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 an XML 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
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| TideParameters |
The Tide specific parameters.
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| TideParametersDialog |
Dialog for the Tide specific settings.
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| TiffFileFilter |
File filter for *.tiff files.
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| TimestampRenderer |
TimestampRenderer.
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| ToolFactory |
This class can be used to start compomics tools.
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| ToolTipComboBoxRenderer |
A combo box renderer that allows tooltip for each element in the combo box
list.
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| Translate |
This class allows the user to translate a DNA sequence into 6 reading frames.
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| Tryptophan |
Tryptophan.
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| Tyrosine |
Tyrosine.
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| 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.
|
| 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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