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.
UniprotTaxonomy
Mapping of the UniProt taxonomy.
UnitOfMeasurement
The unit to use for a measure.
Units
Convenience class providing units.
UnknownElementMassException
This class implements an Exception, thrown when a MassCalc instance is confronted with an element symbol it cannot retrieve in its element lists.
UnspecificCombinationIterator
Iterator for unspecific cleavage.
UnspecificIterator
Iterator for unspecific cleavage.
Updateable
This interface indicates that the implementing class can be updated in permanent storage.
UpdateableCode
This class generates the code to make a DBAccessor an implementation of the Updateable interface.
UrParameter
This interface is used to reference refinement parameters.
Util
Includes general help methods that are used by the other classes.
UtilitiesDemo
This class serves as a demo of how the compomics-utilities library can be used in other projects.
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.
UtilitiesPathParameters
This class sets the path preferences for the files to read/write.
UtilitiesPathParameters.UtilitiesPathKey
Enum of the paths which can be set in utilities.
UtilitiesUserParameters
Utilities user parameters can be used to store user parameters.
ValidationParametersDialog
Dialog for the edition of the sequence matching settings
ValidationQcParameters
This class lists the criteria used for quality control of the validated matches.
ValidationQCParametersDialog
Dialog for the edition of validation QC filters.
Valine
Valine.
Variant
Interface for a variant.
VennDiagram
Class for calculating the groups for Venn diagrams.
VennDiagramDialog
A dialog for creating and displaying Venn diagrams.
VennDiagramLegendLocationDialog
Dialog for setting the location of the legend items in a Venn diagram.
VennDiagramPanel
A panel displaying a Venn diagram based on the provided data.
VennDiagramPanel.VennDiagramType
The supported Venn diagram types.
VisibleTableColumnsDialog
A dialog that lets the user decide which columns to show/hide in a JTable.
VisibleTableColumnsDialogParent
Interface for parents of VisibleTableColumnsDialog.
WaitingActionListener
This class is used to pass actions like cancel while waiting.
WaitingDialog
A dialog displaying progress details.
WaitingDialogExceptionHandler
Exception handler for processes making use of a waiting dialog.
WaitingHandler
An interface for code dealing with how to handle information that is displayed to the user during loading or processing.
WaitingHandlerCLIImpl
This class is an implementation of the WaitingHandler interface to be used when operating through the Command Line Interface.
WaitingHandlerDummy
This class is an implementation of the WaitingHandler interface to be used when a process can be canceled, but no monitoring is needed.
WaveletTree
Wavelet tree.
WebDAO
WebDAO.
WorkbookStyle
This interface sets the style of a workbook export.
WriterBySection
This writer writes the different sections of a file in temp files and bundles them together upon completion.
X
Unknown amino acid (Mascot).
XmlFileFilter
File filter for *.xml files.
XMLValidationErrorHandler
Edited using IntelliJ IDEA Date: 16-Sep-2005 Time: 15:26:12
XTandemIdfileReader
This IdfileReader reads identifications from an X! Tandem xml result file.
XtandemParameters
The X!Tandem specific parameters.
XTandemParametersDialog
Dialog for the X!Tandem specific settings.
XYPlotFiltersDialog
Dialog for editing the data filters for an XYPlottingDialog.
XYPlottingDialog
A dialog that makes it straightforward to inspect compare the values of two columns in a table in a XY plot.
XYPlottingDialog.PlottingDialogPlotType
The plotting dialog types.
XYZDataPoint
Object that stores data about one data point in an XYZ plot.
Z
Glu or Gln: Glx (Mascot).
Zinc
The zinc atom.
ZipUtils
Convenience class for the handling of zip files.
ZstdUtils
Functions needed for compression and decompression.