All Classes
Class | Description |
---|---|
AAIdentityFeature |
Feature based on an amino acid identity.
|
AAIdentityFeatureAbsolute |
An amino acid identity feature at a fixed position on the peptide sequence.
|
AAIdentityFeatureRelative |
An amino acid identity feature at a position relative to the end of an ion on the peptide sequence.
|
AaMass |
Displays the mass of a series of amino acids.
|
AaOccurrence |
This class gathers statistics on the occurrence of amino acids in a fasta
file.
|
AAPropertyFeature |
Feature based on an amino acid property.
|
AAPropertyFeatureAbsolute |
An amino acid property feature at a fixed position on the peptide sequence.
|
AAPropertyFeatureRelative |
An amino acid property feature at a position relative to the end of an ion on the peptide sequence.
|
AAPropertyRelationshipFeature |
Feature based on the relationship between two amino acid features.
|
AAPropertyRelationshipFeature.Relationship |
The different relationships implemented.
|
AASequenceFeature |
Feature based on the amino acid properties of a sequence.
|
AASequenceFeature.Function |
The different functions implemented to compare the amino acid features.
|
AASequenceImpl |
This class represents a sequence for a protein or peptide.
|
AaSubstitutionMatrix |
Matrix of amino acid substitutions.
|
AaSubstitutionMatrixTableModel |
Table model to display the content of an amino acid substitution matrix.
|
AbstractIdentificationParametersCli |
This class serves as a base for the implementation of
IdentificationParametersCLI in specific tools.
|
AccessionMetaData |
Accession meta data.
|
Advocate |
The advocate of a hit can be a search engine, a sequencing algorithm, a
rescoring algorithm, etc.
|
Advocate.AdvocateType |
The different types of advocates.
|
Alanine |
Alanine.
|
AlgorithmParametersDialog |
Interface for an algorithm settings dialog.
|
AlignedListCellRenderer |
ListCellRenderer with alignment functionality.
|
AlignedTableCellRenderer |
TableCellRenderer with alignment functionality.
|
AlignmentBlock |
AlignmentBlock.
|
AlternateRowColoursJTable |
This class provides a simple extension on a JTable, allowing even and uneven rows to
have different colours.
|
AmbiguousSequenceIterator |
Iterator going through the possible sequences of a sequence containing
combinations of amino acids.
|
AminoAcid |
Class representing amino acids.
|
AminoAcid.Property |
Properties of the amino acids.
|
AminoAcidPattern |
An amino acid pattern is a sequence of amino acids.
|
AminoAcidPatternDialog |
This dialog allows the design and test of amino acid patterns.
|
AminoAcidSequence |
This class represents a series of amino acids with associated modifications.
|
AminoAcidSubstitution |
Class representing an amino acid substitution.
|
AndromedaIdfileReader |
This IdfileReader reads identifications from an Andromeda result file.
|
AndromedaParameters |
The Andromeda specific parameters.
|
AndromedaParameters.AndromedaDecoyMode |
The available decoy modes.
|
AndromedaParametersDialog |
Dialog for the Andromeda specific settings.
|
AnnotationParameters |
This class contains the spectrum annotation parameters.
|
AnnotationParameters.IntensityThresholdType |
Enum of the types of intensity thresholds available.
|
AnnotationParametersDialog |
A simple dialog for setting the spectrum annotation preferences.
|
AplFileWriter |
This class writes spectrum files in Andromeda Peak List (APL) format.
|
Arginine |
Arginine.
|
ArrayUtil |
Utility functions to work with arrays.
|
Asparagine |
Asparagine.
|
AsparticAcid |
Aspartic Acid.
|
AssumptionFilter |
Peptide Assumption filter.
|
AssumptionFilterItem |
Enum of the different items an assumption filter can filter on.
|
Atom |
This interface contains information about atoms.
|
AtomChain |
A chain of atoms.
|
AtomChainDialog |
AtomChainDialog.
|
AtomImpl |
Class for a specific atom.
|
AtomPanel |
Panel for selecting atoms.
|
B |
Asn or Asp: Asx (Mascot).
|
BackgroundSpeciesDialog |
Dialog for editing the background species.
|
BareBonesBrowserLaunch |
Class that makes it possible to open a URL in the default browser.
|
BasicMathFunctions |
Class used to perform basic mathematical functions.
|
BigFunctions |
Functions operating with BigDecimal objects.
|
BigMathUtils |
Utils for the manipulation of big numbers.
|
BinaryArrayImpl |
Persistence independent object model implementation class:
|
BinningFilter |
Filters by binning.
|
BinomialDistribution |
Implementation of a binomial distribution.
|
BiomartMapping |
Mapping of the species to BioMart dataset.
|
BlobObject |
Class used to store entire objects in the database as a blob.
|
BoxedObject<K> |
Convenience class allowing the boxing of an object.
|
BugReport |
A simple bug report dialog.
|
ByteArrayRenderer |
ByteArrayRenderer.
|
CacheElement |
The cache element.
|
Calcium |
The calcium atom.
|
Carbon |
Carbon.
|
Charge |
This class contains convenience methods for the handling of charges.
|
ChromatogramPanel |
This class provides a JPanel that can display a profileChromatogram.
|
CliLogger |
Simple logger.
|
CmsFileIterator |
Iterator for a Compomics Mass Spectrometry (cms) file.
|
CmsFileReader |
Reader for Compomics Mass Spectrometry (cms) files.
|
CmsFileUtils |
Utils to store ms files.
|
CmsFileWriter |
Writer for cms files.
|
CmsFolder |
Placeholder for the temp folder to use for cms files.
|
ColorAdapter |
ColorAdapter required to avoid illegal reflective access warnings.
|
ColumnTypeConverter |
This class converts column types into Strings representing
corresponding Java types.
|
CometParameters |
The Comet specific parameters.
|
CometParameters.CometOutputFormat |
The available output formats.
|
CometParametersDialog |
Dialog for the Comet specific settings.
|
CommandLineExceptionHandler |
Exception handler for command line processes.
|
CommandLineParser |
This class provides a generic interface for the parsing of command-line
arguments, options and flags.
|
CommandLineUtils |
This class groups some convenience methods for the use of compomics tools in
command line.
|
CommandParameter |
Convenience methods for the validation of command line parameters.
|
CompareVersionNumbers |
Class for comparing tool version numbers.
|
CompareVersionNumbers |
Comparator for tool version numbers.
|
ComplementaryIonAminoAcidFeature |
Feature based on the amino acid properties of the complementary ion.
|
ComplementaryIonFeature |
Feature based on a property of the complementary ion.
|
CompomicsTools |
This enum types all computational omics tools and libraries that make use of the utilities library.
|
CompomicsWrapper |
A general wrapper for compomics tools.
|
Connectable |
This interface describes the behaviour for classes that can accept an
incoming DB connection.
|
ConnectionDialog |
This class implements a dialog to gather all information concerning a DB connection.
|
Constants |
Convenience class listing constants used throughout the library.
|
Constructors |
This class will generate the code for a default and full constructor for a DBAccessor,
defined by the metadata passed in via the constructor.
|
Contact |
An object for storing Contact details.
|
ContactGroup |
An object for storing ContactGroup details.
|
Copper |
The copper atom.
|
CossIdfileReader |
This IdfileReader reads identifications from a COSS tsv result file.
|
CvTerm |
A simple CvTerm object.
|
Cysteine |
Cysteine.
|
DasAlignment |
DasAlignment.
|
DasAnnotationServerAlingmentReader |
DasAnnotationServerAlingmentReader.
|
DasAnnotationServerResultReader |
DasAnnotationServerResultReader
|
DasFeature |
DasFeature.
|
DataRoc |
This class can be used to draw roc curves from experimental data.
|
DataRoc.RocInterpolation |
Enum listing the possible ways of interpolating points on the ROC.
|
DateChooser |
This class provides a simple date chooser.
|
DatFileFilter |
File filter for *.dat files.
|
DBAccessor |
This class represents an accessor class' sourcecode as generated by the DBAccessorGenerator
class.
|
DBAccessorGenerator |
This class generates an Object that can be used for access to a
given table in a JDBC accessible RDBMS.
|
DBElement |
This interface indicates that the implementing class can be stored, manipulated and deleted in a
permanent storage (typically a RDBMS).
|
DBMetaData |
This class wraps the metadata retrieved from a table on the DB.
|
DbMutex |
Placeholder for the db mutex.
|
DBResultSet |
This class wraps a DB resultset in an 'offline' object.
|
DecoyConverter |
This class appends decoy sequences to the given FASTA file.
|
DefaultOutputLoggerImplementation |
This class implements a default logger (for debugging purposes).
|
DefaultSpectrumAnnotation |
This class provides a default implementation of the SpectrumAnnotation interface.
|
DefaultStyle |
Default style for Excel sheets.
|
Deleteable |
This interface indicates that the implementing class can be deleted from permanent storage.
|
DeleteableCode |
This class genereates the code to make a DBAccessor class an implementation of the Deleteable interface.
|
Deletion |
Class representing an amino acid deletion.
|
DigestionParameters |
This class groups the parameters for the digestion of proteins.
|
DigestionParameters.CleavageParameter |
Enum for the different types of digestion.
|
DigestionParameters.Specificity |
Enum for the different types of enzyme specificity.
|
DirecTagIdfileReader |
An identification file reader for Direct tag results.
|
DirecTagParameters |
The DirecTag specific parameters.
|
DirecTagParametersDialog |
Dialog for editing the DirecTag advanced settings.
|
Distribution |
This class represents a statistical distribution model like a Gaussian
distribution.
|
DistributionRoc |
This class can be used to draw roc curves from experimental data.
|
DoubleMatrix |
Implementation of a matrix for double objects.
|
DownloadLatestZipFromRepo |
Download the latest zip file from the repository.
|
DtaFileFilter |
File filter for *.dta files.
|
DualEnzyme |
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.
|
Dummy | |
DummyFrame |
A simple class used to be able to show a JDialog without a parent frame in
the OS task bar.
|
DummyParameters |
Dummy parameters used to retrieve the parameters type and version.
|
Duration |
Class used to measure duration of a process.
|
ElementaryElement |
This class can be used to retrieve elementary elements like a neutron.
|
ElementaryIon |
This class represents an elementary ion.
|
EmptyCollections |
This class contains empty collections that can be used for empty results without creating new objects.
|
EnsemblGenomesSpecies |
This class provides information about the species mapping in Ensembl Genomes
(Bacteria, Fungi, Metazoa, Plants, Protists).
|
EnsemblGenomesSpecies.EnsemblGenomeDivision |
Enum of the different Ensembl genome divisions.
|
EnsemblSpecies |
Mapping of the Ensembl species.
|
EnsemblVersion |
Class for the handling of Ensembl versions.
|
Enzyme |
This class models an enzyme.
|
Enzyme |
This class implements the functionality for an Enzyme.
|
EnzymeFactory |
This factory will load enzymes from a JSON file and provide them on demand as
a standard class.
|
EnzymeParametersDialog |
Simple dialog for mapping a PRIDE enzyme to a utilities enzyme.
|
EnzymesCLI |
Command line to manage the enzymes.
|
EnzymesCLIInputBean |
This class parses the parameters from an EnzymeCLI.
|
EnzymesCLIParams |
Enum class specifying the EnzymesCLI parameters.
|
EnzymesDialog |
Dialog for the Enzymes.
|
ExcelWriter |
ExportWriter for the export to Excel files.
|
ExceptionHandler |
Interface for the general handling of exceptions.
|
ExperimentObject |
This abstract class provides customization facilities.
|
Export |
Includes export to figure formats for Components and JFreeCharts.
|
ExportFactory |
An export factory manages and generates reports.
|
ExportFeature |
This interface represents an export feature.
|
ExportFormat |
Enum of the different formats available for the exports.
|
ExportFormatSelectionDialog |
Simple dialog for selecting the format type to export to.
|
ExportGraphicsDialog |
Simple dialog for selecting the image type to export a graphics element to.
|
ExportScheme |
This class allows creating a standard output scheme.
|
ExportWriter |
The export writer will write the output in the desired export format.
|
ExtendedPeptide |
This class packages together a peptide, its fixed modifications and its position on the protein.
|
FastaFileFilter |
File filter for *.fasta files.
|
FastaIterator |
Iterator for a FASTA file.
|
FastaMapper |
Interface for a class mapping peptides and tags to a protein.
|
FastaParameters |
The parameters used to parse a FASTA file.
|
FastaParametersCLIParams |
Command line parameters for the FASTA files.
|
FastaParametersDialog |
A dialog for advanced database settings.
|
FastaParametersInputBean |
This class gathers command line parameters for the parsing of FASTA files.
|
FastaSummary |
This class parses a FASTA file and gathers summary statistics.
|
FeaturesGenerator |
This class computes the ms2PIP features from a peptide.
|
FeaturesMap |
This class contains a map of selected features indexed by category.
|
FeaturesMapManager |
This class is used to manage the features maps.
|
FeedBack |
This class is used to report a message to the user.
|
FeedBack.FeedBackType |
The supported report types.
|
FileAdapter |
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.
|
FileAndFileFilter |
Store the selected file and the file type description.
|
FileChooserUtil |
This class contains utilities functions for the file choosers.
|
FileDAO |
FileDAO file access.
|
FileDisplayDialog |
Dialog for showing a list of selected files with the option to remove files
from the list.
|
FileFilterUtils |
Organizes the file filters.
|
FileLoggerImplementation |
This class implements the Logger interface for logging to a file.
|
FilenameExtensionFilter |
This class will implement a FilenameFilter that filters on the extension of files.
|
FileSelectionDialog |
A simple dialog for selecting between different files.
|
FileSystemAccessor |
This class serves as a fast OS independent access point to the file system.
|
FileType |
An enum of the possible file types for the PRIDE file type options.
|
Filter |
Generic interface for a filter.
|
FilterDialog |
Dialog to edit identification matches filters.
|
FilterItem |
Interface for an item used for filtering.
|
FilterItemComparator |
Comparators for filter items.
|
FilterParameters |
This class groups the display filter preferences.
|
FindPdbForUniprotAccessions |
Maps UniProt protein accession numbers to PDB file IDs.
|
Flamable |
This interface describes the behaviour for classes that can handle unrecoverable errors and
exceptions, thrown by child threads etc.
|
FlamableJFrame |
FlamableJFrame.
|
Fluorine |
The fluorine atom.
|
FMIndex |
The FM index.
|
FolderMonitor |
This class will monitor a specified folder for activity.
|
ForwardIonAminoAcidFeature |
Feature based on the amino acid properties of the forward ion.
|
ForwardIonFeature |
Feature based on a property of the forward ion.
|
FractionParameters |
Settings for the handling of fractions.
|
FractionParametersDialog |
FractionSettingsDialog.
|
FragmentAnnotator |
Annotator for b and y ions without neutral losses.
|
FragmentAnnotatorNL |
A fragment annotator for peptide fragment ions with neutral losses.
|
FragmentationMethod |
Enum for the different fragmentation methods.
|
FragmentIonTable |
Creates a fragment ion table with the detected fragment ions.
|
FragmentIonTableCellRenderer |
A cell renderer to use for the FragmentIonTable making it possible to
highlight certain cells.
|
FragmentItensityPredictor |
Predictor for the peptide fragment intensity.
|
FrameExceptionHandler |
Handles exception for a given application and displays warnings using
dialogs.
|
FTP |
This class was modified from a source found on the net (java.sun.com, search in
developer section on 'FtpProtocolException PORT').
|
FTPClient |
This class implements a 'directory listener' to listen for new files and
ftp them to a remote FTP server.
|
FtpConnectionException |
This class handles an FTP connection exception.
|
FTPDownloader |
A simple FTP file downloader.
|
FtpLoginException |
This class handles an FTP login exception.
|
FtpProtocolException |
This class handles an FTP protocol exception.
|
GeneDetailsDialog |
This dialog displays the gene details associated to a protein match.
|
GeneMapping |
Class for the handling of gene mappings.
|
GeneMaps |
The gene maps for a given project.
|
GeneParameters |
Contains methods for downloading gene and GO mappings.
|
GeneParametersDialog |
Dialog for editing the Gene Mapping Preferences.
|
GeneratorException |
This class wraps all exception that can occur while generating code.
|
GenericFastaConverter |
This converter writes a FASTA file with standardized headers.
|
GettersAndSetters |
This class will generate (and subsequently output upon request) all relevant getters and setters
for a DBAccessor.
|
GlutamicAcid |
Glutamic Acid.
|
Glutamine |
Glutamine.
|
Glycan |
This class represents a glycan.
|
Glycine |
Glycine.
|
GoDomains |
Class parsing go domains and storing them in a map.
|
GoMapping |
Class parsing BioMart protein go mappings and storing them in maps.
|
GraphicsPanel |
This class presents a JPanel that will hold and display a mass spectrum or a
chromatogram.
|
GraphicsPanel.DrawingStyle |
An enumerator of the possible GraphicsPanel types.
|
GraphicsPanel.GraphicsPanelType |
An enumerator of the possible GraphicsPanel types.
|
GraphicsPanelTableCellRenderer |
A table cell renderer for GraphicsPanels.
|
GUIFileDAO |
GUIFileDAO.
|
GuiUtilities |
A class containing simple GUI helper methods.
|
GzUtils |
Convenience methods to work with gzipped files.
|
Header |
This class represents the header for a Protein instance.
|
HeaderIterator |
Iterator for the headers of a FASTA file.
|
HeadlessFileDAO |
HeadlessFileDAO.
|
Helium |
The helium atom.
|
HelpDialog |
A dialog used to display help text in HTML format.
|
HelpWindow |
A window used to display help text in HTML format.
|
Histidine |
Histidine.
|
HistogramUtils |
Simple functions to manipulate histograms.
|
Hydrogen |
The hydrogen atom.
|
HyperScore |
Hyperscore as variation of the score implemented in X!Tandem
www.thegpm.org/tandem.
|
Identification |
This class interacts with the back-end database to manage identification
objects.
|
IdentificationAlgorithmParameter |
Interface for the algorithm specific parameters.
|
IdentificationFeaturesCache |
This class caches the identification features calculated by the
IdentificationFeaturesGenerator for later reuse.
|
IdentificationFeaturesCache.ObjectType |
An enumerator of the supported object types.
|
IdentificationFeaturesGenerator |
This class provides identification features and stores them in cache.
|
IdentificationKeys |
Placeholder for the keys of the objects in the identification.
|
IdentificationMatch |
This is an abstract class for an identification match.
|
IdentificationMatch.MatchType |
The type of match.
|
IdentificationMethod |
This class will contain all methods used to obtain identifications.
|
IdentificationParameters |
Generic class grouping the parameters used for protein identification.
|
IdentificationParametersCLI |
The SearchParametersCLI allows creating search parameters files using command
line arguments.
|
IdentificationParametersCLIParams |
Enum class specifying the SearchParameter command line option parameters to
create a SearchParameters object
|
IdentificationParametersEditionDialog |
IdentificationParametersEditionDialog.
|
IdentificationParametersFactory |
Factory for the identification parameters.
|
IdentificationParametersInputBean |
This class parses the parameters from a command line and stores them in a
SearchParameters object.
|
IdentificationParametersMarshaller |
This class is a convenience class to have a DefaultJsonConverter with the
identification parameters interfaces.
|
IdentificationParametersNameDialog | |
IdentificationParametersOverviewDialog |
IdentificationParametersOverviewDialog.
|
IdfileReader |
Generic interface for the parser of a file containing PSMs.
|
IdfileReaderFactory |
This factory will provide the appropriate identification file reader for each
type of file.
|
IdMatchValidationParameters |
Generic class grouping the identification matches validation preferences.
|
ImageType |
Enumerator for supported export plot file types.
|
ImmoniumIon |
Represents an immonium ion.
|
ImmoniumIonAnnotator |
Annotator for immonium and related ions.
|
IndexedMgfReader |
Reader for mgf files based on random access.
|
Insertion |
Class representing an amino acid insertion.
|
InstanceVariables |
This class represents the instance variables for a generated DBAccessor.
|
Instrument |
An object for storing Instrument details.
|
IntDecoder |
Decodes ints from the half bytes in bytes.
|
IntensityHistogram |
Creates an IntensityHistogram plot.
|
InterfaceAdapter<T> |
A generic adapter to parse used interfaces in a class.
|
Iodine |
Iodine.
|
Ion |
This class models an ion.
|
Ion.IonType |
An enumerator of the supported ion types.
|
IonFactory |
This factory generates the expected ions from a peptide.
|
IonFeature |
Feature based on a property of an ion.
|
IonFeature.Property |
Enum for the possible features.
|
IonLabelColorTableModel |
A table model to use for the ion label annotation colors.
|
IonMatch |
This class represents the assignment of a peak to a theoretical ion.
|
IonMatch.MzErrorType |
Enum of the supported error types.
|
IonMatchKeysCache |
Cache for the keys of the ions.
|
IoUtil |
Utils for I/O and file handling.
|
Iron |
The iron atom.
|
Isoleucine |
Isoleucine.
|
IsotopeDistributionGui |
This class is a GUI that visualizes the isotopic calculator.
|
IsotopicDistribution |
This class calculates the isotopic distribution based on a molecular formula.
|
IsotopicDistributionPanel |
This class provides a JPanel that can display a peptide isotopic distribution.
|
IsotopicDistributionSpectrum |
This class is an implementation of the SpectrumFile specific for the isotopic distribution
Created by IntelliJ IDEA.
|
IsotopicElement |
This class represents the isotopically different element with the occurrence
and the dalton difference between this and the natural variant.
|
IteratorFactory |
The iterator goes through a sequence and lists possible peptides with their
fixed modifications.
|
J |
Isoleucine or Leucine.
|
JarFileFilter |
JarFileFilter.
|
JavaHomeDialog |
A dialog for changing the Java Home.
|
JavaHomeOrMemoryDialogParent |
Interface for parents of JavaMemoryDialog and JavaHomeDialog.
|
JavaMemoryDialog |
A dialog for changing the Java memory setting.
|
JavaParametersDialog |
A dialog for showing Java memory settings.
|
JExceptionDialog |
This class implements a JDialog for the specific purpose of showing unrecoverable
errors or exceptions.
|
JFrameForBytes |
This class implements a JFrame, made specifically for the
display of binary data.
|
JLabelAndComponentPanel |
This class implements a JPanel that lays out a set of JLabel and a JComponent
next to each other.
|
JOptionEditorPane |
A dialog to show HTML content with clickable links inside a JOptionsPane.
|
JpegFileFilter |
File filter for *.jpeg files.
|
JsonMarshaller |
This class converts non-specific objects to the JSON format and vice versa.
|
JTableForDB |
This class extends a JTable with specific cellrenderers for fields,
retrieved from DB.
|
KMeansClustering |
K-means clustering.
|
KMeansClusteringSettings |
Settings for k-means clustering.
|
LastSelectedFolder |
Convenience class keeping class of the last selected folders.
|
Leucine |
Leucine.
|
LinearRegression |
Enum of the different implementations for a regression.
|
ListChooser |
Dialog for choosing an item in a list.
|
Lithium |
The Lithium atom.
|
Logger |
This interface describes the behaviour for a class that can log messages.
|
Lysine |
Lysine.
|
Magnesium |
The magnesium atom.
|
MappingWorker | |
MarshallableParameter |
Interface for a parameter which can be marshalled as .par file.
|
MarshallableParameter.Type |
Enum of the type of parameter which can be encountered in a .par file.
|
MascotEnzymeReader |
This class will load Enzyme properties from a Mascot
(www.matrixscience.com)
formatted text file.
|
MascotIdfileReader |
This IdfileReader reads identifications from a Mascot results file.
|
MassCalc |
This class takes care of mass calculation, based on a sequence
in IUPAC format.
|
MassCalcServlet |
This class implements the MassCalc class as a servlet.
|
MassErrorBubblePlot |
Creates a MassErrorBubblePlot displaying the mz values vs the mass error with
the intensity as the size of the bubbles.
|
MassErrorPlot |
Creates a MassErrorPlot displaying the mz values vs the mass error.
|
MassGap |
An undefined mass gap.
|
MassIndexMap |
The mass index map.
|
MatchesImportParametersDialog |
The PeptideShaker import settings dialog.
|
MatchesIterator |
An abstract iterator class to iterate identification matches.
|
MatchFilter |
Abstract representing a filter.
|
MatchFilter.FilterType |
Enum for the type of possible filter.
|
MatchValidationLevel |
Enum listing the different levels of match validation.
|
MatrixContent |
Element for the matrix necessary in pattern search of the FMIndex.
|
MavenJarFile |
MavenJarFile.
|
MDScore |
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.
|
MedianRegression |
Performs a robust linear regression.
|
MemoryConsumptionStatus |
This class provides information on the memory consumption status.
|
MetaDataXMLParser |
MetaDataXMLParser.
|
MetaMorpheusParameters |
The MetaMorpheus specific parameters.
|
MetaMorpheusParameters.MetaMorpheusDecoyType |
The available decoy types.
|
MetaMorpheusParameters.MetaMorpheusDissociationType |
The available dissociation types.
|
MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType |
The available fragmentation terminus types.
|
MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType |
The available initiator methionine behavior types.
|
MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType |
The available mass difference acceptor types.
|
MetaMorpheusParameters.MetaMorpheusSearchType |
The available search types.
|
MetaMorpheusParameters.MetaMorpheusToleranceType |
The available decoy types.
|
MetaMorpheusParametersDialog |
Dialog for the MetaMorpheus specific parameters.
|
Methionine |
Methionine.
|
Metrics |
This class contains metrics gathered during the creation of a PeptideShaker project.
|
MetricsPrefix |
Enumeration of the metrics prefixes.
|
MgfFileFilter |
File filter for *.mgf files.
|
MgfFileIterator |
An iterator of the spectra in an mgf file.
|
MgfFileUtils |
Utilities for the handling of mgf files.
|
MgfFileWriter |
This class writes spectrum files in Mascot Generic File (mgf) format.
|
MgfIndex |
This class contains the indexes of an mgf file after indexing mapped with the
title of the spectrum.
|
MirroredSpectraTestDialog |
Mirrored spectra test class.
|
Modification |
This class models a peptide or protein modification.
|
Modification |
This interface describes the behaviour for a modification on a peptide or aminoacid sequence.
|
ModificationCategory |
Enum for the different modification categories supported.
|
ModificationChooser |
Dialog for choosing an item in a list of modifications.
|
ModificationDialog |
This dialog allows the user to create/edit Modifications.
|
ModificationFactory |
This factory will load Modification from an XML file and provide them on
demand as standard class.
|
ModificationFactory |
This class can be used to generate a Modification instance from a code or title.
|
ModificationFeature |
Feature based on the modification status of an amino acid.
|
ModificationFeature.Property |
Enum for the possible features.
|
ModificationImplementation |
This class implements a specific Modification.
|
ModificationLocalizationMapper |
Function attempting to map modification localization based on their type.
|
ModificationLocalizationParameters |
This class contains the modification localization preferences.
|
ModificationLocalizationParametersDialog |
PTMLocalizationParametersDialog.
|
ModificationLocalizationScore |
An enum of the modification localization scores.
|
ModificationMassMapper |
Function inferring the mass of a modification based on the search engine
used.
|
ModificationMatch |
This class models the match between theoretic PTM and identification results.
|
ModificationNameMapper |
Functions mapping search engine modifications to utilities by name.
|
ModificationParameters |
This class stores the information about the modification parameters (usage,
colors, names).
|
ModificationProfile |
A simple modification profile object.
|
ModificationProvider |
Interface for a modification provider.
|
ModificationsCLI |
Command line to manage the modifications.
|
ModificationsCLIInputBean |
This class parses the parameters from an ModificationsCLI.
|
ModificationsCLIParams |
Enum class specifying the ModificationsCLI parameters.
|
ModificationScoring |
This class contains stores the modification localization scores.
|
ModificationsDialog |
A dialog where the modification details can be modified.
|
ModificationSiteMapping |
This class contains convenience methods to map modifications on potential sites.
|
ModificationTable |
Table containing information about the peak annotation of a modified peptide.
|
ModificationtableContent |
Convenience class for the content of a PTM table.
|
ModificationTemplate |
This class holds a template for a Modification, meaning that it contains all shared characteristics of
a Modification, but not the instance-specific one.
|
ModificationType |
Enum for the different types of modifications supported.
|
ModificationUtils |
This class groups functions that can be used to work with modifications.
|
MolecularElement |
This ENUM types the distinct molecular elements.
|
MolecularFormula |
This class represents the molecular formula.
|
Monitorable |
This interface describes the behaviour for any Object whose progressing state
can be monitored.
|
MonitorableFileInputStream |
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.
|
MonitorableInputStream |
This class provides a specific FilterInputStream that can be monitored for progress.
|
MonitorDimension |
This class makes it possible to set the dimensions of a JFrame of JPanel
to a certain percentage of the screen size.
|
Ms2Exporter |
This class writes spectrum files in MS2 format.
|
Ms2FileFilter |
File filter for *.ms2 files.
|
Ms2FileWriter |
This class writes spectrum files in MS2 format.
|
Ms2pipFeature |
Interface for an ms2pip feature.
|
MsAmandaIdfileReader |
This IdfileReader reads identifications from an MS Amanda csv result file.
|
MsAmandaParameters |
The MS Amanda specific parameters.
|
MsAmandaParametersDialog |
Dialog for the MS Amanda specific settings.
|
MsConvertParameters |
The parameters to use when running msconvert.
|
MsConvertParametersDialog |
Dialog for the creation and edition of msconvert parameters.
|
MsFileExporter |
This class writes ms files in various formats.
|
MsFileExporter.Format |
Enum of the supported export formats.
|
MsFileHandler |
A spectrum provider for mass spectrometry files based on Compomics Mass
Spectrometry (cms) files.
|
MsFileIterator |
Interface for mass spectrometry file readers.
|
MsFilePerformance |
This script test the speed of the ms file access.
|
MsgfParameters |
The MS-GF+ specific parameters.
|
MsgfParametersDialog |
Dialog for the MS-GF+ specific settings.
|
MSNumpress |
MSNumpress.
|
MultipleAAPropertyFeature |
Interface for the ms2pip features having multiple amino acid properties.
|
MutexMap |
Mutex map for the features cache.
|
MyriMatchParameters |
The MyriMatch specific parameters.
|
MyriMatchParametersDialog |
Dialog for the MyriMatch specific settings.
|
MzDataFileFilter |
File filter for *.mzData files.
|
MzIdentMLIdfileReader |
This IdfileReader reads identifications from an mzIdentML result file.
|
MzIdentMLIdfileReader.RawValueConversionType |
Enum for the raw value to e-value conversion.
|
MzIdentMLIdfileSearchParametersConverter |
Reads basic search parameters from mzIdentML result files.
|
MzIdentMLVersion |
Enum of the versions of the mzIdentML format supported.
|
MzMlFileFilter |
File filter for *.mzML files.
|
MzmlFileIterator |
An iterator of the spectra in an mzml file.
|
MzmlFileIterator.Precision |
The supported precision types for the binary data as defined in the mzML
specifications and the PSI-MS ontology.
|
MzmlFileUtils |
Utilities for the handling of mzml files.
|
MzXmlFileFilter |
File filter for *.mzXML files.
|
NeutralLoss |
This class represents a neutral loss.
|
NeutralLossCombination |
This class represents a combination of multiple neutral losses.
|
NeutralLossesMap |
This class contains the informations relative to the accounting of neutral
losses
|
NewEnzymeDialog |
This dialog allows the user to create a new enzyme.
|
Nitrogen |
The nitrogen atom.
|
NoDigestionCombinationIterator |
Iterator for no digestion of a sequence containing amino acid combinations.
|
NoDigestionIterator |
Iterator for no digestion.
|
NonSymmetricalNormalDistribution |
This class represents a non symmetrical normal distribution.
|
NormalDistribution |
This class represents a normal distribution.
|
NormalizationFactors |
Class grouping the normalization factors used to normalize quantification
results.
|
NormalKernelDensityEstimator |
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.
|
NotesDialog |
A simple dialog for displaying notes.
|
NotificationDialog |
An undecorated dialog for displaying notifications.
|
NotificationDialogParent |
A NotificationDialog parent interface.
|
NovorIdfileReader |
This IdfileReader reads identifications from a Novor csv result file.
|
NovorParameters |
Novor specific parameters.
|
NovorParametersDialog |
Dialog for editing Novor advanced settings.
|
NucleotideSequence |
This class combines a protein Header with a nucleotide sequence.
|
NucleotideSequenceImpl |
This class represents a nucleotide sequence (RNA or DNA).
|
ObjectMutex |
This mutex can be used to manage threads editing experiment objects using
their key.
|
ObjectsCache |
An object cache can be combined to an ObjectDB to improve its performance.
|
ObjectsDB |
A database which can easily be used to store objects.
|
OmssaParameters |
The OMSSA specific parameters.
|
OmssaParametersDialog |
Dialog for the OMSSA specific parameters.
|
OmxFileFilter |
File filter for *.omx files.
|
OnyaseIdfileReader |
Id file reader for the scripts in Onyase.
|
OperatingSystemEnum |
This ENUM types the distinct OS systems.
|
OutFileFilter |
File filter for *.out files.
|
OutputParameters |
This enum lists the possible output options.
|
Oxygen |
The oxygen atom.
|
PathKey |
Interface for a path key.
|
PathParametersDialog |
Dialog used to set paths.
|
Patient |
This class groups the information about the patient from whom the sample is
taken
|
PatientInformation |
Information about the patient.
|
PdbBlock |
PdbBlock.
|
PdbParameter |
PdbParameter.
|
PdfFileFilter |
File filter for *.pdf files.
|
Peak |
This class represents a peak.
|
PeffFileFilter |
File filter for *.peff files.
|
PepnovoAssumptionDetails |
This class contains pepnovo assumption details which are not contained in the
tag assumption class which will be saved as additional parameter.
|
PepNovoIdfileReader |
This class can be used to parse PepNovo identification files.
|
PepnovoParameters |
PepNovo specific parameters.
|
PepNovoParametersDialog |
Dialog for editing the PepNovo advanced settings.
|
Peptide |
This class represents a peptide.
|
PeptideAminoAcidFeature |
Feature based on the amino acid properties of a peptide.
|
PeptideAndProteinBuilder |
This class builds peptides and proteins based on PSMs.
|
PeptideAssumption |
This object models the assumption made by an advocate.
|
PeptideAssumptionFilter |
This class filters peptide assumptions based on various properties.
|
PeptideDraft |
Draft of a peptide used during protein sequence digestion.
|
PeptideFeature |
Feature based on a peptide property.
|
PeptideFeature.Property |
Enum for the possible features.
|
PeptideFilter |
Peptide filter.
|
PeptideFilterItem |
Enum of the different items a peptide filter can filter on.
|
PeptideFragmentationModel |
Enum for the different peptide fragmentation models implemented.
|
PeptideFragmentIon |
This class models a peptide fragment ion.
|
PeptideInference |
Functions related to peptide inference.
|
PeptideMapperCLI |
Command line peptide mapping.
|
PeptideMatch |
This class models a peptide match.
|
PeptideMatchesIterator |
An iterator for peptide matches.
|
PeptideProteinMapping |
Class used to model the mapping of a peptide to a protein sequence.
|
PeptideShakerSetupDialog |
A dialog used to set up the connection to PeptideShaker.
|
PeptideSpectrumAnnotator |
Annotates a spectrum with peptide fragments.
|
PeptideUtils |
This class groups functions that can be used to work with peptides.
|
PeptideVariantMatches |
This class represents a set of variants found on a peptide.
|
PeptideVariantsParameters |
Preferences for the allowed variants in peptide sequences.
|
PeptideVariantsParameters.VariantType |
Enum indicating all three variant types
|
PeptideVariantsParametersDialog |
FractionSettingsDialog.
|
PepXmlFileFilter |
File filter for *.pep.xml, *.pepxml and *.xml files.
|
PepxmlIdfileReader |
Simple IdfileReader for Pepxml files.
|
Persistable |
This interface indicates that the implementing class can be persisted in permanent storage.
|
PersistableCode |
This class generates the code to make a DBAccessor an implementation of the Persistable
interface.
|
Phenylalanine |
Phenylalanine.
|
PhosphoRS |
This class estimates the PhosphoRS score as described in
https://www.ncbi.nlm.nih.gov/pubmed/22073976.
|
Phosphorus |
The phosphorus atom.
|
PickUp |
This interface describes the behaviour for a class that can pick up results.
|
PklFile |
Contains information about the contents of one PKL file.
|
PklFileFilter |
File filter for *.pkl files.
|
PklSpoFileFilter |
File filter for *.pkl.spo files.
|
PkxFileFilter |
File filter for *.pkx files.
|
PngFileFilter |
File filter for *.png files.
|
PNovoIdfileReader |
This class can be used to parse pNovo identification files.
|
PNovoParameters |
pNovo specific parameters.
|
PNovoParametersDialog |
Dialog for editing pNovo advanced settings.
|
Potassium |
The potassium atom.
|
Precursor |
This class models a precursor.
|
PrecursorAccuracy |
The precursor accuracy as a score.
|
PrecursorAnnotator |
Annotator for the precursor peaks.
|
PrecursorIon |
A precursor ion.
|
PrecursorMap |
This map stores the precursors indexed by mass.
|
PrideFilter |
An object to set up a filter for use in a query to the PRIDE webservice.
|
PrideFilterType |
An enum of the possible filters for the PRIDE Filter options.
|
PrideMarshaller |
A json marshaller for use with the PRIDE webservice.
|
PrideObject |
Interface for a PRIDE object.
|
PrideObjectsFactory |
This factory manages the pride objects saved in the user folder.
|
PrideQuery |
An enum that constructs the template queries for the PRIDE webservice.
|
PrideWebService |
A java representation of the PRIDE web service.
|
PrideXmlValidator |
PRIDE XML schema validation.
|
PrivacyParametersDialog |
The privacy settings dialog allows the user to set the privacy settings.
|
ProbabilityFilter |
Filter removing points with outlying slope.
|
ProcessingParameters |
ProcessingPreferences.
|
ProcessingParameters.ProcessingType |
Class indicating the type of processing.
|
ProcessingParametersDialog |
Dialog to edit the processing parameters.
|
ProgressDialog |
This class implements a modal dialog that is displayed during a longer-lasting task.
|
ProgressDialogX |
A dialog for displaying information about progress.
|
ProjectParameters |
This class contains project specific parameters.
|
ProjectType |
This enum lists the different types of projects that can be created using PeptideShaker.
|
Proline |
Proline.
|
PropertiesManager |
This class holds all user properties for ms_lims.
|
Protein |
This class models a protein.
|
Protein |
This class implements the behaviour for a Protein instance.
|
ProteinDatabase |
Enum of the supported protein databases.
|
ProteinDetailsProvider |
Interface for a class able to provide metadata on proteins.
|
ProteinFilter |
Protein filter.
|
ProteinFilterItem |
Enum of the different items a protein filter can filter on.
|
ProteinGeneDetailsProvider |
Class used to map proteins to gene information.
|
ProteinInferenceParameters |
Generic class grouping the protein inference preferences.
|
ProteinInferenceParametersDialog |
Dialog for the edition of the protein inference settings.
|
ProteinIterator |
Interface for a protein iterator.
|
ProteinIteratorUtils |
This class contains utilities used during the iteration of protein sequences.
|
ProteinMatch |
This class models a protein match.
|
ProteinMatchesIterator |
An iterator of protein matches.
|
ProteinSequencePane |
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.
|
ProteinUtils |
Convenience functions for the handling of proteins.
|
ProteoWizardFilter |
Filters which can be applied to msconvert.
|
ProteoWizardMsFormat |
The mass spectrometry formats supported by ProteoWizard.
|
ProteoWizardSetupDialog |
A dialog used to set up the connection to ProteoWizard.
|
Protocol |
An object for storing Protocol details.
|
ProtXmlFileFilter |
File filter for *.prot.xml, *.protxml and *.xml files.
|
PsAnnotationFeature |
This class lists the annotation export features.
|
PsFragmentFeature |
This class lists the fragment identification features.
|
PsIdentificationAlgorithmMatchesFeature |
This class lists the Algorithm identification features.
|
PsInputFilterFeature |
This enum lists the export features related to the import features.
|
PsmFilter |
PSM filter.
|
PsmFilterItem |
Enum of the different items a PSM filter can filter on.
|
PSModificationScores |
This class contains the scores for the locations of the possible
modifications.
|
PsmScore |
Enum listing the PSM scores implemented in compomics utilities.
|
PsmScoresEstimator |
This class can be used to estimate PSM scores.
|
PsmScoringParameters |
Generic class for peptide spectrum match scoring.
|
PsmScoringParametersDialog |
Dialog for the edition of the PSM scoring settings.
|
PSParameter |
PeptideShaker compomics utilities experiment customizable parameter.
|
PsPeptideFeature |
This class lists the peptide identification features.
|
PsProjectFeature |
This class lists the PSM identification features.
|
PsProteinFeature |
This class lists the protein identification features.
|
PsPsmFeature |
This class lists the PSM identification features.
|
PsPtmScoringFeature |
This enum groups the export features related to PTM scoring.
|
PsSearchFeature |
This class lists the export features linked to the spectrum identification.
|
PsSpectrumCountingFeature |
This class lists all the export features related to the spectrum counting.
|
PsValidationFeature |
This enum lists the export features linked to the validation process.
|
PTMFactoryMarshaller |
This class is a convenience class to have a DefaultJsonConverter with the
search parameter interfaces.
|
PtmToPrideMap |
Map linking user modification names to Unimod CV terms.
|
PushBackStringReader |
This class implements a PushBackReader for Strings which allows the reading
of entire lines as well as the pushing back of entire lines.
|
Pyrrolysine |
Pyrrolysine.
|
Quantification |
An abstract quantification class.
|
Quantification.QuantificationMethod |
The implemented quantification methods.
|
Rank |
Rank as used in the FM index.
|
Reagent |
A reporter ion labeling reagent.
|
RecalibrationUtils |
Utility functions for spectrum recalibration.
|
Reference |
A simple publication reference object.
|
ReferenceArea |
A reference area to be added to a GraphicsPanel.
|
ReferenceGroup |
An object for storing ReferenceGroup details.
|
RegExEnzyme |
This class implements the functionality of an Enzyme by
simulating digestion based on a regular expression.
|
RegressionStatistics |
Results of a linear regression of equation y = a.x + b and Pearson
correlation r.
|
RelatedIon |
Represents a related ion, i.e., an ion that is related to a given amino acid,
and is its own factory.
|
ReportEditor |
Dialog for editing reports.
|
ReporterExportFeature |
Reporter extension of the utilities export features.
|
ReporterIon |
This class models a reporter ion and is its own factory.
|
ReporterIonAnnotator |
Annotator for reporter ions.
|
ReporterIonQuantification |
This class contains quantification parameters.
|
ReporterMethod |
This class contains information relative to a reporter quantification method.
|
ReporterMethodFactory |
This factory imports reporter methods details from an XMl file.
|
ReporterPeptideFeature |
This enum lists all the peptide export features available from reporter
complementarily to the ones available in PeptideShaker.
|
ReporterProteinFeatures |
This enum lists all the protein export features available from reporter
complementarily to the ones available in PeptideShaker.
|
ReporterPsmFeatures |
This enum lists all the PSM export features available from reporter
complementarily to the ones available in PeptideShaker.
|
ReporterSetupDialog |
A dialog used to set up the connection to Reporter.
|
RescalingEvent |
This class implements a resizing event that occurred on a SpectrumPanel.
|
Retrievable |
This interface indicates that the implementing class can be retrieved from permanent storage.
|
RetrievableCode |
This class generates the code to make a DBAccessor an implementation of the Retrieveable
interface.
|
ROC |
This class can be used to draw ROC curves.
|
Sample |
An object for storing Sample details.
|
SampleSelection |
Class which allows the selection of the right identification.
|
ScalingFactorsEstimators |
This class estimates spectrum counting scaling factors.
|
SearchGuiSetupDialog |
A dialog used to set up the connection between PeptideShaker and SearchGUI.
|
SearchParameters |
This class groups the parameters used for identification.
|
SearchParameters.MassAccuracyType |
Possible mass accuracy types.
|
SearchParametersDialog |
The search settings dialog.
|
Selenium |
Selenium.
|
Selenocysteine |
SeC (U) (Mascot)-
|
SelfUpdatingTableModel |
These table models include a self updating function.
|
Sequence |
This interface defines the default behavior of any kind of
sequence with a certain mass - be it DNA, protein or something
else.
|
SequenceDbDetailsDialog |
This dialog displays information about a sequence database.
|
SequenceFragmentationPanel |
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.
|
SequenceIterator |
Interface for an iterator returning peptides along a protein sequence.
|
SequenceMatchingParameters |
The sequence matching options.
|
SequenceMatchingParameters.MatchingType |
The different types of amino acid matching.
|
SequenceMatchingParametersDialog |
Dialog for the edition of the sequence matching settings.
|
SequenceModificationPanel |
A panel for displaying modification profiles.
|
SequenceProvider |
Interface for a class able to retrieve the sequence of a given protein.
|
SequestFragmentationModel |
Fragmentation model originally described in the Sequest algorithm
(https://www.ncbi.nlm.nih.gov/pubmed/24226387) adapted to utilities objects.
|
SequestParamsFileFilter |
File filter for sequest.params files.
|
SerializationUtils |
This class implements convenience methods for serialization and
deserialization.
|
Serine |
Serine.
|
SimpleFileReader |
Interface for file readers.
|
SimpleFileWriter |
Simple gz file writer that is thread safe and throws exceptions as runtime
exceptions.
|
SimpleGzReader |
Simple wrapper for a gz file reader.
|
SimpleLinearRegression |
Performs a simple linear regression.
|
SimpleMzIdentMLExporter |
Simple mzIdentML exporter for PSM-level results.
|
SimpleNoiseDistribution |
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.
|
SimplePeptideAnnotator |
A simple annotator for peptides.
|
SimplePeptideAnnotator.IonSeries |
The type of ion series to annotate.
|
SimpleSemaphore |
A simple semaphore where thread interrupted exception are thrown as runtime exception.
|
SimpleTextReader |
Simple wrapper for a flat file reader.
|
SimpleXmlWriter |
Simple writer for xml files.
|
SingleAAPropertyFeature |
Interface for the ms2pip features having a single amino acid property.
|
SingleProteinSequenceProvider |
Sequence provider for a single protein.
|
SNPElement | |
SnrScore |
This score uses the intensity distribution of the peaks to evaluate an SNR
score.
|
Sodium |
The sodium atom.
|
SparklineColorsDialog |
Dialog for user selection of the colors used by the sparklines.
|
SpeciesDialog | Deprecated.
use the GenePreferencesDialog instead
|
SpeciesFactory |
Class related to the handling of species.
|
SpecificAnnotationParameters |
The spectrum annotation preferences specific to a spectrum and an
identification assumption.
|
SpecificSingleEnzymeCombinationIterator |
Iterator for enzymatic digestion.
|
SpecificSingleEnzymeIterator |
Iterator for enzymatic digestion.
|
Spectrum |
This class models a spectrum.
|
SpectrumAnnotation |
This interface describes the behaviour for a spectrum annotation.
|
SpectrumAnnotator |
The spectrum annotator annotates peaks in a spectrum.
|
SpectrumAnnotator.TiesResolution |
Enum of the possibilities for ties resolution when multiple peaks can be
annotated.
|
SpectrumCountingMethod |
Enum of the implemented spectrum counting methods.
|
SpectrumCountingParameters |
This class contains the spectrum counting parameters.
|
SpectrumFile |
This interface describes the behaviour for a spectrum file
(ie., PKL file, Mascot Generic file, dat file, ...).
|
SpectrumIdentificationAssumption |
Spectrum identification assumption made by an identification algorithm.
|
SpectrumIndex |
This map stores the fragment ions indexed by mass.
|
SpectrumMatch |
This class models a spectrum match.
|
SpectrumMatchesIterator |
An iterator for spectrum matches.
|
SpectrumPanel |
This class presents a JPanel that will hold and display a mass spectrum in
centroid or profile mode.
|
SpectrumPanelListener |
This interface describes the behaviour for a listener that wants to receive information
about events that occurred on a SpectrumPanel.
|
SpectrumProvider |
Interface for objects providing spectra.
|
SpectrumUtil |
Utilities functions to handle spectra.
|
SplashScreen |
Class that takes care of converting an svg file to a png file using the
command line version of apache batik.
|
StandardMasses |
Enum of standard masses.
|
StandardUnit |
The standard units implemented.
|
StartBrowser |
This class starts a browser for the given URL.
|
StartEndPosition |
StartEndPosition.
|
StreamGobbler |
A stream gobbler.
|
StreamUtil |
Convenience methods to work with lambdas.
|
StringListChooser |
Dialog for choosing an item in a list of String.
|
Substitution |
Class representing an amino acid substitution.
|
Sulfur |
The sulfur atom.
|
SvgFileFilter |
File filter for *.svg files.
|
Swap |
Class representing an amino acid swap.
|
SwingUtils |
Swing utilities methods.
|
SwingWorker |
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.
|
TableMap |
In a chain of data manipulators some behaviour is common.
|
TableMouseWheelListener |
MouseWheelListener for SelfUpdatingTableModels that supports scrolling in a
more efficient way.
|
TableProperties |
This class groups properties for the tables
|
TableScrollBarListener |
AdjustmentListener for SelfUpdatingTableModels supporting scrolling in a more
efficient way.
|
TableSorter |
A sorter for TableModels.
|
TableValueWrapper |
This interface describes the behaviour for a class that wraps a table element.
|
Tag |
This class represents a sequence mass tag.
|
TagAssumption |
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
|
TagComponent |
Interface for a sequence tag component.
|
TagElement |
The tag element.
|
TagFactory |
Convenience class for sequence tag generation.
|
TagFragmentIon |
A fragment ion obtained from a tag.
|
TagSpectrumAnnotator |
Annotates a spectrum with information from a tag.
|
TagUtils |
This class groups functions that can be used to work with peptides.
|
TarUtils |
This class contains convenience methods for taring files.
|
TempByteArray |
Convenience class for storing an array buffer and a length.
|
TempFilesManager |
This class can be used to reference temp files and manage them.
|
TestCaseLM |
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.
|
TextWriter |
ExportWriter for the export to text files.
|
ThermoRawFileParserOutputFormat |
The mass spectrometry output formats supported by ThermoRawFileParser.
|
ThermoRawFileParserParameters |
The parameters to use when running ThermoRawFileParser.
|
ThermoRawFileParserParametersDialog |
Dialog for the creation and edition of ThermoRawFileParser parameters.
|
Threonine |
Threonine.
|
TideIdfileReader |
This IdfileReader reads identifications from an Tide tsv results file.
|
TideParameters |
The Tide specific parameters.
|
TideParametersDialog |
Dialog for the Tide specific settings.
|
TiffFileFilter |
File filter for *.tiff files.
|
TimestampRenderer |
TimestampRenderer.
|
ToolFactory |
This class can be used to start compomics tools.
|
ToolTipComboBoxRenderer |
A combo box renderer that allows tooltip for each element in the combo box
list.
|
Translate |
This class allows the user to translate a DNA sequence into 6 reading frames.
|
Tryptophan |
Tryptophan.
|
Tyrosine |
Tyrosine.
|
UniformFragmentation |
Dummy intensity predictor that returns 1.0 for every ion.
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UniprotTaxonomy |
Mapping of the UniProt taxonomy.
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UnitOfMeasurement |
The unit to use for a measure.
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Units |
Convenience class providing units.
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UnknownElementMassException |
This class implements an Exception, thrown when a MassCalc instance
is confronted with an element symbol it cannot retrieve in its
element lists.
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UnspecificCombinationIterator |
Iterator for unspecific cleavage.
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UnspecificIterator |
Iterator for unspecific cleavage.
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Updateable |
This interface indicates that the implementing class can be updated in permanent storage.
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UpdateableCode |
This class generates the code to make a DBAccessor an implementation of the Updateable
interface.
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UrParameter |
This interface is used to reference refinement parameters.
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Util |
Includes general help methods that are used by the other classes.
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UtilitiesDemo |
This class serves as a demo of how the compomics-utilities library can be
used in other projects.
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UtilitiesGUIDefaults |
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.
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UtilitiesPathParameters |
This class sets the path preferences for the files to read/write.
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UtilitiesPathParameters.UtilitiesPathKey |
Enum of the paths which can be set in utilities.
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UtilitiesUserParameters |
Utilities user parameters can be used to store user parameters.
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ValidationParametersDialog |
Dialog for the edition of the sequence matching settings
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ValidationQcParameters |
This class lists the criteria used for quality control of the validated
matches.
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ValidationQCParametersDialog |
Dialog for the edition of validation QC filters.
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Valine |
Valine.
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Variant |
Interface for a variant.
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VennDiagram |
Class for calculating the groups for Venn diagrams.
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VennDiagramDialog |
A dialog for creating and displaying Venn diagrams.
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VennDiagramLegendLocationDialog |
Dialog for setting the location of the legend items in a Venn diagram.
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VennDiagramPanel |
A panel displaying a Venn diagram based on the provided data.
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VennDiagramPanel.VennDiagramType |
The supported Venn diagram types.
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VisibleTableColumnsDialog |
A dialog that lets the user decide which columns to show/hide in a JTable.
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VisibleTableColumnsDialogParent |
Interface for parents of VisibleTableColumnsDialog.
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WaitingActionListener |
This class is used to pass actions like cancel while waiting.
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WaitingDialog |
A dialog displaying progress details.
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WaitingDialogExceptionHandler |
Exception handler for processes making use of a waiting dialog.
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WaitingHandler |
An interface for code dealing with how to handle information that is
displayed to the user during loading or processing.
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WaitingHandlerCLIImpl |
This class is an implementation of the WaitingHandler interface to be used
when operating through the Command Line Interface.
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WaitingHandlerDummy |
This class is an implementation of the WaitingHandler interface to be used
when a process can be canceled, but no monitoring is needed.
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WaveletTree |
Wavelet tree.
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WebDAO |
WebDAO.
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WorkbookStyle |
This interface sets the style of a workbook export.
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WriterBySection |
This writer writes the different sections of a file in temp files and bundles
them together upon completion.
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X |
Unknown amino acid (Mascot).
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XmlFileFilter |
File filter for *.xml files.
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XMLValidationErrorHandler |
Edited using IntelliJ IDEA Date: 16-Sep-2005 Time: 15:26:12
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XTandemIdfileReader |
This IdfileReader reads identifications from an X! Tandem xml result file.
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XtandemParameters |
The X!Tandem specific parameters.
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XTandemParametersDialog |
Dialog for the X!Tandem specific settings.
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XYPlotFiltersDialog |
Dialog for editing the data filters for an XYPlottingDialog.
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XYPlottingDialog |
A dialog that makes it straightforward to inspect compare the values of two
columns in a table in a XY plot.
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XYPlottingDialog.PlottingDialogPlotType |
The plotting dialog types.
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XYZDataPoint |
Object that stores data about one data point in an XYZ plot.
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Z |
Glu or Gln: Glx (Mascot).
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Zinc |
The zinc atom.
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ZipUtils |
Convenience class for the handling of zip files.
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ZstdUtils |
Functions needed for compression and decompression.
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