All Classes
AASequenceImpl
Advocate
AdvocateFactory
Alanine
AlignedListCellRenderer
AlignedTableCellRenderer
AlignmentBlock
AlternateRowColoursJTable
AminoAcid
AndromedaIdfileReader
AnnotationPreferences
Arginine
Asparagine
AsparticAcid
Atom
B
BareBonesBrowserLaunch
BasicMathFunctions
BinaryArrayImpl
ByteArrayRenderer
Carbon
Charge
ChromatogramPanel
ColumnTypeConverter
CommandLineParser
CompomicsTools
Connectable
ConnectionDialog
Constructors
Contact
CorrectionFactor
CvTerm
Cysteine
DasAlignment
DasAnnotationServerAlingmentReader
DasAnnotationServerResultReader
DasFeature
DateChooser
DatFileFilter
DBAccessor
DBAccessorGenerator
DBElement
DBMetaData
DBResultSet
DefaultOutputLoggerImplementation
DefaultSpectrumAnnotation
Deleteable
DeleteableCode
DtaFileFilter
DualEnzyme
ElementaryIon
Enzyme
Enzyme
EnzymeFactory
ExperimentIO
ExperimentObject
Export
FastaFileFilter
FastaIndex
FileFilterUtils
FileLoggerImplementation
FilenameExtensionFilter
FileSystemAccessor
FindPdbForUniprotAccessions
Flamable
FlamableJFrame
FolderMonitor
FragmentIonTable
FragmentIonTableCellRenderer
FTP
FTPClient
FtpConnectionException
FtpLoginException
FtpProtocolException
GeneratorException
GettersAndSetters
GlutamicAcid
Glutamine
Glycine
Glycon
GlyconFactory
GraphicsPanel
GraphicsPanel.GraphicsPanelType
GraphicsPanelTableCellRenderer
Header
Header.DatabaseType
HelpDialog
HelpWindow
Histidine
Hydrogen
Identification
IdentificationDB
IdentificationMatch
IdentificationMatch.MatchType
IdentificationMethod
IdentificationParametersReader
IdfileReader
IdfileReaderFactory
ImageType
ImmoniumIon
InstanceVariables
Instrument
IntensityHistogram
Ion
Ion.IonType
IonFactory
IonLabelColorTableModel
IonMatch
Isoleucine
IsotopeDistributionGui
IsotopicDistribution
IsotopicDistributionPanel
IsotopicDistributionSpectrum
IsotopicElement
J
JExceptionDialog
JFrameForBytes
JLabelAndComponentPanel
JpegFileFilter
JTableForDB
Leucine
Logger
Lysine
MascotEnzymeReader
MascotIdfileReader
MascotScore
MassCalc
MassCalcServlet
MassErrorBubblePlot
MassErrorPlot
Methionine
MgfFileFilter
MgfIndex
MgfReader
Modification
ModificationFactory
ModificationImplementation
ModificationMatch
ModificationProfile
ModificationTemplate
MolecularElement
MolecularFormula
Monitorable
MonitorableFileInputStream
MonitorableInputStream
MonitorDimension
MS1Spectrum
Ms2FileFilter
Ms2Identification
MsExperiment
MSnSpectrum
MzDataFileFilter
MzMlFileFilter
MzXmlFileFilter
NeutralLoss
NeutralLossesMap
Nitrogen
NucleotideSequence
NucleotideSequenceImpl
ObjectsCache
ObjectsDB
OMSSAIdfileReader
OmxFileFilter
OperatingSystemEnum
OutFileFilter
Oxygen
PdbBlock
PdbParameter
PdfFileFilter
Peak
PeffFileFilter
Peptide
PeptideAssumption
PeptideFragmentIon
PeptideMatch
PeptideQuantification
PepXmlFileFilter
Persistable
PersistableCode
Phenylalanine
Phosphorus
PickUp
PklFile
PklFileFilter
PklSpoFileFilter
PkxFileFilter
PngFileFilter
PostProcessor
Precursor
PrecursorIon
PrideObject
PrideObjectsFactory
ProgressDialog
ProgressDialogX
Proline
PropertiesManager
Protein
Protein
ProteinMatch
ProteinQuantification
ProteinSequencePane
ProteomicAnalysis
Protocol
ProtXmlFileFilter
PsmQuantification
PTM
PtmDialog
PtmDialogParent
PTMFactory
PTMLocationScores
PtmtableContent
PtmToPrideMap
PushBackStringReader
Pyrrolysine
Quantification
Quantification.QuantificationMethod
QuantificationDB
QuantificationMatch
QuantificationMatch.MatchType
Ratio
Reference
ReferenceArea
RegExEnzyme
ReporterIon
ReporterIonQuantification
ReporterMethod
ReporterMethodFactory
RescalingEvent
Retrievable
RetrievableCode
Sample
Sample
SampleAnalysisSet
SampleSelection
SearchEngine
Selenocysteine
Sequence
SequenceFactory
SequenceFragmentationPanel
SequenceModificationPanel
SequestParamsFileFilter
Serine
Spectrum
SpectrumAnnotation
SpectrumAnnotator
SpectrumCounting
SpectrumCounting.SpectrumCountingMethod
SpectrumFactory
SpectrumFile
SpectrumMatch
SpectrumPanel
SpectrumPanelListener
StartBrowser
StartEndPosition
Sulfur
SvgFileFilter
SwingWorker
TableMap
TableSorter
TableValueWrapper
Threonine
TiffFileFilter
TimestampRenderer
ToolTipComboBoxRenderer
Translate
Tryptophan
Tyrosine
UnknownElementMassException
Updateable
UpdateableCode
UrParameter
Util
UtilitiesDemo
UtilitiesGUIDefaults
UtilitiesUserPreferences
Valine
WaitingDialog
WaitingHandler
WaitingHandlerCLIImpl
X
XmlFileFilter
XTandemIdfileReader
XYZDataPoint
Z