents an export feature.
Enum of the different formats available for the exports.
Simple dialog for selecting the format type to export to.
Simple dialog for selecting the image type to export a graphics element to.
This class allows creating a standard output scheme.
The export writer will write the output in the desired export format.
This class packages together a peptide, its fixed modifications and its position on the protein.
File filter for *.fasta files.
Iterator for a FASTA file.
Interface for a class mapping peptides and tags to a protein.
The parameters used to parse a FASTA file.
Command line parameters for the FASTA files.
A dialog for advanced database settings.
This class gathers command line parameters for the parsing of FASTA files.
This class parses a FASTA file and gathers summary statistics.
This class computes the ms2PIP features from a peptide.
This class contains a map of selected features indexed by category.
This class is used to manage the features maps.
This class is used to report a message to the user.
The supported report types.
This class is intended to avoid the default behavior of the GSON parser to
append the current path to the absolute path of a file.
Store the selected file and the file type description.
This class contains utilities functions for the file choosers.
FileDAO file access.
Dialog for showing a list of selected files with the option to remove files
from the list.
Organizes the file filters.
This class implements the Logger interface for logging to a file.
This class will implement a FilenameFilter that filters on the extension of files.
A simple dialog for selecting between different files.
This class serves as a fast OS independent access point to the file system.
An enum of the possible file types for the PRIDE file type options.
Generic interface for a filter.
Dialog to edit identification matches filters.
Interface for an item used for filtering.
Comparators for filter items.
This class groups the display filter preferences.
Maps UniProt protein accession numbers to PDB file IDs.
This interface describes the behaviour for classes that can handle unrecoverable errors and
exceptions, thrown by child threads etc.
FlamableJFrame.
The fluorine atom.
The FM index.
This class will monitor a specified folder for activity.
Feature based on the amino acid properties of the forward ion.
Feature based on a property of the forward ion.
Settings for the handling of fractions.
FractionSettingsDialog.
Annotator for b and y ions without neutral losses.
A fragment annotator for peptide fragment ions with neutral losses.
Enum for the different fragmentation methods.
Creates a fragment ion table with the detected fragment ions.
A cell renderer to use for the FragmentIonTable making it possible to
highlight certain cells.
Predictor for the peptide fragment intensity.
Handles exception for a given application and displays warnings using
dialogs.
This class was modified from a source found on the net (java.sun.com, search in
developer section on 'FtpProtocolException PORT').
This class implements a 'directory listener' to listen for new files and
ftp them to a remote FTP server.
This class handles an FTP connection exception.
A simple FTP file downloader.
This class handles an FTP login exception.
This class handles an FTP protocol exception.
This dialog displays the gene details associated to a protein match.
Class for the handling of gene mappings.
The gene maps for a given project.
Contains methods for downloading gene and GO mappings.
Dialog for editing the Gene Mapping Preferences.
This class wraps all exception that can occur while generating code.
This converter writes a FASTA file with standardized headers.
This class will generate (and subsequently output upon request) all relevant getters and setters
for a DBAccessor.
Glutamic Acid.
Glutamine.
This class represents a glycan.
Glycine.
Class parsing GO domains and storing them in a map.
Class parsing BioMart protein GO mappings and storing them in maps.
This class presents a JPanel that will hold and display a mass spectrum or a
chromatogram.
An enumerator of the possible GraphicsPanel types.
An enumerator of the possible GraphicsPanel types.
A table cell renderer for GraphicsPanels.
GUIFileDAO.
A class containing simple GUI helper methods.
Convenience methods to work with gzipped files.
This class represents the header for a Protein instance.
Iterator for the headers of a FASTA file.
HeadlessFileDAO.
The helium atom.
A dialog used to display help text in HTML format.
A window used to display help text in HTML format.
Histidine.
Simple functions to manipulate histograms.
Convenience class extracting the data needed to plot the modification
matching.
The hydrogen atom.
Hyperscore as variation of the score implemented in X!Tandem
www.thegpm.org/tandem.
This class interacts with the back-end database to manage identification
objects.
Interface for the algorithm specific parameters.
This class caches the identification features calculated by the
IdentificationFeaturesGenerator for later reuse.
An enumerator of the supported object types.
This class provides identification features and stores them in cache.
Placeholder for the keys of the objects in the identification.
This is an abstract class for an identification match.
The type of match.
This class will contain all methods used to obtain identifications.
Generic class grouping the parameters used for protein identification.
The IdentificationParametersCLI allows creating search parameters files using
command line arguments.
Enum class specifying the SearchParameter command line option parameters to
create a SearchParameters object
IdentificationParametersEditionDialog.
Factory for the identification parameters.
This class parses the parameters from a command line and stores them in a
SearchParameters object.
This class is a convenience class to have a DefaultJsonConverter with the
identification parameters interfaces.
IdentificationParametersOverviewDialog.
Generic interface for the parser of a file containing PSMs.
This factory will provide the appropriate identification file reader for each
type of file.
Generic class grouping the identification matches validation preferences.
Enumerator for supported export plot file types.
Represents an immonium ion.
Annotator for immonium and related ions.
Reader for mgf files based on random access.
Class representing an amino acid insertion.
This class represents the instance variables for a generated DBAccessor.
An object for storing Instrument details.
Decodes ints from the half bytes in bytes.
Creates an IntensityHistogram plot.
A generic adapter to parse used interfaces in a class.
Iodine.
This class models an ion.
An enumerator of the supported ion types.
This factory generates the expected ions from a peptide.
Feature based on a property of an ion.
Enum for the possible features.
A table model to use for the ion label annotation colors.
This class represents the assignment of a peak to a theoretical ion.
Enum of the supported error types.
Cache for the keys of the ions.
Utils for I/O and file handling.
The iron atom.
Isoleucine.
This class is a GUI that visualizes the isotopic calculator.
This class calculates the isotopic distribution based on a molecular formula.
This class provides a JPanel that can display a peptide isotopic distribution.
This class is an implementation of the SpectrumFile specific for the isotopic distribution
Created by IntelliJ IDEA.
This class represents the isotopically different element with the occurrence
and the dalton difference between this and the natural variant.
The iterator goes through a sequence and lists possible peptides with their
fixed modifications.
Isoleucine or Leucine.
JarFileFilter.
A dialog for changing the Java Home.
Interface for parents of JavaMemoryDialog and JavaHomeDialog.
A dialog for changing the Java memory setting.
A dialog for showing Java memory settings.
This class implements a JDialog for the specific purpose of showing unrecoverable
errors or exceptions.
This class implements a JFrame, made specifically for the
display of binary data.
This class implements a JPanel that lays out a set of JLabel and a JComponent
next to each other.
A dialog to show HTML content with clickable links inside a JOptionsPane.
File filter for *.jpeg files.
This class converts non-specific objects to the JSON format and vice versa.
This class extends a JTable with specific cellrenderers for fields,
retrieved from DB.
K-means clustering.
Settings for k-means clustering.
Convenience class keeping class of the last selected folders.
Leucine.
Enum of the different implementations for a regression.
Dialog for choosing an item in a list.
The Lithium atom.
This interface describes the behaviour for a class that can log messages.
Lysine.
The magnesium atom.
The Manganese atom.
MappingWorker.
Interface for a parameter which can be marshalled as .par file.
Enum of the type of parameter which can be encountered in a .par file.
This class will load Enzyme properties from a Mascot
(www.matrixscience.com)
formatted text file.
This IdfileReader reads identifications from a Mascot results file.
This class takes care of mass calculation, based on a sequence
in IUPAC format.
This class implements the MassCalc class as a servlet.
Creates a MassErrorBubblePlot displaying the mz values vs the mass error with
the intensity as the size of the bubbles.
Creates a MassErrorPlot displaying the mz values vs the mass error.
An undefined mass gap.
The mass index map.
The PeptideShaker import settings dialog.
An abstract iterator class to iterate identification matches.
Abstract representing a filter.
Enum for the type of possible filter.
Enum listing the different levels of match validation.
Element for the matrix necessary in pattern search of the FMIndex.
MavenJarFile.
This class estimates the MD score as described in
https://www.ncbi.nlm.nih.gov/pubmed/21057138 Note: this implementation of the
MD score is not restricted to phosphorylation.
Performs a robust linear regression.
This class provides information on the memory consumption status.
MetaDataXMLParser.
The MetaMorpheus specific parameters.
The available decoy types.
The available dissociation types.
The available fragmentation terminus types.
The available initiator methionine behavior types.
The available mass difference acceptor types.
The available search types.
The available decoy types.
Dialog for the MetaMorpheus specific parameters.
Methionine.
This class contains metrics gathered during the creation of a PeptideShaker project.
Enumeration of the metrics prefixes.
File filter for *.mgf files.
An iterator of the spectra in an mgf file.
Utilities for the handling of mgf files.
This class writes spectrum files in Mascot Generic File (mgf) format.
This class contains the indexes of an mgf file after indexing mapped with the
title of the spectrum.
Mirrored spectra test class.
This class models a peptide or protein modification.
This interface describes the behaviour for a modification on a peptide or aminoacid sequence.
Enum for the different modification categories supported.
Dialog for choosing an item in a list of modifications.
This dialog allows the user to create/edit Modifications.
This factory will load Modification from an XML file and provide them on
demand as standard class.
This class can be used to generate a Modification instance from a code or title.
Feature based on the modification status of an amino acid.
Enum for the possible features.
This class implements a specific Modification.
Function attempting to map modification localization based on their type.
Function attempting to map modification localization based on their type.
This class contains the modification localization preferences.
PTMLocalizationParametersDialog.
An enum of the modification localization scores.
Function inferring the mass of a modification based on the search engine
used.
Function inferring the mass of a modification based on the search engine
used.
This class models the match between theoretic PTM and identification results.
Functions mapping search engine modifications to utilities by name.
Functions mapping search engine modifications to utilities by name.
This class stores the information about the modification parameters (usage,
colors, names).
Functions for the mapping of modifications on peptides.
A simple modification profile object.
Interface for a modification provider.
Command line to manage the modifications.
This class parses the parameters from an ModificationsCLI.
Enum class specifying the ModificationsCLI parameters.
This class contains stores the modification localization scores.
A dialog where the modification details can be modified.
This class contains convenience methods to map modifications on potential sites.
Table containing information about the peak annotation of a modified peptide.
Convenience class for the content of a PTM table.
This class holds a template for a Modification, meaning that it contains all shared characteristics of
a Modification, but not the instance-specific one.
Enum for the different types of modifications supported.
This class groups functions that can be used to work with modifications.
This ENUM types the distinct molecular elements.
This class represents the molecular formula.
This interface describes the behaviour for any Object whose progressing state
can be monitored.
This class implements an InputStream that reports on the progress of reading
a file in integer quantities, even though the underlying file may have a binary size that is outside
of integer range.
This class provides a specific FilterInputStream that can be monitored for progress.
This class makes it possible to set the dimensions of a JFrame of JPanel
to a certain percentage of the screen size.
This class writes spectrum files in MS2 format.
File filter for *.ms2 files.
This class writes spectrum files in MS2 format.
Interface for an ms2pip feature.
This IdfileReader reads identifications from an MS Amanda csv result file.
The MS Amanda specific parameters.
Dialog for the MS Amanda specific settings.
The parameters to use when running msconvert.
Dialog for the creation and edition of msconvert parameters.
This class writes ms files in various formats.
Enum of the supported export formats.
A spectrum provider for mass spectrometry files based on Compomics Mass
Spectrometry (cms) files.
Interface for mass spectrometry file readers.
This script test the speed of the ms file access.
The MS-GF+ specific parameters.
Dialog for the MS-GF+ specific settings.
MSNumpress.
Interface for the ms2pip features having multiple amino acid properties.
Mutex map for the features cache.
The MyriMatch specific parameters.
Dialog for the MyriMatch specific settings.
File filter for *.mzData files.
This IdfileReader reads identifications from an mzIdentML result file.
Enum for the raw value to e-value conversion.
Reads basic search parameters from mzIdentML result files.
Enum of the versions of the mzIdentML format supported.
File filter for *.mzML files.
An iterator of the spectra in an mzml file.
The supported precision types for the binary data as defined in the mzML
specifications and the PSI-MS ontology.
Utilities for the handling of mzml files.
File filter for *.mzXML files.
This class represents a neutral loss.
This class represents a combination of multiple neutral losses.
This class contains the informations relative to the accounting of neutral
losses
This dialog allows the user to create a new enzyme.
The Nickel atom.
The nitrogen atom.
Iterator for no digestion of a sequence containing amino acid combinations.
Iterator for no digestion.
This class represents a non symmetrical normal distribution.
This class represents a normal distribution.
Class grouping the normalization factors used to normalize quantification
results.
This class makes use of "SSJ: Stochastic Simulation in Java" library from
iro.umontreal.ca to estimate probability density function of an array of
double.
A simple dialog for displaying notes.
An undecorated dialog for displaying notifications.
A NotificationDialog parent interface.
This IdfileReader reads identifications from a Novor csv result file.
Novor specific parameters.
Dialog for editing Novor advanced settings.
This class combines a protein Header with a nucleotide sequence.
This class represents a nucleotide sequence (RNA or DNA).
This mutex can be used to manage threads editing experiment objects using
their key.
An object cache can be combined to an ObjectDB to improve its performance.
A database which can easily be used to store objects.
The OMSSA specific parameters.
Dialog for the OMSSA specific parameters.
File filter for *.omx files.
Id file reader for the scripts in Onyase.
This ENUM types the distinct OS systems.
File filter for *.out files.
This enum lists the possible output options.
The oxygen atom.
Interface for a path key.
Dialog used to set paths.
Allows the user to set the path settings in command line.
Parses the command line and retrieves the user input.
Parameters for the path settings command line.
This class groups the information about the patient from whom the sample is
taken
Information about the patient.
PdbBlock.
PdbParameter.
File filter for *.pdf files.
This class represents a peak.
File filter for *.peff files.
This class contains pepnovo assumption details which are not contained in the
tag assumption class which will be saved as additional parameter.
This class can be used to parse PepNovo identification files.
PepNovo specific parameters.
Dialog for editing the PepNovo advanced settings.
This class represents a peptide.
Feature based on the amino acid properties of a peptide.
This class builds peptides and proteins based on PSMs.
This object models the assumption made by an advocate.
This class filters peptide assumptions based on various properties.
Parameter for storing additional non-mandatory peptide assumption
information.
Draft of a peptide used during protein sequence digestion.
Feature based on a peptide property.
Enum for the possible features.
Peptide filter.
Enum of the different items a peptide filter can filter on.
Enum for the different peptide fragmentation models implemented.
This class models a peptide fragment ion.
Functions related to peptide inference.
Command line peptide mapping.
This class models a peptide match.
An iterator for peptide matches.
Class used to model the mapping of a peptide to a protein sequence.
A dialog used to set up the connection to PeptideShaker.
Annotates a spectrum with peptide fragments.
This class groups functions that can be used to work with peptides.
This class represents a set of variants found on a peptide.
Preferences for the allowed variants in peptide sequences.
Enum indicating all three variant types
FractionSettingsDialog.
File filter for *.pep.xml, *.pepxml and *.xml files.
Simple IdfileReader for Pepxml files.
Enum for the features of Percolator kept in cache.
This class serves as a cache for Percolator features.
Performance benchmark for the ModificationPeptideMapping class.
Runnable for the benchmark.
This interface indicates that the implementing class can be persisted in permanent storage.
This class generates the code to make a DBAccessor an implementation of the Persistable
interface.
Phenylalanine.
This class estimates the PhosphoRS score as described in
https://www.ncbi.nlm.nih.gov/pubmed/22073976.
The phosphorus atom.
This interface describes the behaviour for a class that can pick up results.
Contains information about the contents of one PKL file.
File filter for *.pkl files.
File filter for *.pkl.spo files.
File filter for *.pkx files.
File filter for *.png files.
This class can be used to parse pNovo identification files.
pNovo specific parameters.
Dialog for editing pNovo advanced settings.
The potassium atom.
This class models a precursor.
The precursor accuracy as a score.
Annotator for the precursor peaks.
A precursor ion.
This map stores the precursors indexed by mass.
Parameter for storing additional non-mandatory precursor information.
An object to set up a filter for use in a query to the PRIDE webservice.
An enum of the possible filters for the PRIDE Filter options.
A json marshaller for use with the PRIDE webservice.
Interface for a PRIDE object.
This factory manages the pride objects saved in the user folder.
An enum that constructs the template queries for the PRIDE webservice.
A java representation of the PRIDE web service.
PRIDE XML schema validation.
The privacy settings dialog allows the user to set the privacy settings.
Filter removing points with outlying slope.
ProcessingPreferences.
Class indicating the type of processing.
Dialog to edit the processing parameters.
This class implements a modal dialog that is displayed during a longer-lasting task.
A dialog for displaying information about progress.
This class contains project specific parameters.
This enum lists the different types of projects that can be created using
PeptideShaker.
Proline.
This class holds all user properties for ms_lims.
This class models a protein.
This class implements the behaviour for a Protein instance.
Enum of the supported protein databases.
Interface for a class able to provide metadata on proteins.
Protein filter.
Enum of the different items a protein filter can filter on.
Class used to map proteins to gene information.
Generic class grouping the protein inference preferences.
Dialog for the edition of the protein inference settings.
Interface for a protein iterator.
This class contains utilities used during the iteration of protein sequences.
This class models a protein match.
An iterator of protein matches.
This class contains a method that formats a given protein sequence such that
both the covered parts of the sequence and the peptide selected in the peptide
table is highlighted.
Convenience functions for the handling of proteins.
Filters which can be applied to msconvert.
The mass spectrometry formats supported by ProteoWizard.
A dialog used to set up the connection to ProteoWizard.
An object for storing Protocol details.
File filter for *.prot.xml, *.protxml and *.xml files.
This class lists the annotation export features.
This class lists the fragment identification features.
This class lists the Algorithm identification features.
This enum lists the export features related to the import features.
PSM filter.
Enum of the different items a PSM filter can filter on.
This class contains the scores for the locations of the possible
modifications.
Enum listing the PSM scores implemented in compomics utilities.
This class can be used to estimate PSM scores.
Generic class for peptide spectrum match scoring.
Dialog for the edition of the PSM scoring settings.
PeptideShaker compomics utilities experiment customizable parameter.
This class lists the peptide identification features.
This class lists the PSM identification features.
This class lists the protein identification features.
This class lists the PSM identification features.
This enum groups the export features related to PTM scoring.
This class lists the export features linked to the spectrum identification.
This class lists all the export features related to the spectrum counting.
This enum lists the export features linked to the validation process.
This class is a convenience class to have a DefaultJsonConverter with the
search parameter interfaces.
Map linking user modification names to Unimod CV terms.
This class implements a PushBackReader for Strings which allows the reading
of entire lines as well as the pushing back of entire lines.
Pyrrolysine.
An abstract quantification class.
The implemented quantification methods.
Rank as used in the FM index.
A reporter ion labeling reagent.
Utility functions for spectrum recalibration.
A simple publication reference object.
A reference area to be added to a GraphicsPanel.
An object for storing ReferenceGroup details.
This class implements the functionality of an Enzyme by
simulating digestion based on a regular expression.
Results of a linear regression of equation y = a.x + b and Pearson
correlation r.
Represents a related ion, i.e., an ion that is related to a given amino acid,
and is its own factory.
Dialog for editing reports.
Reporter extension of the utilities export features.
This class models a reporter ion and is its own factory.
Annotator for reporter ions.
This class contains quantification parameters.
This class contains information relative to a reporter quantification method.
This factory imports reporter methods details from an XMl file.
This enum lists all the peptide export features available from reporter
complementarily to the ones available in PeptideShaker.
This enum lists all the protein export features available from reporter
complementarily to the ones available in PeptideShaker.
This enum lists all the PSM export features available from reporter
complementarily to the ones available in PeptideShaker.
A dialog used to set up the connection to Reporter.
This class implements a resizing event that occurred on a SpectrumPanel.
This interface indicates that the implementing class can be retrieved from permanent storage.
This class generates the code to make a DBAccessor an implementation of the Retrieveable
interface.
This class can be used to draw ROC curves.
This IdfileReader reads identifications from a Sage tsv file.
The Sage specific parameters.
Dialog for the Sage specific settings.
An object for storing Sample details.
Class which allows the selection of the right identification.
This class estimates spectrum counting scaling factors.
This class exports a draft of sdrf file.
A dialog used to set up the connection between PeptideShaker and SearchGUI.
This class groups the parameters used for identification.
Possible mass accuracy types.
The search settings dialog.
Selenium.
SeC (U) (Mascot)-
These table models include a self updating function.
This interface defines the default behavior of any kind of
sequence with a certain mass - be it DNA, protein or something
else.
This dialog displays information about a sequence database.
This class was imported from the Peptizer and MascotDatfile parser, and was
developed to display fragmentation information on the modified sequence as
inspired by X!Tandem.
Interface for an iterator returning peptides along a protein sequence.
The sequence matching options.
The different types of amino acid matching.
Dialog for the edition of the sequence matching settings.
A panel for displaying modification profiles.
Interface for a class able to retrieve the sequence of a given protein.
Fragmentation model originally described in the Sequest algorithm
(https://www.ncbi.nlm.nih.gov/pubmed/24226387) adapted to utilities objects.
File filter for sequest.params files.
This class implements convenience methods for serialization and
deserialization.
Serine.
Interface for file readers.
Simple gz file writer that is thread safe and throws exceptions as runtime
exceptions.
Simple wrapper for a gz file reader.
Performs a simple linear regression.
Simple mzIdentML exporter for PSM-level results.
This class makes a simple modeling of the noise using a normal distribution
on the log of the peak intensities and returns the associated binned
cumulative probability for a given intensity.
A simple annotator for peptides.
The type of ion series to annotate.
A simple semaphore where thread interrupted exception are thrown as runtime exception.
Simple wrapper for a flat file reader.
Simple writer for xml files.
Interface for the ms2pip features having a single amino acid property.
Sequence provider for a single protein.
This score uses the intensity distribution of the peaks to evaluate an SNR
score.
The sodium atom.
Dialog for user selection of the colors used by the sparklines.
Class related to the handling of species.
The spectrum annotation preferences specific to a spectrum and an
identification assumption.
Iterator for enzymatic digestion.
Iterator for enzymatic digestion.
This class models a spectrum.
This interface describes the behaviour for a spectrum annotation.
The spectrum annotator annotates peaks in a spectrum.
Enum of the possibilities for ties resolution when multiple peaks can be
annotated.
Enum of the implemented spectrum quantification methods.
This class contains the spectrum counting parameters.
This interface describes the behaviour for a spectrum file
(ie., PKL file, Mascot Generic file, dat file, ...).
Spectrum identification assumption made by an identification algorithm.
This map stores the fragment ions indexed by mass.
This class models a spectrum match.
An iterator for spectrum matches.
This class presents a JPanel that will hold and display a mass spectrum in
centroid or profile mode.
This interface describes the behaviour for a listener that wants to receive information
about events that occurred on a SpectrumPanel.
Interface for objects providing spectra.
Utilities functions to handle spectra.
Class that takes care of converting an svg file to a png file using the
command line version of apache batik.
Enum of standard masses.
The standard units implemented.
This class starts a browser for the given URL.
StartEndPosition.
A stream gobbler.
Convenience methods to work with lambdas.
Dialog for choosing an item in a list of String.
Class representing an amino acid substitution.
The sulfur atom.
File filter for *.svg files.
Class representing an amino acid swap.
Swing utilities methods.
This is the 3rd version of SwingWorker (also known as
SwingWorker 3), an abstract class that you subclass to
perform GUI-related work in a dedicated thread.
In a chain of data manipulators some behaviour is common.
MouseWheelListener for SelfUpdatingTableModels that supports scrolling in a
more efficient way.
This class groups properties for the tables
AdjustmentListener for SelfUpdatingTableModels supporting scrolling in a more
efficient way.
A sorter for TableModels.
This interface describes the behaviour for a class that wraps a table element.
This class represents a sequence mass tag.
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
Interface for a sequence tag component.
The tag element.
Convenience class for sequence tag generation.
A fragment ion obtained from a tag.
Annotates a spectrum with information from a tag.
This class groups functions that can be used to work with peptides.
This class contains convenience methods for taring files.
Convenience class for storing an array buffer and a length.
This class can be used to reference temp files and manage them.
This TestCase extension contains some useful methods for loading Properties files
from the classpath and getting general files' full name or an InputStream from
the classpath.
ExportWriter for the export to text files.
The mass spectrometry output formats supported by ThermoRawFileParser.
The parameters to use when running ThermoRawFileParser.
Dialog for the creation and edition of ThermoRawFileParser parameters.
Threonine.
This IdfileReader reads identifications from an Tide tsv results file.
The Tide specific parameters.
Dialog for the Tide specific settings.
File filter for *.tiff files.
TimestampRenderer.
This class can be used to start compomics tools.
A combo box renderer that allows tooltip for each element in the combo box
list.
This class allows the user to translate a DNA sequence into 6 reading frames.
Tryptophan.
Tyrosine.
Dummy intensity predictor that returns 1.0 for every ion.
Mapping of the UniProt species taken from
https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt.
The unit to use for a measure.
Convenience class providing units.
This class implements an Exception, thrown when a MassCalc instance
is confronted with an element symbol it cannot retrieve in its
element lists.
Iterator for unspecific cleavage.
Iterator for unspecific cleavage.
This interface indicates that the implementing class can be updated in permanent storage.
This class generates the code to make a DBAccessor an implementation of the Updateable
interface.
This interface is used to reference refinement parameters.
Includes general help methods that are used by the other classes.
This class serves as a demo of how the compomics-utilities library can be
used in other projects.
This class contains a list of GUI defaults to be used across the tools
using the utilities library to make sure that the tools have the same
look and feel.
This class sets the path preferences for the files to read/write.
Enum of the paths which can be set in utilities.
Utilities user parameters can be used to store user parameters.
Dialog for the edition of the sequence matching settings
This class lists the criteria used for quality control of the validated
matches.
Dialog for the edition of validation QC filters.
Valine.
Interface for a variant.
Class for calculating the groups for Venn diagrams.
A dialog for creating and displaying Venn diagrams.
Dialog for setting the location of the legend items in a Venn diagram.
A panel displaying a Venn diagram based on the provided data.
The supported Venn diagram types.
A dialog that lets the user decide which columns to show/hide in a JTable.
Interface for parents of VisibleTableColumnsDialog.
This class is used to pass actions like cancel while waiting.
A dialog displaying progress details.
Exception handler for processes making use of a waiting dialog.
An interface for code dealing with how to handle information that is
displayed to the user during loading or processing.
This class is an implementation of the WaitingHandler interface to be used
when operating through the Command Line Interface.
This class is an implementation of the WaitingHandler interface to be used
when a process can be canceled, but no monitoring is needed.
Wavelet tree.
WebDAO.
This interface sets the style of a workbook export.
This writer writes the different sections of a file in temp files and bundles
them together upon completion.
Unknown amino acid (Mascot).
File filter for *.xml files.
Edited using IntelliJ IDEA Date: 16-Sep-2005 Time: 15:26:12
This IdfileReader reads identifications from an X! Tandem xml result file.
The X!Tandem specific parameters.
Dialog for the X!Tandem specific settings.
Dialog for editing the data filters for an XYPlottingDialog.
A dialog that makes it straightforward to inspect compare the values of two
columns in a table in a XY plot.
The plotting dialog types.
Object that stores data about one data point in an XYZ plot.
Glu or Gln: Glx (Mascot).
The zinc atom.
Convenience class for the handling of zip files.
Functions needed for compression and decompression.