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Package com.compomics.util |
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Class com.compomics.util.AlternateRowColoursJTable extends JTable implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Color iEvenRowColor
Color iUnevenRowColor
Package com.compomics.util.db |
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Class com.compomics.util.db.DBResultSet extends AbstractTableModel implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
int iColCount
int iRowCount
String[] iColNames
Object[][] iData
Class com.compomics.util.db.GeneratorException extends Exception implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Exception iNested
Class com.compomics.util.db.ObjectsDB extends Object implements Serializable |
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serialVersionUID: -8595805180622832745L
Serialized Fields |
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String dbName
Connection dbConnection
ArrayList<E> longKeys
ObjectsCache objectsCache
BufferedWriter debugWriter
File debugFolder
boolean debug
Package com.compomics.util.examples |
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Class com.compomics.util.examples.HelpWindow extends JFrame implements Serializable |
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Serialized Fields |
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JButton closeJButton
JScrollPane jScrollPane1
JEditorPane textJEditorPane
Class com.compomics.util.examples.UtilitiesDemo extends JFrame implements Serializable |
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Serialized Fields |
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HashMap<K,V> peffAnnotationsColorMap
HashMap<K,V> peffAnnotationsTooltipMap
boolean peffFormat
TreeMap<K,V> keyValuePairs
File currentSequenceFile
BufferedReader currentPeffBufferedReader
String currentSequence
String currentSequenceLine
HashMap<K,V> linkedSpectrumPanels
HashMap<K,V> allAnnotations
SpectrumPanel spectrumAPanel
SpectrumPanel spectrumBPanel
int spectrumPanelMaxPadding
int chromatogramPanelMaxPadding
MascotEnzymeReader mascotEnzymeReader
String cleanProteinSequence
HashMap<K,V> selectedAnnotationTypes
ArrayList<E> sequenceAnnotationColumnHeaderTooltips
Color sparklineColor
JCheckBox H2OIonsJCheckBox
JCheckBox NH3IonsJCheckBox
JCheckBox aIonsJCheckBox
JCheckBox allPeaksJCheckBox
JCheckBox bIonsJCheckBox
JButton browseJButton
JCheckBox cIonsJCheckBox
JCheckBox chargeOneJCheckBox
JCheckBox chargeOverTwoJCheckBox
JSpinner chargePeptideAJSpinner
JSpinner chargePeptideBJSpinner
JCheckBox chargeTwoJCheckBox
JPanel chromatogramAJPanel
JPanel chromatogramJPanel
JLabel chromatogramPanelHelpJLabel
JLabel chromatogramPanelInfoJLabel
JComboBox enzymesJComboBox
JButton exportJButton
JLabel inSilicoDigestionHelpJLabel
JEditorPane informationJEditorPane
JPanel informationJPanel
JScrollPane informationJScrollPane
JTextField inhibitorsJTextField
JPanel ionSelectionJPanel
JPanel isotopicDistributionAJPanel
JLabel isotopicDistributionCalculatorHelpJLabel
JLabel isotopicDistributionCalculatorInfoJLabel
JPanel isotopicDistributionJPanel
JLabel jLabel1
JLabel jLabel10
JLabel jLabel11
JLabel jLabel12
JLabel jLabel13
JLabel jLabel14
JLabel jLabel15
JLabel jLabel16
JLabel jLabel17
JLabel jLabel18
JLabel jLabel19
JLabel jLabel2
JLabel jLabel20
JLabel jLabel21
JLabel jLabel24
JLabel jLabel3
JLabel jLabel4
JLabel jLabel5
JLabel jLabel6
JLabel jLabel7
JLabel jLabel8
JLabel jLabel9
JPanel jPanel1
JPanel jPanel10
JPanel jPanel11
JPanel jPanel12
JPanel jPanel2
JPanel jPanel3
JPanel jPanel4
JPanel jPanel5
JPanel jPanel6
JPanel jPanel7
JPanel jPanel8
JPanel jPanel9
JRadioButton jRadioButton1
JScrollPane jScrollPane1
JScrollPane jScrollPane2
JScrollPane jScrollPane3
JSeparator jSeparator1
JSeparator jSeparator2
JSeparator jSeparator3
JSeparator jSeparator4
JSeparator jSeparator5
JSeparator jSeparator6
JSeparator jSeparator9
JTabbedPane jTabbedPane
JCheckBox linkedSpectraJCheckBox
JSpinner lowerMassJSpinner
JSpinner missedCleavagesJSpinner
JButton nextJButton
JCheckBox otherIonsJCheckBox
JTable peffAnnotationsJTable
JTable peffHeaderJTable
JPanel peptideAColorJPanel
JTextField peptideACompositionJTextField
JScrollPane peptideAJScrollPane
org.jdesktop.swingx.JXTable peptideAJXTable
JTextField peptideAMzJTextField
JPanel peptideBColorJPanel
JTextField peptideBCompositionJTextField
JScrollPane peptideBJScrollPane
org.jdesktop.swingx.JXTable peptideBJXTable
JTextField peptideBMzJTextField
JTextField peptideSequenceAJTextField
JTextField peptideSequenceBJTextField
JPanel peptidesJPanel
JTable peptidesJTable
JScrollPane peptidesScrollPane
JTextField positionJTextField
JCheckBox profileSpectrumJCheckBox
JScrollPane proteinCoverageJScrollPane
JLabel proteinDigestionJLabel
JPanel proteinDigestionJPanel
JTable proteinHeaderJTable
JEditorPane proteinSequenceCoverageJEditorPane
JPanel sequenceCoverageJPanel
JTextField sequenceFileJTextField
JTabbedPane sequenceJTabbedPane
JComboBox silacLabelPeptideAJComboBox
JComboBox silacLabelPeptideBJComboBox
JTextField siteJTextField
JPanel spectraJPanel
JPanel spectrumAJPanel
JPanel spectrumBJPanel
JPanel spectrumJPanel
JLabel spectrumPanelHelpJLabel
JLabel spectrumPanelInfoJLabel
JSpinner upperMassJSpinner
JCheckBox xIonsJCheckBox
JCheckBox yIonsJCheckBox
JCheckBox zIonsJCheckBox
Package com.compomics.util.experiment |
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Class com.compomics.util.experiment.MsExperiment extends ExperimentObject implements Serializable |
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serialVersionUID: 4330394623824512352L
Serialized Fields |
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String reference
HashMap<K,V> samples
HashMap<K,V> analysis
Class com.compomics.util.experiment.ProteomicAnalysis extends ExperimentObject implements Serializable |
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serialVersionUID: -6738411343333889777L
Serialized Fields |
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int index
HashMap<K,V> quantification
HashMap<K,V> identification
Class com.compomics.util.experiment.SampleAnalysisSet extends ExperimentObject implements Serializable |
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serialVersionUID: -5399187779025810060L
Serialized Fields |
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Sample sample
HashMap<K,V> analysis
Package com.compomics.util.experiment.biology |
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Class com.compomics.util.experiment.biology.Atom extends ExperimentObject implements Serializable |
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Serialized Fields |
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double mass
String name
String letter
Class com.compomics.util.experiment.biology.Enzyme extends ExperimentObject implements Serializable |
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serialVersionUID: -1852087173903613377L
Serialized Fields |
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int id
String name
ArrayList<E> aminoAcidBefore
ArrayList<E> aminoAcidAfter
ArrayList<E> restrictionBefore
ArrayList<E> restrictionAfter
Class com.compomics.util.experiment.biology.Ion extends ExperimentObject implements Serializable |
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Serialized Fields |
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Ion.IonType type
double theoreticMass
Class com.compomics.util.experiment.biology.NeutralLoss extends ExperimentObject implements Serializable |
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serialVersionUID: 5540846193082177391L
Serialized Fields |
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double mass
String name
Boolean fixed
Class com.compomics.util.experiment.biology.Peptide extends ExperimentObject implements Serializable |
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serialVersionUID: 5632064601627536034L
Serialized Fields |
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String sequence
Double mass
ArrayList<E> parentProteins
ArrayList<E> modifications
Class com.compomics.util.experiment.biology.Protein extends ExperimentObject implements Serializable |
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serialVersionUID: 1987224639519365761L
Serialized Fields |
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String accession
boolean decoy
String sequence
Header.DatabaseType databaseType
Class com.compomics.util.experiment.biology.PTM extends ExperimentObject implements Serializable |
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serialVersionUID: -545472596243822505L
Serialized Fields |
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int type
ArrayList<E> residuesArray
String name
String shortName
double mass
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
Class com.compomics.util.experiment.biology.PTMFactory extends Object implements Serializable |
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serialVersionUID: 7935264190312934466L
Class com.compomics.util.experiment.biology.Sample extends ExperimentObject implements Serializable |
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serialVersionUID: 303393644914835325L
Serialized Fields |
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String reference
Package com.compomics.util.experiment.biology.atoms |
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Class com.compomics.util.experiment.biology.atoms.Carbon extends Atom implements Serializable |
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Class com.compomics.util.experiment.biology.atoms.Hydrogen extends Atom implements Serializable |
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Class com.compomics.util.experiment.biology.atoms.Nitrogen extends Atom implements Serializable |
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Class com.compomics.util.experiment.biology.atoms.Oxygen extends Atom implements Serializable |
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Class com.compomics.util.experiment.biology.atoms.Phosphorus extends Atom implements Serializable |
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Class com.compomics.util.experiment.biology.atoms.Sulfur extends Atom implements Serializable |
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Package com.compomics.util.experiment.biology.ions |
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Class com.compomics.util.experiment.biology.ions.ElementaryIon extends Ion implements Serializable |
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serialVersionUID: -1578136397635015592L
Serialized Fields |
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String name
int subType
Class com.compomics.util.experiment.biology.ions.Glycon extends Ion implements Serializable |
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serialVersionUID: -2278483206647518565L
Serialized Fields |
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HashMap<K,V> theoreticMasses
String name
String longName
Class com.compomics.util.experiment.biology.ions.ImmoniumIon extends Ion implements Serializable |
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serialVersionUID: -3403620196563864756L
Serialized Fields |
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int subType
Class com.compomics.util.experiment.biology.ions.PeptideFragmentIon extends Ion implements Serializable |
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serialVersionUID: 8283809283803740651L
Serialized Fields |
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ArrayList<E> neutralLosses
int number
int subType
Class com.compomics.util.experiment.biology.ions.PrecursorIon extends Ion implements Serializable |
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serialVersionUID: -2630586959372309153L
Serialized Fields |
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ArrayList<E> neutralLosses
Class com.compomics.util.experiment.biology.ions.ReporterIon extends Ion implements Serializable |
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serialVersionUID: 1109011048958734120L
Serialized Fields |
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String name
int subtype
Package com.compomics.util.experiment.identification |
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Class com.compomics.util.experiment.identification.FastaIndex extends ExperimentObject implements Serializable |
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Serialized Fields |
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HashMap<K,V> indexes
String fileName
boolean isDecoy
int nTarget
Class com.compomics.util.experiment.identification.Identification extends ExperimentObject implements Serializable |
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serialVersionUID: -2551700699384242554L
Serialized Fields |
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ArrayList<E> proteinIdentification
ArrayList<E> peptideIdentification
ArrayList<E> spectrumIdentification
HashMap<K,V> proteinMap
int methodUsed
String serializationDirectory
HashMap<K,V> urParameters
ArrayList<E> longKeys
Boolean isDB
IdentificationDB identificationDB
String reference
Class com.compomics.util.experiment.identification.IdentificationDB extends Object implements Serializable |
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serialVersionUID: 691986038787590646L
Serialized Fields |
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String dbName
String proteinTableName
String proteinParametersTableSuffix
String peptideTableName
String peptideParametersTableSuffix
String psmTableSuffix
String psmParametersTableSuffix
String parametersSuffix
ArrayList<E> psmTables
ArrayList<E> psmParametersTables
ArrayList<E> peptideParametersTables
ArrayList<E> proteinParametersTables
ArrayList<E> matchParametersTables
ObjectsDB objectsDB
Class com.compomics.util.experiment.identification.IdentificationMatch extends ExperimentObject implements Serializable |
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serialVersionUID: -9132138792119651421L
Class com.compomics.util.experiment.identification.IdentificationMethod extends ExperimentObject implements Serializable |
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serialVersionUID: 4601179275244591663L
Serialized Fields |
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int index
Class com.compomics.util.experiment.identification.NeutralLossesMap extends Object implements Serializable |
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serialVersionUID: -4690159937753713106L
Serialized Fields |
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HashMap<K,V> bBoundaries
HashMap<K,V> yBoundaries
Class com.compomics.util.experiment.identification.PeptideAssumption extends ExperimentObject implements Serializable |
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serialVersionUID: 3606509518581203063L
Serialized Fields |
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int rank
Peptide peptide
int advocate
Charge identificationCharge
double eValue
String file
Boolean isDecoy
Package com.compomics.util.experiment.identification.advocates |
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Class com.compomics.util.experiment.identification.advocates.PostProcessor extends ExperimentObject implements Serializable |
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serialVersionUID: 1892975432623296983L
Serialized Fields |
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int id
Class com.compomics.util.experiment.identification.advocates.SearchEngine extends ExperimentObject implements Serializable |
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serialVersionUID: 9162799394758139976L
Serialized Fields |
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int id
Package com.compomics.util.experiment.identification.identifications |
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Class com.compomics.util.experiment.identification.identifications.Ms2Identification extends Identification implements Serializable |
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serialVersionUID: -7242302146506873391L
Package com.compomics.util.experiment.identification.matches |
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Class com.compomics.util.experiment.identification.matches.IonMatch extends ExperimentObject implements Serializable |
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serialVersionUID: 5753142782728884464L
Serialized Fields |
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Peak peak
Ion ion
Charge charge
Class com.compomics.util.experiment.identification.matches.ModificationMatch extends ExperimentObject implements Serializable |
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serialVersionUID: 7129515983284796207L
Serialized Fields |
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String theoreticPtm
boolean variable
int modifiedSite
Class com.compomics.util.experiment.identification.matches.PeptideMatch extends IdentificationMatch implements Serializable |
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serialVersionUID: 7195830246336841081L
Serialized Fields |
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Peptide theoreticPeptide
String mainMatchKey
ArrayList<E> spectrumMatches
Boolean isDecoy
Class com.compomics.util.experiment.identification.matches.ProteinMatch extends IdentificationMatch implements Serializable |
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serialVersionUID: -6061842447053092696L
Serialized Fields |
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ArrayList<E> theoreticProtein
String mainMatch
ArrayList<E> peptideMatches
Class com.compomics.util.experiment.identification.matches.SpectrumMatch extends IdentificationMatch implements Serializable |
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serialVersionUID: 3227760855215444318L
Serialized Fields |
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String spectrumKey
HashMap<K,V> assumptions
PeptideAssumption bestAssumption
HashMap<K,V> firstHits
ArrayList<E> advocates
Integer spectrumNumber
Package com.compomics.util.experiment.io.identifications.idfilereaders |
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Class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader extends ExperimentObject implements Serializable |
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Serialized Fields |
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HashMap<K,V> index
RandomAccessFile randomAccessFile
String fileName
Class com.compomics.util.experiment.io.identifications.idfilereaders.MascotIdfileReader extends ExperimentObject implements Serializable |
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Serialized Fields |
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File inspectedFile
com.compomics.mascotdatfile.util.interfaces.MascotDatfileInf iMascotDatfile
Class com.compomics.util.experiment.io.identifications.idfilereaders.OMSSAIdfileReader extends ExperimentObject implements Serializable |
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Serialized Fields |
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File identificationFile
File modsFile
File userModsFile
PTMFactory ptmFactory
de.proteinms.omxparser.OmssaOmxFile omxFile
Class com.compomics.util.experiment.io.identifications.idfilereaders.XTandemIdfileReader extends ExperimentObject implements Serializable |
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Serialized Fields |
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de.proteinms.xtandemparser.xtandem.XTandemFile xTandemFile
de.proteinms.xtandemparser.xtandem.ModificationMap modificationMap
de.proteinms.xtandemparser.xtandem.ProteinMap proteinMap
de.proteinms.xtandemparser.xtandem.PeptideMap peptideMap
Package com.compomics.util.experiment.io.massspectrometry |
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Class com.compomics.util.experiment.io.massspectrometry.MgfIndex extends ExperimentObject implements Serializable |
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serialVersionUID: -5591103342266964263L
Serialized Fields |
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HashMap<K,V> indexMap
ArrayList<E> spectrumTitles
String fileName
Double maxRT
Double minRT
Double maxMz
Double maxIntensity
Package com.compomics.util.experiment.massspectrometry |
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Class com.compomics.util.experiment.massspectrometry.Charge extends ExperimentObject implements Serializable |
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serialVersionUID: -7119215126058492261L
Serialized Fields |
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int sign
int value
Class com.compomics.util.experiment.massspectrometry.MS1Spectrum extends Spectrum implements Serializable |
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serialVersionUID: -7328539274222920271L
Class com.compomics.util.experiment.massspectrometry.MSnSpectrum extends Spectrum implements Serializable |
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serialVersionUID: -7144961253807359274L
Serialized Fields |
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Precursor precursor
Class com.compomics.util.experiment.massspectrometry.Peak extends ExperimentObject implements Serializable |
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serialVersionUID: -7425947046833405676L
Serialized Fields |
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double mz
double rt
double intensity
Class com.compomics.util.experiment.massspectrometry.Precursor extends ExperimentObject implements Serializable |
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serialVersionUID: -2711244157697138296L
Serialized Fields |
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double rt
Double rtMin
Double rtMax
double mz
double intensity
ArrayList<E> possibleCharges
Class com.compomics.util.experiment.massspectrometry.Spectrum extends ExperimentObject implements Serializable |
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serialVersionUID: 7152424141470431489L
Serialized Fields |
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String spectrumTitle
String fileName
int level
HashMap<K,V> peakList
String scanNumber
double scanStartTime
Package com.compomics.util.experiment.personalization |
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Class com.compomics.util.experiment.personalization.ExperimentObject extends Object implements Serializable |
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serialVersionUID: 1929697552061121072L
Serialized Fields |
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HashMap<K,V> urParams
Package com.compomics.util.experiment.quantification |
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Class com.compomics.util.experiment.quantification.Quantification extends ExperimentObject implements Serializable |
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Serialized Fields |
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Quantification.QuantificationMethod methodUsed
ArrayList<E> proteinQuantification
ArrayList<E> peptideQuantification
HashMap<K,V> modifiedPeptidesQuantification
HashMap<K,V> psmIDentificationToQuantification
QuantificationDB quantificationDB
Class com.compomics.util.experiment.quantification.QuantificationDB extends Object implements Serializable |
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serialVersionUID: 4600091320219653637L
Serialized Fields |
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String dbName
String proteinTableName
String proteinParametersTableSuffix
String peptideTableName
String peptideParametersTableSuffix
String psmTableSuffix
String psmParametersTableSuffix
ArrayList<E> psmTables
ArrayList<E> psmParametersTables
ArrayList<E> peptideParametersTables
ArrayList<E> proteinParametersTables
ObjectsDB objectsDB
Class com.compomics.util.experiment.quantification.QuantificationMatch extends ExperimentObject implements Serializable |
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Serialized Fields |
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HashMap<K,V> ratios
Class com.compomics.util.experiment.quantification.Ratio extends ExperimentObject implements Serializable |
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Serialized Fields |
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int measureLabel
double ratio
Package com.compomics.util.experiment.quantification.matches |
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Class com.compomics.util.experiment.quantification.matches.PeptideQuantification extends QuantificationMatch implements Serializable |
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Serialized Fields |
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String peptideKey
ArrayList<E> psmQuantification
Class com.compomics.util.experiment.quantification.matches.ProteinQuantification extends QuantificationMatch implements Serializable |
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Serialized Fields |
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String proteinKey
ArrayList<E> peptideQuantification
Class com.compomics.util.experiment.quantification.matches.PsmQuantification extends QuantificationMatch implements Serializable |
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Serialized Fields |
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String spectrumKey
String spectrumMatchKey
HashMap<K,V> reporterMatches
HashMap<K,V> deisotopedIntensities
double referenceIntensity
Package com.compomics.util.experiment.quantification.reporterion |
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Class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification extends Quantification implements Serializable |
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Serialized Fields |
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HashMap<K,V> sampleAssignement
ReporterMethod reporterMethod
Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable |
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Package com.compomics.util.experiment.refinementparameters |
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Class com.compomics.util.experiment.refinementparameters.MascotScore extends Object implements Serializable |
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serialVersionUID: 1781298332459022056L
Serialized Fields |
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double score
Package com.compomics.util.general |
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Class com.compomics.util.general.UnknownElementMassException extends Exception implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
String element
Package com.compomics.util.general.servlet |
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Class com.compomics.util.general.servlet.MassCalcServlet extends javax.servlet.http.HttpServlet implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Package com.compomics.util.gui |
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Class com.compomics.util.gui.FlamableJFrame extends JFrame implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Class com.compomics.util.gui.JExceptionDialog extends JDialog implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
String[] iMessages
Throwable iThrowable
Class com.compomics.util.gui.JFrameForBytes extends JFrame implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
byte[] iData
JTextArea txtData
JButton btnUnzip
JButton btnSave
Class com.compomics.util.gui.JLabelAndComponentPanel extends JPanel implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
Class com.compomics.util.gui.JTableForDB extends AlternateRowColoursJTable implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
String iDateTimeFormat
Vector<E> iFrames
Package com.compomics.util.gui.dialogs |
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Class com.compomics.util.gui.dialogs.ConnectionDialog extends JDialog implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
ArrayList<E> iConnections
JComboBox cmbConfigurations
JTextField txtDriver
JTextField txtUrl
JTextField txtUser
JPasswordField txtPassword
JButton btnOK
JButton btnCancel
Connectable iTarget
String iPropsFile
String iLastInitiatedConfiguration
Class com.compomics.util.gui.dialogs.DateChooser extends JDialog implements Serializable |
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Serialized Fields |
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Calendar iSelectedCalendar
Calendar iShownCalendar
int iSelectedDayIndex
JLabel[] lblDayNames
JLabel[] lblDays
Integer[] iDays
JLabel lblCurrentMonthYear
Class com.compomics.util.gui.dialogs.HelpDialog extends JDialog implements Serializable |
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Serialized Fields |
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int windowWidth
int windowHeightReduction
Frame frameParent
JDialog dialogParent
Image aboutIcon
Image helpIcon
JPanel backgroundPanel
JButton closeJButton
JScrollPane jScrollPane1
JEditorPane textJEditorPane
Class com.compomics.util.gui.dialogs.ProgressDialog extends JDialog implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
JProgressBar iProgress
Class com.compomics.util.gui.dialogs.PtmDialog extends JDialog implements Serializable |
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Serialized Fields |
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PtmDialogParent ptmDialogParent
PTMFactory ptmFactory
List<E> aminoAcids
PTM currentPtm
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
PtmToPrideMap ptmToPrideMap
CvTerm cvTerm
boolean editable
JButton addNeutralLoss
JButton addReporterIon
JPanel backgroundPanel
JButton cancelButton
JPanel detailsPanel
JButton helpJButton
JLabel jLabel1
JLabel jLabel2
JLabel jLabel3
JLabel jLabel4
JLabel jLabel5
JLabel jLabel6
JLabel jLabel7
JPanel jPanel1
JTextField massTxt
JTextField nameTxt
JPanel neutralLossesAndReporterIonsPanel
JScrollPane neutralLossesJScrollPane
JTable neutralLossesTable
JButton okButton
JButton olsJButton
JTextField psiModMappingJTextField
JPanel psiModMappingPanel
JButton removeNeutralLoss
JButton removerReporterIon
JScrollPane reporterIonsJScrollPane
JTable reporterIonsTable
JTextField residuesTxt
JComboBox typeCmb
Class com.compomics.util.gui.dialogs.SampleSelection extends JDialog implements Serializable |
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Serialized Fields |
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String[] samples
String choice
JPanel backgroundPanel
JComboBox comboBox
JLabel jLabel1
JLabel jLabel2
JButton okButton
JLabel titleLbl
Package com.compomics.util.gui.isotopic_calculator |
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Class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui extends JFrame implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
JTextArea txtSequence
JLabel lblComp
JLabel lblMass
JButton calculateButton
AlternateRowColoursJTable table1
JPanel jpanContent
JPanel headerTable
JPanel spectrumPanel
JSpinner spinCharge
JLabel lblPeptide
AASequenceImpl iSequence
HashMap<K,V> iElements
double iCharge
Package com.compomics.util.gui.protein |
---|
Class com.compomics.util.gui.protein.SequenceModificationPanel extends JPanel implements Serializable |
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Serialized Fields |
---|
HashMap<K,V> fragmentIonRectangles
String[] iSequenceComponents
ArrayList<E> profiles
Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
int iYStart
boolean isModifiedSequence
Package com.compomics.util.gui.renderers |
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Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends DefaultListCellRenderer implements Serializable |
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Serialized Fields |
---|
int align
Class com.compomics.util.gui.renderers.ByteArrayRenderer extends DefaultTableCellRenderer implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
byte[] iData
Class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer extends JLabel implements Serializable |
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Serialized Fields |
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double minXAxisValue
double maxXAxisValue
TableCellRenderer delegate
Class com.compomics.util.gui.renderers.TimestampRenderer extends DefaultTableCellRenderer implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends BasicComboBoxRenderer implements Serializable |
---|
Serialized Fields |
---|
Vector<E> tooltips
int align
int MAX_TOOLTIP_WIDTH
Package com.compomics.util.gui.spectrum |
---|
Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
---|
Color iChromatogramColor
Color iChromatogramPointColor
Class com.compomics.util.gui.spectrum.FragmentIonTable extends JTable implements Serializable |
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Serialized Fields |
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ArrayList<E> currentFragmentIonTypes
NeutralLossesMap neutralLosses
boolean singleCharge
boolean twoCharges
ArrayList<E> tooltips
Peptide currentPeptide
String peptideSequence
ArrayList<E> allAnnotations
ArrayList<E> allSpectra
Class com.compomics.util.gui.spectrum.GraphicsPanel extends JPanel implements Serializable |
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Serialized Fields |
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float peakWidth
float backgroundPeakWidth
boolean subscriptAnnotationNumbers
Color peakWaterMarkColor
boolean scientificXAxis
boolean scientificYAxis
String scientificPattern
HashMap<K,V> referenceAreasXAxis
HashMap<K,V> referenceAreasYAxis
boolean miniature
boolean yDataIsPositive
float alphaLevel
boolean useMassDeltaCombinations
double deltaMassWindow
String iXAxisLabel
String iYAxisLabel
Color iFilenameColor
ArrayList<E> iDataPointAndLineColor
ArrayList<E> iAreaUnderCurveColor
Integer iPointSize
String iFilename
ArrayList<E> iSpecPanelListeners
int iPointDetectionTolerance
int iStartXLoc
int iStartYLoc
int iEndXLoc
double xAxisZoomRangeLowerValue
double xAxisZoomRangeUpperValue
int iDragXLoc
double iXScaleUnit
double iYScaleUnit
int iXUnit
int iYUnit
int iXPadding
int iTopPadding
boolean iXAxisStartAtZero
boolean iDragged
int xTagCount
int yTagCount
int padding
int currentPadding
int maxPadding
boolean showFileName
boolean showPrecursorDetails
boolean showResolution
ArrayList<E> iXAxisData
double iXAxisMin
double iXAxisMax
double iYAxisMin
double iYAxisMax
double iAnnotationYAxisThreshold
ArrayList<E> iYAxisData
double iPrecursorMZ
String iPrecursorCharge
ArrayList<E> iXAxisDataInPixels
ArrayList<E> iYAxisDataInPixels
boolean iHighLight
int iHighLightIndex
int iHighLightDatasetIndex
boolean iClicked
int iClickedIndex
int iClickedDataSetIndex
Vector<E> iClickedList
Vector<E> iClickedListDatasetIndices
Vector<E> iStoredSequence
Vector<E> iStoredSequenceDatasetIndices
Vector<E> iAnnotations
int iMinDrag
int iDrawStyle
int iDotRadius
int iMSLevel
boolean showAllPeaks
boolean yAxisZoomExcludesBackgroundPeaks
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
Class com.compomics.util.gui.spectrum.IntensityHistogram extends JPanel implements Serializable |
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Serialized Fields |
---|
org.jfree.chart.ChartPanel chartPanel
Class com.compomics.util.gui.spectrum.IonLabelColorTableModel extends DefaultTableModel implements Serializable |
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Serialized Fields |
---|
HashMap<K,V> ionMap
ArrayList<E> keys
Class com.compomics.util.gui.spectrum.IsotopicDistributionPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
Color aSpectrumPeakColor
Color aSpectrumProfileModeLineColor
ArrayList<E> peptideSequences
ArrayList<E> peptideCharges
HashMap<K,V> iElements
Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends JPanel implements Serializable |
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Serialized Fields |
---|
boolean useRelativeError
ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
Class com.compomics.util.gui.spectrum.MassErrorPlot extends JPanel implements Serializable |
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Serialized Fields |
---|
ArrayList<E> annotations
ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
boolean useRelativeError
Class com.compomics.util.gui.spectrum.SequenceFragmentationPanel extends JPanel implements Serializable |
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Serialized Fields |
---|
HashMap<K,V> tooltipRectangles
String[] iSequenceComponents
ArrayList<E> iIonMatches
double[] bIons
double[] yIons
Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
boolean isModifiedSequence
boolean iHighlightModifications
HashMap<K,V> iModificationColors
, etc.
HashMap<K,V> iModificationNames
int forwardIon
int rewindIon
Color forwardColor
Color rewindColor
Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
---|
Color aSpectrumPeakColor
Color aSpectrumProfileModeLineColor
Package com.compomics.util.gui.waiting.waitinghandlers |
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Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX extends JDialog implements Serializable |
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Serialized Fields |
---|
boolean doNothingOnClose
boolean unstoppable
boolean canceled
boolean finished
Image waitingIcon
Image normalIcon
Frame waitingHandlerParentFrame
JDialog waitingHandlerParentDialog
JProgressBar progressBar
Class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog extends JDialog implements Serializable |
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Serialized Fields |
---|
JDialog dialog
Point naturalLocation
Timer shakeTimer
boolean runFinished
boolean runCanceled
String tab
ArrayList<E> tips
int currentTipIndex
String lastSelectedFolder
Image waitingIcon
Image normalIcon
Frame waitingHandlerParent
boolean shakeWhenFinished
String processName
JPanel backgroundPanel
JCheckBox closeDialogWhenImportCompletesCheckBox
JButton closeJButton
JLayeredPane layeredPane
JButton nextJButton
JButton okButton
JPanel processProgressPanel
JProgressBar progressBar
JTextArea reportArea
JScrollPane reportAreaScrollPane
JLabel saveReportLabel
JProgressBar secondaryJProgressBar
JSplitPane secondaryProgressBarSplitPane
JCheckBox showTipOfTheDayCheckBox
JProgressBar tempJProgressBar
JEditorPane tipOfTheDayEditorPane
JPanel tipOfTheDayJPanel
JLayeredPane tipOfTheDayLayeredPane
JScrollPane tipOfTheDayScrollPane
Package com.compomics.util.io |
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Class com.compomics.util.io.FtpConnectionException extends FtpProtocolException implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
Class com.compomics.util.io.FtpLoginException extends FtpProtocolException implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
Class com.compomics.util.io.FtpProtocolException extends IOException implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
Package com.compomics.util.preferences |
---|
Class com.compomics.util.preferences.AnnotationPreferences extends Object implements Serializable |
---|
serialVersionUID: -524156803097913546L
Serialized Fields |
---|
boolean yAxisZoomExcludesBackgroundPeaks
boolean intensityIonTable
boolean showBars
boolean showAllPeaks
double intensityLimit
boolean automaticAnnotation
HashMap<K,V> selectedIons
NeutralLossesMap neutralLossesMap
boolean neutralLossesSequenceDependant
ArrayList<E> selectedCharges
double fragmentIonAccuracy
Peptide currentPeptide
int currentPrecursorCharge
boolean showForwardIonDeNovoTags
boolean showRewindIonDeNovoTags
int deNovoCharge
Class com.compomics.util.preferences.UtilitiesUserPreferences extends Object implements Serializable |
---|
serialVersionUID: -4343570286224891504L
Serialized Fields |
---|
Float spectrumAnnotatedPeakWidth
Float spectrumBackgroundPeakWidth
Color spectrumAnnotatedPeakColor
Color spectrumBackgroundPeakColor
Color sparklineColorValidated
Color sparklineColorNonValidated
Color sparklineColorNotFound
Color sparklineColorPossible
Color peptideSelected
int memoryPreference
String searchGuiPath
String peptideShakerPath
String reporterPath
String relimsPath
Package com.compomics.util.pride |
---|
Class com.compomics.util.pride.CvTerm extends Object implements Serializable |
---|
serialVersionUID: -2890434198335005181L
Serialized Fields |
---|
String ontology
String accession
String name
String value
Class com.compomics.util.pride.PtmToPrideMap extends Object implements Serializable |
---|
serialVersionUID: 7368502853292052566L
Serialized Fields |
---|
HashMap<K,V> modToCvMap
Package com.compomics.util.pride.prideobjects |
---|
Class com.compomics.util.pride.prideobjects.Contact extends Object implements Serializable |
---|
serialVersionUID: -9182316910747747823L
Serialized Fields |
---|
String name
String eMail
String institution
Class com.compomics.util.pride.prideobjects.Instrument extends Object implements Serializable |
---|
serialVersionUID: -8802861658166703745L
Serialized Fields |
---|
String name
ArrayList<E> cvTerms
CvTerm source
CvTerm detector
Class com.compomics.util.pride.prideobjects.Protocol extends Object implements Serializable |
---|
serialVersionUID: -9045298216154032632L
Serialized Fields |
---|
String name
ArrayList<E> cvTerms
Class com.compomics.util.pride.prideobjects.Reference extends Object implements Serializable |
---|
serialVersionUID: -5449836209751629549L
Serialized Fields |
---|
String reference
String pmid
String doi
Class com.compomics.util.pride.prideobjects.Sample extends Object implements Serializable |
---|
serialVersionUID: -7142471175737857227L
Serialized Fields |
---|
String name
ArrayList<E> cvTerms
Package com.compomics.util.protein |
---|
Class com.compomics.util.protein.Header extends Object implements Serializable |
---|
serialVersionUID: 7665784733371863163L
Serialized Fields |
---|
String iID
String iForeignID
String iAccession
Header.DatabaseType databaseType
String iForeignAccession
String iDescription
String iForeignDescription
String iRest
StringBuffer iAddenda
int iStart
int iEnd
Class com.compomics.util.protein.ModificationImplementation extends Object implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
ModificationTemplate iTemplate
int iLocation
Package com.compomics.util.sun |
---|
Class com.compomics.util.sun.TableMap extends AbstractTableModel implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
TableModel model
Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable |
---|
Serialized Fields |
---|
org.apache.log4j.Logger logger
int[] indexes
Vector<E> sortingColumns
boolean ascending
int compares
MouseAdapter listMouseListener
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