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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
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
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
JScrollPane peptidesJScrollPane
org.jdesktop.swingx.JXTable peptidesJXTable
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
SpectrumCollection spectrumCollection
HashMap<K,V> quantification
HashMap<K,V> identification
SequenceDataBase sequenceDataBase
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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double theoreticMass
int familyType
Class com.compomics.util.experiment.biology.NeutralLoss extends ExperimentObject implements Serializable |
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Serialized Fields |
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double mass
String name
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
HashSet<E> theoreticPeptideFragmentIons
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
String 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
String[] residuesArray
String name
double mass
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.Glycon extends Ion implements Serializable |
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Serialized Fields |
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HashMap<K,V> theoreticMasses
String name
String shortName
Class com.compomics.util.experiment.biology.ions.PeptideFragmentIon extends Ion implements Serializable |
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Serialized Fields |
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PeptideFragmentIon.PeptideFragmentIonType type
ArrayList<E> neutralLosses
int number
String residue
Class com.compomics.util.experiment.biology.ions.Proton extends Ion implements Serializable |
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Class com.compomics.util.experiment.biology.ions.ReporterIon extends Ion implements Serializable |
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Serialized Fields |
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int index
String name
Package com.compomics.util.experiment.biology.neutrallosses |
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Class com.compomics.util.experiment.biology.neutrallosses.CH4OS extends NeutralLoss implements Serializable |
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Class com.compomics.util.experiment.biology.neutrallosses.H2O extends NeutralLoss implements Serializable |
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Class com.compomics.util.experiment.biology.neutrallosses.H3PO4 extends NeutralLoss implements Serializable |
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Class com.compomics.util.experiment.biology.neutrallosses.HPO3 extends NeutralLoss implements Serializable |
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Class com.compomics.util.experiment.biology.neutrallosses.NH3 extends NeutralLoss implements Serializable |
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Package com.compomics.util.experiment.identification |
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Class com.compomics.util.experiment.identification.Identification extends ExperimentObject implements Serializable |
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serialVersionUID: -2551700699384242554L
Serialized Fields |
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HashMap<K,V> proteinIdentification
HashMap<K,V> peptideIdentification
HashMap<K,V> spectrumIdentification
HashMap<K,V> proteinMap
int methodUsed
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.PeptideAssumption extends ExperimentObject implements Serializable |
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serialVersionUID: 3606509518581203063L
Serialized Fields |
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int rank
Peptide peptide
int advocate
double measuredMass
double eValue
int c13
double ppmMassError
HashSet<E> annotations
String file
Boolean isDecoy
Class com.compomics.util.experiment.identification.SequenceDataBase extends ExperimentObject implements Serializable |
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serialVersionUID: -8651416887737619199L
Serialized Fields |
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String name
String version
HashMap<K,V> proteinMap
HashMap<K,V> headerMap
int nTargetSequences
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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PTM theoreticPtm
boolean variable
int modifiedSite
Class com.compomics.util.experiment.identification.matches.PeptideMatch extends ExperimentObject implements Serializable |
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serialVersionUID: 7195830246336841081L
Serialized Fields |
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Peptide theoreticPeptide
SpectrumMatch mainMatch
HashMap<K,V> spectrumMatches
Boolean isDecoy
Class com.compomics.util.experiment.identification.matches.ProteinMatch extends ExperimentObject implements Serializable |
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serialVersionUID: -6061842447053092696L
Serialized Fields |
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HashMap<K,V> theoreticProtein
Protein mainMatch
HashMap<K,V> peptideMatches
Class com.compomics.util.experiment.identification.matches.SpectrumMatch extends ExperimentObject 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
Package com.compomics.util.experiment.io.identifications.idfilereaders |
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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
SpectrumCollection spectrumCollection
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
Integer msResponseScale
PTMFactory ptmFactory
SpectrumCollection spectrumCollection
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
SpectrumCollection spectrumCollection
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 mz
double intensity
Charge charge
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
HashSet<E> peakList
String scanNumber
double scanStartTime
Class com.compomics.util.experiment.massspectrometry.SpectrumCollection extends ExperimentObject implements Serializable |
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serialVersionUID: -7894588835760914088L
Serialized Fields |
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HashMap<K,V> spectrumMap
int sourceType
HashMap<K,V> mzMLUnmarshallerMap
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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int methodUsed
HashMap<K,V> proteinQuantification
Class com.compomics.util.experiment.quantification.QuantificationMethod extends ExperimentObject implements Serializable |
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Serialized Fields |
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int index
String name
Class com.compomics.util.experiment.quantification.Ratio extends ExperimentObject implements Serializable |
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Serialized Fields |
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int referenceLabel
int measureLabel
double ratio
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
int referenceLabel
ReporterMethod reporterMethod
Class com.compomics.util.experiment.quantification.reporterion.ReporterMethod extends QuantificationMethod implements Serializable |
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Serialized Fields |
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ArrayList<E> reporterIons
ArrayList<E> correctionFactors
Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable |
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Serialized Fields |
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ArrayList<E> methods
Package com.compomics.util.experiment.quantification.reporterion.quantification |
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Class com.compomics.util.experiment.quantification.reporterion.quantification.PeptideQuantification extends ExperimentObject implements Serializable |
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Serialized Fields |
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String peptideKey
HashMap<K,V> psmQuantification
HashMap<K,V> ratios
Class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification extends ExperimentObject implements Serializable |
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Serialized Fields |
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String proteinKey
HashMap<K,V> peptideQuantification
HashMap<K,V> proteinRatios
Class com.compomics.util.experiment.quantification.reporterion.quantification.PsmQuantification extends ExperimentObject implements Serializable |
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Serialized Fields |
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String spectrumKey
String spectrumMatchKey
HashMap<K,V> reporterMatches
HashMap<K,V> ratios
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 |
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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.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.ProgressDialogX extends JDialog implements Serializable |
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Serialized Fields |
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ProgressDialogParent progressDialogFrame
boolean doNothingOnClose
JProgressBar progressBar
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 |
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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.renderers |
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Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends DefaultListCellRenderer implements Serializable |
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Serialized Fields |
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int align
Class com.compomics.util.gui.renderers.ByteArrayRenderer extends DefaultTableCellRenderer implements Serializable |
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Serialized Fields |
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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 |
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org.apache.log4j.Logger logger
Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends BasicComboBoxRenderer implements Serializable |
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Serialized Fields |
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Vector<E> tooltips
int align
int MAX_TOOLTIP_WIDTH
Package com.compomics.util.gui.spectrum |
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Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
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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
boolean singleCharge
boolean twoCharges
ArrayList<E> tooltips
Peptide currentPeptide
String peptideSequence
ArrayList<E> allAnnotations
ArrayList<E> annotations
ArrayList<E> allSpectra
Class com.compomics.util.gui.spectrum.GraphicsPanel extends JPanel implements Serializable |
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Serialized Fields |
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Color peakWaterMarkColor
boolean scientificXAxis
boolean scientificYAxis
String scientificPattern
HashMap<K,V> referenceAreasXAxis
HashMap<K,V> referenceAreasYAxis
boolean miniature
boolean yDataIsPositive
float alphaLevel
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
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
Class com.compomics.util.gui.spectrum.IntensityHistogram extends JPanel implements Serializable |
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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 |
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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 |
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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 |
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HashMap<K,V> fragmentIonRectangles
String[] iSequenceComponents
ArrayList<E> iIonMatches
double[] bIons
double[] yIons
Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
boolean iBoolHighlightSequence
boolean isModifiedSequence
Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
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Color aSpectrumPeakColor
Color aSpectrumProfileModeLineColor
Package com.compomics.util.io |
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Class com.compomics.util.io.FtpConnectionException extends FtpProtocolException implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Class com.compomics.util.io.FtpLoginException extends FtpProtocolException implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Class com.compomics.util.io.FtpProtocolException extends IOException implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
Package com.compomics.util.protein |
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Class com.compomics.util.protein.Header extends Object implements Serializable |
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serialVersionUID: 7665784733371863163L
Serialized Fields |
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String iID
String iForeignID
String iAccession
String iDatabaseType
String iForeignAccession
String iDescription
String iForeignDescription
String iRest
StringBuffer iAddenda
int iStart
int iEnd
Class com.compomics.util.protein.ModificationImplementation extends Object implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
ModificationTemplate iTemplate
int iLocation
Package com.compomics.util.sun |
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Class com.compomics.util.sun.TableMap extends AbstractTableModel implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
TableModel model
Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
int[] indexes
Vector<E> sortingColumns
boolean ascending
int compares
MouseAdapter listMouseListener
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