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Package Hierarchies:
com.compomics.software
,
com.compomics.software.autoupdater
,
com.compomics.software.dialogs
,
com.compomics.util
,
com.compomics.util.db
,
com.compomics.util.db.components
,
com.compomics.util.db.interfaces
,
com.compomics.util.denovo
,
com.compomics.util.enumeration
,
com.compomics.util.examples
,
com.compomics.util.experiment
,
com.compomics.util.experiment.annotation.gene
,
com.compomics.util.experiment.annotation.go
,
com.compomics.util.experiment.biology
,
com.compomics.util.experiment.biology.aminoacids
,
com.compomics.util.experiment.biology.atoms
,
com.compomics.util.experiment.biology.ions
,
com.compomics.util.experiment.identification
,
com.compomics.util.experiment.identification.advocates
,
com.compomics.util.experiment.identification.identifications
,
com.compomics.util.experiment.identification.matches
,
com.compomics.util.experiment.identification.protein_inference.proteintree
,
com.compomics.util.experiment.identification.ptm
,
com.compomics.util.experiment.identification.ptm.ptmscores
,
com.compomics.util.experiment.identification.scoring
,
com.compomics.util.experiment.io
,
com.compomics.util.experiment.io.identifications
,
com.compomics.util.experiment.io.identifications.idfilereaders
,
com.compomics.util.experiment.io.massspectrometry
,
com.compomics.util.experiment.massspectrometry
,
com.compomics.util.experiment.personalization
,
com.compomics.util.experiment.quantification
,
com.compomics.util.experiment.quantification.matches
,
com.compomics.util.experiment.quantification.reporterion
,
com.compomics.util.experiment.quantification.spectrumcounting
,
com.compomics.util.experiment.refinementparameters
,
com.compomics.util.general
,
com.compomics.util.general.servlet
,
com.compomics.util.gui
,
com.compomics.util.gui.error_handlers
,
com.compomics.util.gui.events
,
com.compomics.util.gui.export_graphics
,
com.compomics.util.gui.filehandling
,
com.compomics.util.gui.gene_mapping
,
com.compomics.util.gui.interfaces
,
com.compomics.util.gui.isotopic_calculator
,
com.compomics.util.gui.protein
,
com.compomics.util.gui.ptm
,
com.compomics.util.gui.renderers
,
com.compomics.util.gui.searchsettings
,
com.compomics.util.gui.spectrum
,
com.compomics.util.gui.tablemodels
,
com.compomics.util.gui.utils
,
com.compomics.util.gui.waiting.waitinghandlers
,
com.compomics.util.interfaces
,
com.compomics.util.io
,
com.compomics.util.io.filefilters
,
com.compomics.util.junit
,
com.compomics.util.math
,
com.compomics.util.messages
,
com.compomics.util.nucleotide
,
com.compomics.util.pdbfinder
,
com.compomics.util.pdbfinder.das.readers
,
com.compomics.util.pdbfinder.pdb
,
com.compomics.util.preferences
,
com.compomics.util.preferences.gui
,
com.compomics.util.pride
,
com.compomics.util.pride.prideobjects
,
com.compomics.util.pride.validation
,
com.compomics.util.protein
,
com.compomics.util.sun
,
com.compomics.util.waiting
Class Hierarchy
java.lang.
Object
com.compomics.util.protein.
AASequenceImpl
(implements com.compomics.util.interfaces.
Sequence
)
javax.swing.table.
AbstractTableModel
(implements java.io.
Serializable
, javax.swing.table.
TableModel
)
com.compomics.util.db.
DBResultSet
javax.swing.table.
DefaultTableModel
(implements java.io.
Serializable
)
com.compomics.util.gui.spectrum.
IonLabelColorTableModel
com.compomics.util.gui.tablemodels.
SelfUpdatingTableModel
com.compomics.util.sun.
TableMap
(implements javax.swing.event.
TableModelListener
)
com.compomics.util.sun.
TableSorter
com.compomics.util.experiment.identification.
AdvocateFactory
com.compomics.util.gui.renderers.
AlignedTableCellRenderer
(implements javax.swing.table.
TableCellRenderer
)
com.compomics.util.pdbfinder.das.readers.
AlignmentBlock
com.compomics.util.experiment.biology.
AminoAcid
(implements java.io.
Serializable
)
com.compomics.util.experiment.biology.aminoacids.
Alanine
com.compomics.util.experiment.biology.aminoacids.
Arginine
com.compomics.util.experiment.biology.aminoacids.
Asparagine
com.compomics.util.experiment.biology.aminoacids.
AsparticAcid
com.compomics.util.experiment.biology.aminoacids.
B
com.compomics.util.experiment.biology.aminoacids.
Cysteine
com.compomics.util.experiment.biology.aminoacids.
GlutamicAcid
com.compomics.util.experiment.biology.aminoacids.
Glutamine
com.compomics.util.experiment.biology.aminoacids.
Glycine
com.compomics.util.experiment.biology.aminoacids.
Histidine
com.compomics.util.experiment.biology.aminoacids.
Isoleucine
com.compomics.util.experiment.biology.aminoacids.
J
com.compomics.util.experiment.biology.aminoacids.
Leucine
com.compomics.util.experiment.biology.aminoacids.
Lysine
com.compomics.util.experiment.biology.aminoacids.
Methionine
com.compomics.util.experiment.biology.aminoacids.
Phenylalanine
com.compomics.util.experiment.biology.aminoacids.
Proline
com.compomics.util.experiment.biology.aminoacids.
Pyrrolysine
com.compomics.util.experiment.biology.aminoacids.
Selenocysteine
com.compomics.util.experiment.biology.aminoacids.
Serine
com.compomics.util.experiment.biology.aminoacids.
Threonine
com.compomics.util.experiment.biology.aminoacids.
Tryptophan
com.compomics.util.experiment.biology.aminoacids.
Tyrosine
com.compomics.util.experiment.biology.aminoacids.
Valine
com.compomics.util.experiment.biology.aminoacids.
X
com.compomics.util.experiment.biology.aminoacids.
Z
com.compomics.util.experiment.biology.
AminoAcidPattern
(implements java.io.
Serializable
)
com.compomics.util.preferences.
AnnotationPreferences
(implements java.io.
Serializable
)
com.compomics.util.experiment.identification.ptm.ptmscores.
AScore
com.compomics.util.examples.
BareBonesBrowserLaunch
com.compomics.util.math.
BasicMathFunctions
com.compomics.util.
BinaryArrayImpl
com.compomics.util.db.
ColumnTypeConverter
com.compomics.util.general.
CommandLineParser
com.compomics.software.
CommandLineUtils
com.compomics.software.autoupdater.
CompareVersionNumbers
(implements java.util.
Comparator
<T>)
com.compomics.util.
CompareVersionNumbers
(implements java.util.
Comparator
<T>)
com.compomics.software.
CompomicsWrapper
java.awt.
Component
(implements java.awt.image.
ImageObserver
, java.awt.
MenuContainer
, java.io.
Serializable
)
java.awt.
Container
javax.swing.
JComponent
(implements java.io.
Serializable
)
javax.swing.
JLabel
(implements javax.accessibility.
Accessible
, javax.swing.
SwingConstants
)
javax.swing.plaf.basic.
BasicComboBoxRenderer
(implements javax.swing.
ListCellRenderer
, java.io.
Serializable
)
com.compomics.util.gui.renderers.
ToolTipComboBoxRenderer
javax.swing.
DefaultListCellRenderer
(implements javax.swing.
ListCellRenderer
, java.io.
Serializable
)
com.compomics.util.gui.renderers.
AlignedListCellRenderer
javax.swing.table.
DefaultTableCellRenderer
(implements java.io.
Serializable
, javax.swing.table.
TableCellRenderer
)
com.compomics.util.gui.renderers.
ByteArrayRenderer
com.compomics.util.gui.renderers.
TimestampRenderer
com.compomics.util.gui.renderers.
GraphicsPanelTableCellRenderer
(implements javax.swing.table.
TableCellRenderer
)
javax.swing.
JPanel
(implements javax.accessibility.
Accessible
)
com.compomics.util.gui.spectrum.
GraphicsPanel
com.compomics.util.gui.spectrum.
ChromatogramPanel
com.compomics.util.gui.spectrum.
IsotopicDistributionPanel
com.compomics.util.gui.spectrum.
SpectrumPanel
com.compomics.util.gui.spectrum.
IntensityHistogram
com.compomics.util.gui.
JLabelAndComponentPanel
com.compomics.util.gui.spectrum.
MassErrorBubblePlot
com.compomics.util.gui.spectrum.
MassErrorPlot
com.compomics.util.gui.spectrum.
SequenceFragmentationPanel
com.compomics.util.gui.protein.
SequenceModificationPanel
javax.swing.
JTable
(implements javax.accessibility.
Accessible
, javax.swing.event.
CellEditorListener
, javax.swing.event.
ListSelectionListener
, javax.swing.event.
RowSorterListener
, javax.swing.
Scrollable
, javax.swing.event.
TableColumnModelListener
, javax.swing.event.
TableModelListener
)
com.compomics.util.
AlternateRowColoursJTable
com.compomics.util.gui.
JTableForDB
com.compomics.util.gui.spectrum.
FragmentIonTable
java.awt.
Window
(implements javax.accessibility.
Accessible
)
java.awt.
Dialog
javax.swing.
JDialog
(implements javax.accessibility.
Accessible
, javax.swing.
RootPaneContainer
, javax.swing.
WindowConstants
)
com.compomics.util.gui.
AminoAcidPatternDialog
com.compomics.util.gui.error_handlers.
BugReport
com.compomics.util.gui.utils.
ConnectionDialog
com.compomics.util.gui.utils.
DateChooser
com.compomics.util.gui.searchsettings.
EnzymeSelectionDialog
com.compomics.util.gui.export_graphics.
ExportGraphicsDialog
com.compomics.util.gui.filehandling.
FileSelectionDialog
com.compomics.util.gui.
GeneDetailsDialog
com.compomics.util.gui.error_handlers.
HelpDialog
com.compomics.util.preferences.gui.
ImportSettingsDialog
com.compomics.software.dialogs.
JavaOptionsDialog
com.compomics.util.gui.
JExceptionDialog
com.compomics.util.examples.
MirroredSpectraTestDialog
com.compomics.util.gui.ptm.
ModificationsDialog
(implements com.compomics.util.gui.ptm.
PtmDialogParent
)
com.compomics.software.dialogs.
PeptideShakerSetupDialog
com.compomics.util.preferences.gui.
ProcessingPreferencesDialog
com.compomics.util.gui.waiting.waitinghandlers.
ProgressDialog
com.compomics.util.gui.waiting.waitinghandlers.
ProgressDialogX
(implements com.compomics.util.waiting.
WaitingHandler
)
com.compomics.util.gui.ptm.
PtmDialog
(implements no.uib.olsdialog.OLSInputable)
com.compomics.software.dialogs.
RelimsSetupDialog
com.compomics.software.dialogs.
ReporterSetupDialog
com.compomics.util.gui.
SampleSelection
com.compomics.software.dialogs.
SearchGuiSetupDialog
com.compomics.util.gui.searchsettings.
SearchSettingsDialog
(implements com.compomics.util.gui.ptm.
PtmDialogParent
)
com.compomics.util.gui.protein.
SequenceDbDetailsDialog
com.compomics.util.gui.gene_mapping.
SpeciesDialog
com.compomics.util.gui.
VennDiagramDialog
(implements com.compomics.util.gui.export_graphics.
ExportGraphicsDialogParent
)
com.compomics.util.gui.
VennDiagramLegendLocationDialog
com.compomics.util.gui.
VisibleTableColumnsDialog
com.compomics.util.gui.waiting.waitinghandlers.
WaitingDialog
(implements com.compomics.util.waiting.
WaitingHandler
)
com.compomics.util.gui.
XYPlotFiltersDialog
com.compomics.util.gui.
XYPlottingDialog
(implements com.compomics.util.gui.export_graphics.
ExportGraphicsDialogParent
, com.compomics.util.gui.
VisibleTableColumnsDialogParent
)
java.awt.
Frame
(implements java.awt.
MenuContainer
)
javax.swing.
JFrame
(implements javax.accessibility.
Accessible
, javax.swing.
RootPaneContainer
, javax.swing.
WindowConstants
)
com.compomics.util.gui.
DummyFrame
com.compomics.util.gui.
FlamableJFrame
(implements com.compomics.util.interfaces.
Flamable
)
com.compomics.util.examples.
HelpWindow
com.compomics.util.gui.isotopic_calculator.
IsotopeDistributionGui
com.compomics.util.gui.
JFrameForBytes
com.compomics.util.examples.
UtilitiesDemo
com.compomics.util.db.components.
Constructors
com.compomics.util.pride.prideobjects.
Contact
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.pride.prideobjects.
ContactGroup
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.experiment.quantification.reporterion.
CorrectionFactor
com.compomics.util.pride.
CvTerm
(implements java.io.
Serializable
)
com.compomics.util.pdbfinder.das.readers.
DasAlignment
com.compomics.util.pdbfinder.das.readers.
DasAnnotationServerAlingmentReader
com.compomics.util.pdbfinder.das.readers.
DasAnnotationServerResultReader
com.compomics.util.pdbfinder.das.readers.
DasFeature
com.compomics.util.db.
DBAccessor
com.compomics.util.db.
DBAccessorGenerator
com.compomics.util.db.
DBMetaData
com.compomics.util.general.
DefaultOutputLoggerImplementation
(implements com.compomics.util.interfaces.
Logger
)
com.compomics.util.gui.spectrum.
DefaultSpectrumAnnotation
(implements com.compomics.util.gui.interfaces.
SpectrumAnnotation
)
com.compomics.util.db.components.
DeleteableCode
com.compomics.software.autoupdater.
DownloadLatestZipFromRepo
com.compomics.util.experiment.biology.
ElementaryElement
com.compomics.util.protein.
Enzyme
(implements java.lang.
Cloneable
)
com.compomics.util.protein.
DualEnzyme
com.compomics.util.protein.
RegExEnzyme
com.compomics.util.experiment.biology.
EnzymeFactory
com.compomics.util.general.
ExceptionHandler
com.compomics.util.experiment.io.
ExperimentIO
com.compomics.util.experiment.personalization.
ExperimentObject
(implements java.lang.
Cloneable
, java.io.
Serializable
)
com.compomics.util.experiment.io.identifications.idfilereaders.
AndromedaIdfileReader
(implements com.compomics.util.experiment.io.identifications.
IdfileReader
)
com.compomics.util.experiment.biology.
Atom
com.compomics.util.experiment.biology.atoms.
Carbon
com.compomics.util.experiment.biology.atoms.
Hydrogen
com.compomics.util.experiment.biology.atoms.
Nitrogen
com.compomics.util.experiment.biology.atoms.
Oxygen
com.compomics.util.experiment.biology.atoms.
Phosphorus
com.compomics.util.experiment.biology.atoms.
Sulfur
com.compomics.util.experiment.massspectrometry.
Charge
com.compomics.util.experiment.biology.
Enzyme
com.compomics.util.experiment.identification.
FastaIndex
com.compomics.util.experiment.identification.
Identification
com.compomics.util.experiment.identification.identifications.
Ms2Identification
com.compomics.util.experiment.identification.
IdentificationMatch
com.compomics.util.experiment.identification.matches.
PeptideMatch
com.compomics.util.experiment.identification.matches.
ProteinMatch
com.compomics.util.experiment.identification.matches.
SpectrumMatch
com.compomics.util.experiment.identification.
IdentificationMethod
com.compomics.util.experiment.biology.
Ion
com.compomics.util.experiment.biology.ions.
ElementaryIon
com.compomics.util.experiment.biology.ions.
Glycon
com.compomics.util.experiment.biology.ions.
ImmoniumIon
com.compomics.util.experiment.biology.ions.
PeptideFragmentIon
com.compomics.util.experiment.biology.ions.
PrecursorIon
com.compomics.util.experiment.biology.ions.
ReporterIon
com.compomics.util.experiment.identification.matches.
IonMatch
com.compomics.util.experiment.io.massspectrometry.
MgfIndex
com.compomics.util.experiment.identification.matches.
ModificationMatch
com.compomics.util.experiment.
MsExperiment
com.compomics.util.experiment.biology.
NeutralLoss
com.compomics.util.experiment.massspectrometry.
Peak
com.compomics.util.experiment.biology.
Peptide
com.compomics.util.experiment.identification.
PeptideAssumption
com.compomics.util.experiment.identification.advocates.
PostProcessor
(implements com.compomics.util.experiment.identification.
Advocate
)
com.compomics.util.experiment.massspectrometry.
Precursor
com.compomics.util.experiment.biology.
Protein
com.compomics.util.experiment.
ProteomicAnalysis
com.compomics.util.experiment.biology.
PTM
com.compomics.util.experiment.quantification.
Quantification
com.compomics.util.experiment.quantification.reporterion.
ReporterIonQuantification
com.compomics.util.experiment.quantification.
QuantificationMatch
com.compomics.util.experiment.quantification.matches.
PeptideQuantification
com.compomics.util.experiment.quantification.matches.
ProteinQuantification
com.compomics.util.experiment.quantification.matches.
PsmQuantification
com.compomics.util.experiment.quantification.
Ratio
com.compomics.util.experiment.quantification.reporterion.
ReporterMethodFactory
com.compomics.util.experiment.biology.
Sample
com.compomics.util.experiment.
SampleAnalysisSet
com.compomics.util.experiment.identification.advocates.
SearchEngine
(implements com.compomics.util.experiment.identification.
Advocate
)
com.compomics.util.experiment.massspectrometry.
Spectrum
com.compomics.util.experiment.massspectrometry.
MS1Spectrum
com.compomics.util.experiment.massspectrometry.
MSnSpectrum
com.compomics.util.
Export
com.compomics.util.messages.
FeedBack
com.compomics.software.autoupdater.
FileDAO
com.compomics.software.autoupdater.
GUIFileDAO
com.compomics.software.autoupdater.
HeadlessFileDAO
javax.swing.filechooser.
FileFilter
com.compomics.util.io.filefilters.
DatFileFilter
com.compomics.util.io.filefilters.
DtaFileFilter
com.compomics.util.io.filefilters.
FastaFileFilter
com.compomics.util.io.
FilenameExtensionFilter
(implements java.io.
FilenameFilter
)
com.compomics.util.io.filefilters.
JpegFileFilter
com.compomics.util.io.filefilters.
MgfFileFilter
com.compomics.util.io.filefilters.
Ms2FileFilter
com.compomics.util.io.filefilters.
MzDataFileFilter
com.compomics.util.io.filefilters.
MzMlFileFilter
com.compomics.util.io.filefilters.
MzXmlFileFilter
com.compomics.util.io.filefilters.
OmxFileFilter
com.compomics.util.io.filefilters.
OutFileFilter
com.compomics.util.io.filefilters.
PdfFileFilter
com.compomics.util.io.filefilters.
PeffFileFilter
com.compomics.util.io.filefilters.
PepXmlFileFilter
com.compomics.util.io.filefilters.
PklFileFilter
com.compomics.util.io.filefilters.
PklSpoFileFilter
com.compomics.util.io.filefilters.
PkxFileFilter
com.compomics.util.io.filefilters.
PngFileFilter
com.compomics.util.io.filefilters.
ProtXmlFileFilter
com.compomics.util.io.filefilters.
SequestParamsFileFilter
com.compomics.util.io.filefilters.
SvgFileFilter
com.compomics.util.io.filefilters.
TiffFileFilter
com.compomics.util.io.filefilters.
XmlFileFilter
com.compomics.util.io.filefilters.
FileFilterUtils
com.compomics.util.general.
FileLoggerImplementation
(implements com.compomics.util.interfaces.
Logger
)
com.compomics.util.io.
FileSystemAccessor
com.compomics.util.pdbfinder.
FindPdbForUniprotAccessions
com.compomics.util.io.
FolderMonitor
(implements java.lang.
Runnable
)
com.compomics.util.gui.renderers.
FragmentIonTableCellRenderer
(implements javax.swing.table.
TableCellRenderer
)
com.compomics.util.io.
FTP
com.compomics.util.io.
FTPClient
com.compomics.util.experiment.annotation.gene.
GeneFactory
com.compomics.util.preferences.
GenePreferences
(implements java.io.
Serializable
)
javax.servlet.GenericServlet (implements java.io.
Serializable
, javax.servlet.Servlet, javax.servlet.ServletConfig)
javax.servlet.http.HttpServlet (implements java.io.
Serializable
)
com.compomics.util.general.servlet.
MassCalcServlet
com.compomics.util.db.components.
GettersAndSetters
com.compomics.util.experiment.biology.
GlyconFactory
com.compomics.util.experiment.annotation.go.
GOFactory
com.compomics.util.gui.
GuiUtilities
com.compomics.util.protein.
Header
(implements java.lang.
Cloneable
, java.io.
Serializable
)
com.compomics.util.experiment.identification.
IdentificationDB
(implements java.io.
Serializable
)
com.compomics.util.experiment.io.identifications.
IdentificationParametersReader
com.compomics.util.experiment.io.identifications.
IdfileReaderFactory
com.compomics.util.preferences.
IdFilter
(implements java.io.
Serializable
)
java.io.
InputStream
(implements java.io.
Closeable
)
java.io.
FilterInputStream
com.compomics.util.io.
MonitorableInputStream
(implements com.compomics.util.interfaces.
Monitorable
)
com.compomics.util.io.
MonitorableFileInputStream
com.compomics.util.db.components.
InstanceVariables
com.compomics.util.pride.prideobjects.
Instrument
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.experiment.biology.
IonFactory
com.compomics.util.general.
IsotopicDistribution
com.compomics.util.general.
IsotopicDistributionSpectrum
(implements com.compomics.util.interfaces.
SpectrumFile
)
com.compomics.util.general.
IsotopicElement
com.compomics.software.autoupdater.
JarFileFilter
(implements java.io.
FilenameFilter
)
com.compomics.util.io.
MascotEnzymeReader
com.compomics.util.experiment.refinementparameters.
MascotScore
(implements com.compomics.util.experiment.personalization.
UrParameter
)
com.compomics.util.general.
MassCalc
com.compomics.util.experiment.identification.ptm.ptmscores.
MDScore
com.compomics.software.autoupdater.
MetaDataXMLParser
com.compomics.util.experiment.io.massspectrometry.
MgfReader
com.compomics.util.protein.
ModificationFactory
com.compomics.util.protein.
ModificationImplementation
(implements java.lang.
Cloneable
, com.compomics.util.interfaces.
Modification
, java.io.
Serializable
)
com.compomics.util.gui.protein.
ModificationProfile
com.compomics.util.preferences.
ModificationProfile
(implements java.io.
Serializable
)
com.compomics.util.protein.
ModificationTemplate
com.compomics.util.protein.
MolecularFormula
com.compomics.util.gui.
MonitorDimension
com.compomics.util.experiment.biology.
Mutation
com.compomics.util.experiment.biology.
MutationFactory
com.compomics.util.experiment.identification.
NeutralLossesMap
(implements java.io.
Serializable
)
com.compomics.util.experiment.identification.protein_inference.proteintree.
Node
(implements java.io.
Serializable
)
com.compomics.util.nucleotide.
NucleotideSequence
com.compomics.util.nucleotide.
NucleotideSequenceImpl
(implements com.compomics.util.interfaces.
Sequence
)
com.compomics.util.db.
ObjectsCache
com.compomics.util.db.
ObjectsDB
(implements java.io.
Serializable
)
com.compomics.util.pdbfinder.pdb.
PdbBlock
com.compomics.util.pdbfinder.pdb.
PdbParameter
com.compomics.util.denovo.
PeptideAssumptionDetails
(implements com.compomics.util.experiment.personalization.
UrParameter
)
com.compomics.util.db.components.
PersistableCode
com.compomics.util.io.
PklFile
com.compomics.util.pride.
PrideObjectsFactory
com.compomics.util.pride.validation.
PrideXmlValidator
com.compomics.util.preferences.
ProcessingPreferences
(implements java.io.
Serializable
)
com.compomics.util.io.
PropertiesManager
com.compomics.util.protein.
Protein
com.compomics.util.gui.protein.
ProteinSequencePane
com.compomics.util.experiment.identification.protein_inference.proteintree.
ProteinTree
com.compomics.util.experiment.identification.protein_inference.proteintree.
ProteinTree.PeptideIterator
(implements java.util.
Iterator
<E>)
com.compomics.util.experiment.identification.protein_inference.proteintree.
ProteinTreeComponentsFactory
com.compomics.util.pride.prideobjects.
Protocol
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.experiment.identification.scoring.
PsmScores
com.compomics.util.experiment.biology.
PTMFactory
(implements java.io.
Serializable
)
com.compomics.util.preferences.
PTMScoringPreferences
(implements java.io.
Serializable
)
com.compomics.util.experiment.identification.ptm.
PtmSiteMapping
com.compomics.util.experiment.identification.ptm.
PtmtableContent
com.compomics.util.pride.
PtmToPrideMap
(implements java.io.
Serializable
)
com.compomics.util.io.
PushBackStringReader
com.compomics.util.experiment.quantification.
QuantificationDB
(implements java.io.
Serializable
)
com.compomics.util.pride.prideobjects.
Reference
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.gui.spectrum.
ReferenceArea
com.compomics.util.pride.prideobjects.
ReferenceGroup
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.experiment.quantification.reporterion.
ReporterMethod
com.compomics.util.gui.events.
RescalingEvent
com.compomics.util.db.components.
RetrievableCode
javax.swing.
RowFilter
<M,I>
com.compomics.util.gui.
XYPlottingDialog.SelectedValuesTableFilter
com.compomics.util.pride.prideobjects.
Sample
(implements com.compomics.util.pride.
PrideObject
, java.io.
Serializable
)
com.compomics.util.experiment.identification.
SearchParameters
(implements java.io.
Serializable
)
com.compomics.util.experiment.identification.
SearchParametersInputBean
com.compomics.util.experiment.identification.
SequenceFactory
com.compomics.util.io.
SerializationUtils
com.compomics.util.experiment.identification.
SpectrumAnnotator
com.compomics.util.experiment.quantification.spectrumcounting.
SpectrumCounting
com.compomics.util.experiment.massspectrometry.
SpectrumFactory
com.compomics.software.
SplashScreen
com.compomics.util.io.
StartBrowser
com.compomics.util.pdbfinder.das.readers.
StartEndPosition
com.compomics.util.io.
StreamGobbler
(implements java.lang.
Runnable
)
com.compomics.util.sun.
SwingWorker
com.compomics.util.experiment.identification.
TagFactory
com.compomics.util.io.
TarUtils
com.compomics.util.junit.
TestCaseLM
java.lang.
Throwable
(implements java.io.
Serializable
)
java.lang.
Exception
com.compomics.util.db.
GeneratorException
java.io.
IOException
com.compomics.util.io.
FtpProtocolException
com.compomics.util.io.
FtpConnectionException
com.compomics.util.io.
FtpLoginException
com.compomics.util.general.
UnknownElementMassException
com.compomics.software.
ToolFactory
com.compomics.util.general.
Translate
com.compomics.util.db.components.
UpdateableCode
com.compomics.util.
Util
com.compomics.util.gui.
UtilitiesGUIDefaults
com.compomics.util.preferences.
UtilitiesUserPreferences
(implements java.io.
Serializable
)
com.compomics.util.gui.waiting.waitinghandlers.
WaitingHandlerCLIImpl
(implements com.compomics.util.waiting.
WaitingHandler
)
com.compomics.software.autoupdater.
WebDAO
com.compomics.util.pride.validation.
XMLValidationErrorHandler
(implements org.xml.sax.
ErrorHandler
)
com.compomics.util.gui.
XYPlottingDialog.NormalKernelDensityEstimator
com.compomics.util.
XYZDataPoint
java.util.zip.
ZipFile
java.util.jar.
JarFile
com.compomics.software.autoupdater.
MavenJarFile
Interface Hierarchy
java.lang.
Comparable
<T>
com.compomics.util.interfaces.
Modification
com.compomics.util.interfaces.
SpectrumFile
com.compomics.util.interfaces.
Connectable
com.compomics.util.db.interfaces.
DBElement
com.compomics.util.db.interfaces.
Deleteable
com.compomics.util.gui.export_graphics.
ExportGraphicsDialogParent
com.compomics.util.interfaces.
Flamable
com.compomics.util.experiment.io.identifications.
IdfileReader
com.compomics.software.dialogs.
JavaOptionsDialogParent
com.compomics.util.interfaces.
Logger
com.compomics.util.interfaces.
Monitorable
com.compomics.util.db.interfaces.
Persistable
com.compomics.util.interfaces.
PickUp
com.compomics.util.pride.
PrideObject
com.compomics.util.gui.ptm.
PtmDialogParent
com.compomics.util.db.interfaces.
Retrievable
com.compomics.util.gui.searchsettings.
SearchSettingsDialogParent
com.compomics.util.interfaces.
Sequence
java.io.
Serializable
com.compomics.util.experiment.identification.
Advocate
com.compomics.util.experiment.personalization.
UrParameter
com.compomics.util.gui.interfaces.
SpectrumAnnotation
com.compomics.util.gui.interfaces.
SpectrumPanelListener
com.compomics.util.interfaces.
TableValueWrapper
com.compomics.util.db.interfaces.
Updateable
com.compomics.util.gui.
VisibleTableColumnsDialogParent
com.compomics.util.waiting.
WaitingActionListener
com.compomics.util.waiting.
WaitingHandler
Enum Hierarchy
java.lang.
Object
java.lang.
Enum
<E> (implements java.lang.
Comparable
<T>, java.io.
Serializable
)
com.compomics.util.enumeration.
OperatingSystemEnum
com.compomics.util.enumeration.
MolecularElement
com.compomics.util.enumeration.
ImageType
com.compomics.util.enumeration.
CompomicsTools
com.compomics.util.experiment.biology.
Ion.IonType
com.compomics.util.experiment.identification.
SearchParametersInputBean.ToolType
com.compomics.util.experiment.identification.
SearchParametersCLIParams
com.compomics.util.experiment.identification.
SearchParameters.PrecursorAccuracyType
com.compomics.util.experiment.identification.
IdentificationMatch.MatchType
com.compomics.util.experiment.identification.matches.
ProteinMatch.MatchingType
com.compomics.util.experiment.quantification.
QuantificationMatch.MatchType
com.compomics.util.experiment.quantification.
Quantification.QuantificationMethod
com.compomics.util.experiment.quantification.spectrumcounting.
SpectrumCounting.SpectrumCountingMethod
com.compomics.util.gui.
VennDiagramDialog.VennDiagramType
com.compomics.util.gui.spectrum.
GraphicsPanel.DrawingStyle
com.compomics.util.gui.spectrum.
GraphicsPanel.GraphicsPanelType
com.compomics.util.messages.
FeedBack.FeedBackType
com.compomics.util.protein.
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