All Classes
AAIntensityRankScore
AAMS2MzFidelityScore
AASequenceImpl
AbstractIdentificationParametersCli
AdvancedProteinDatabaseDialog
Advocate
Advocate.AdvocateType
Alanine
AlignedListCellRenderer
AlignedTableCellRenderer
AlignmentBlock
AlternateRowColoursJTable
AminoAcid
AminoAcidPattern
AminoAcidPattern.MatchingType
AminoAcidPatternDialog
AndromedaIdfileReader
AnnotationPreferences
Arginine
AScore
Asparagine
AsparticAcid
Atom
B
BareBonesBrowserLaunch
BasicMathFunctions
BinaryArrayImpl
BugReport
ByteArrayRenderer
Carbon
Charge
ChromatogramPanel
ColumnTypeConverter
CommandLineParser
CommandLineUtils
CompareVersionNumbers
CompareVersionNumbers
ComplementarityScore
CompomicsTools
CompomicsWrapper
Connectable
ConnectionDialog
Constructors
Contact
ContactGroup
CvTerm
Cysteine
DasAlignment
DasAnnotationServerAlingmentReader
DasAnnotationServerResultReader
DasFeature
DateChooser
DatFileFilter
DBAccessor
DBAccessorGenerator
DBElement
DBMetaData
DBResultSet
DefaultOutputLoggerImplementation
DefaultSpectrumAnnotation
Deleteable
DeleteableCode
DerbyUtil
DirecTagIdfileReader
DirecTagParameters
Distribution
DoubleMatrix
DownloadLatestZipFromRepo
DtaFileFilter
DualEnzyme
DummyFrame
ElementaryElement
ElementaryIon
Enzyme
Enzyme
EnzymeFactory
EnzymeSelectionDialog
ExceptionHandler
ExperimentIO
ExperimentObject
Export
ExportFactory
ExportFeature
ExportGraphicsDialog
ExportGraphicsDialogParent
ExportScheme
FastaFileFilter
FastaIndex
FeedBack
FeedBack.FeedBackType
FileDAO
FileDisplayDialog
FileFilterUtils
FileLoggerImplementation
FilenameExtensionFilter
FileSelectionDialog
FileSystemAccessor
FindPdbForUniprotAccessions
Flamable
FlamableJFrame
FolderMonitor
FragmentIonTable
FragmentIonTableCellRenderer
FTP
FTPClient
FtpConnectionException
FTPDownloader
FtpLoginException
FtpProtocolException
GeneDetailsDialog
GeneFactory
GenePreferences
GeneratorException
GettersAndSetters
GlutamicAcid
Glutamine
Glycine
Glycon
GlyconFactory
GOFactory
GraphicsPanel
GraphicsPanel.DrawingStyle
GraphicsPanel.GraphicsPanelType
GraphicsPanelTableCellRenderer
GUIFileDAO
GuiUtilities
Header
Header.DatabaseType
HeadlessFileDAO
HelpDialog
HelpWindow
Histidine
Hydrogen
Identification
IdentificationAlgorithmParameter
IdentificationDB
IdentificationMatch
IdentificationMatch.MatchType
IdentificationMethod
IdentificationParametersCLIParams
IdentificationParametersInputBean
IdentificationParametersReader
IdfileReader
IdfileReaderFactory
IdFilter
ImageType
ImmoniumIon
ImportSettingsDialog
InstanceVariables
Instrument
IntensityHistogram
IntensityRankScore
Ion
Ion.IonType
IonFactory
IonLabelColorTableModel
IonMatch
Isoleucine
IsotopeDistributionGui
IsotopicDistribution
IsotopicDistributionPanel
IsotopicDistributionSpectrum
IsotopicElement
J
JarFileFilter
JavaMemoryDialog
JavaMemoryDialogParent
JavaSettingsDialog
JExceptionDialog
JFrameForBytes
JLabelAndComponentPanel
JOptionEditorPane
JpegFileFilter
JTableForDB
Leucine
Logger
Lysine
MascotEnzymeReader
MascotScore
MassCalc
MassCalcServlet
MassErrorBubblePlot
MassErrorPlot
MassGap
MavenJarFile
MDScore
MetaDataXMLParser
Methionine
MgfFileFilter
MgfIndex
MgfReader
MirroredSpectraTestDialog
Modification
ModificationFactory
ModificationImplementation
ModificationMatch
ModificationProfile
ModificationProfile
ModificationsDialog
ModificationTemplate
MolecularElement
MolecularFormula
Monitorable
MonitorableFileInputStream
MonitorableInputStream
MonitorDimension
MS1Spectrum
Ms2FileFilter
Ms2Identification
MS2MzFidelityScore
MsAmandaIdfileReader
MsAmandaParameters
MsAmandaScore
MsAmandaSettingsDialog
MsExperiment
MsgfParameters
MsgfSettingsDialog
MSnSpectrum
Mutation
MutationFactory
MzDataFileFilter
MzIdentMLIdfileReader
MzIdentMLIdfileSearchParametersConverter
MzIdentMLValidator
MzMlFileFilter
MzXmlFileFilter
NeutralLoss
NeutralLossesMap
Nitrogen
Node
NonSymmetricalNormalDistribution
NormalDistribution
NotesDialog
NotificationDialog
NotificationDialogParent
NucleotideSequence
NucleotideSequenceImpl
ObjectsCache
ObjectsDB
OmssaParameters
OmssaSettingsDialog
OmxFileFilter
OperatingSystemEnum
OutFileFilter
Oxygen
Patient
PatientInformation
PdbBlock
PdbParameter
PdfFileFilter
Peak
PeffFileFilter
PepnovoAssumptionDetails
PepNovoIdfileReader
PepnovoParameters
Peptide
PeptideAssumption
PeptideFragmentIon
PeptideMatch
PeptideShakerSetupDialog
PeptideSpectrumAnnotator
PepXmlFileFilter
Persistable
PersistableCode
Phenylalanine
PhosphoRS
Phosphorus
PickUp
PklFile
PklFileFilter
PklSpoFileFilter
PkxFileFilter
PngFileFilter
Precursor
PrecursorAccuracy
PrecursorIon
PrideObject
PrideObjectsFactory
PrideXmlValidator
PrivacySettingsDialog
ProcessingPreferences
ProcessingPreferencesDialog
ProgressDialog
ProgressDialogX
Proline
PropertiesManager
Protein
Protein
ProteinMatch
ProteinSequencePane
ProteinTree
ProteinTreeComponentsFactory
ProteomicAnalysis
Protocol
ProtXmlFileFilter
PsmScores
PTM
PtmChooser
PtmDialog
PtmDialogParent
PTMFactory
PtmScore
PTMScoringPreferences
PtmSiteMapping
PtmtableContent
PtmToPrideMap
PushBackStringReader
Pyrrolysine
Quantification
Quantification.QuantificationMethod
Reagent
Reference
ReferenceArea
ReferenceGroup
RegExEnzyme
RelimsSetupDialog
ReportEditor
ReporterIon
ReporterIonQuantification
ReporterMethod
ReporterMethodFactory
ReporterSetupDialog
RescalingEvent
Retrievable
RetrievableCode
ROC
Sample
Sample
SampleAnalysisSet
SampleSelection
SearchGuiSetupDialog
SearchParameters
SearchParameters.MassAccuracyType
SearchParameters.PrecursorAccuracyType
SearchSettingsDialog
SearchSettingsDialogParent
Selenocysteine
SelfUpdatingTableModel
Sequence
SequenceDbDetailsDialog
SequenceFactory
SequenceFragmentationPanel
SequenceModificationPanel
SequestParamsFileFilter
SerializationUtils
Serine
SpeciesDialog
Spectrum
SpectrumAnnotation
SpectrumAnnotator
SpectrumCounting
SpectrumCounting.SpectrumCountingMethod
SpectrumFactory
SpectrumFile
SpectrumIdentificationAssumption
SpectrumMatch
SpectrumPanel
SpectrumPanelListener
SplashScreen
StartBrowser
StartEndPosition
StreamGobbler
Sulfur
SvgFileFilter
SwingUtils
SwingWorker
TableMap
TableMouseWheelListener
TableProperties
TableScrollBarListener
TableSorter
TableValueWrapper
Tag
TagAssumption
TagComponent
TagFactory
TagFragmentIon
TagSpectrumAnnotator
TarUtils
TestCaseLM
Threonine
TiffFileFilter
TimestampRenderer
ToolFactory
ToolTipComboBoxRenderer
Translate
Tryptophan
Tyrosine
UnknownElementMassException
Updateable
UpdateableCode
UrParameter
Util
UtilitiesDemo
UtilitiesGUIDefaults
UtilitiesPathPreferences
UtilitiesPathPreferences.UtilitiesPathKey
UtilitiesUserPreferences
Valine
VennDiagram
VennDiagramDialog
VennDiagramLegendLocationDialog
VennDiagramPanel
VennDiagramPanel.VennDiagramType
VisibleTableColumnsDialog
VisibleTableColumnsDialogParent
WaitingActionListener
WaitingDialog
WaitingHandler
WaitingHandlerCLIImpl
WebDAO
X
XmlFileFilter
XMLValidationErrorHandler
XtandemParameters
XTandemSettingsDialog
XYPlotFiltersDialog
XYPlottingDialog
XYZDataPoint
Z