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Package com.compomics.util |
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Class com.compomics.util.AlternateRowColoursJTable extends javax.swing.JTable implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
java.awt.Color iEvenRowColor
java.awt.Color iUnevenRowColor
Package com.compomics.util.db |
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Class com.compomics.util.db.DBResultSet extends javax.swing.table.AbstractTableModel implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
int iColCount
int iRowCount
java.lang.String[] iColNames
java.lang.Object[][] iData
Class com.compomics.util.db.GeneratorException extends java.lang.Exception implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
java.lang.Exception iNested
Package com.compomics.util.examples |
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Class com.compomics.util.examples.HelpWindow extends javax.swing.JFrame implements Serializable |
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Serialized Fields |
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javax.swing.JButton closeJButton
javax.swing.JScrollPane jScrollPane1
javax.swing.JEditorPane textJEditorPane
Class com.compomics.util.examples.UtilitiesDemo extends javax.swing.JFrame implements Serializable |
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Serialized Fields |
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java.util.HashMap<K,V> peffAnnotationsColorMap
java.util.HashMap<K,V> peffAnnotationsTooltipMap
boolean peffFormat
java.util.TreeMap<K,V> keyValuePairs
java.io.File currentSequenceFile
java.io.BufferedReader currentPeffBufferedReader
java.lang.String currentSequence
java.lang.String currentSequenceLine
java.util.HashMap<K,V> linkedSpectrumPanels
java.util.HashMap<K,V> allAnnotations
SpectrumPanel spectrumAPanel
SpectrumPanel spectrumBPanel
int spectrumPanelMaxPadding
int chromatogramPanelMaxPadding
MascotEnzymeReader mascotEnzymeReader
java.lang.String cleanProteinSequence
java.util.HashMap<K,V> selectedAnnotationTypes
java.util.ArrayList<E> sequenceAnnotationColumnHeaderTooltips
java.awt.Color sparklineColor
javax.swing.JCheckBox H2OIonsJCheckBox
javax.swing.JCheckBox NH3IonsJCheckBox
javax.swing.JCheckBox aIonsJCheckBox
javax.swing.JCheckBox allPeaksJCheckBox
javax.swing.JCheckBox bIonsJCheckBox
javax.swing.JButton browseJButton
javax.swing.JCheckBox cIonsJCheckBox
javax.swing.JCheckBox chargeOneJCheckBox
javax.swing.JCheckBox chargeOverTwoJCheckBox
javax.swing.JSpinner chargePeptideAJSpinner
javax.swing.JSpinner chargePeptideBJSpinner
javax.swing.JCheckBox chargeTwoJCheckBox
javax.swing.JPanel chromatogramAJPanel
javax.swing.JPanel chromatogramJPanel
javax.swing.JLabel chromatogramPanelHelpJLabel
javax.swing.JLabel chromatogramPanelInfoJLabel
javax.swing.JComboBox enzymesJComboBox
javax.swing.JButton exportJButton
javax.swing.JLabel inSilicoDigestionHelpJLabel
javax.swing.JEditorPane informationJEditorPane
javax.swing.JPanel informationJPanel
javax.swing.JScrollPane informationJScrollPane
javax.swing.JTextField inhibitorsJTextField
javax.swing.JPanel ionSelectionJPanel
javax.swing.JPanel isotopicDistributionAJPanel
javax.swing.JLabel isotopicDistributionCalculatorHelpJLabel
javax.swing.JLabel isotopicDistributionCalculatorInfoJLabel
javax.swing.JPanel isotopicDistributionJPanel
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel10
javax.swing.JLabel jLabel11
javax.swing.JLabel jLabel12
javax.swing.JLabel jLabel13
javax.swing.JLabel jLabel14
javax.swing.JLabel jLabel15
javax.swing.JLabel jLabel16
javax.swing.JLabel jLabel17
javax.swing.JLabel jLabel18
javax.swing.JLabel jLabel19
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel20
javax.swing.JLabel jLabel21
javax.swing.JLabel jLabel24
javax.swing.JLabel jLabel3
javax.swing.JLabel jLabel4
javax.swing.JLabel jLabel5
javax.swing.JLabel jLabel6
javax.swing.JLabel jLabel7
javax.swing.JLabel jLabel8
javax.swing.JLabel jLabel9
javax.swing.JPanel jPanel1
javax.swing.JPanel jPanel10
javax.swing.JPanel jPanel11
javax.swing.JPanel jPanel12
javax.swing.JPanel jPanel2
javax.swing.JPanel jPanel3
javax.swing.JPanel jPanel4
javax.swing.JPanel jPanel5
javax.swing.JPanel jPanel6
javax.swing.JPanel jPanel7
javax.swing.JPanel jPanel8
javax.swing.JPanel jPanel9
javax.swing.JRadioButton jRadioButton1
javax.swing.JScrollPane jScrollPane1
javax.swing.JScrollPane jScrollPane2
javax.swing.JScrollPane jScrollPane3
javax.swing.JSeparator jSeparator1
javax.swing.JSeparator jSeparator2
javax.swing.JSeparator jSeparator3
javax.swing.JSeparator jSeparator4
javax.swing.JSeparator jSeparator5
javax.swing.JSeparator jSeparator6
javax.swing.JSeparator jSeparator9
javax.swing.JTabbedPane jTabbedPane
javax.swing.JCheckBox linkedSpectraJCheckBox
javax.swing.JSpinner lowerMassJSpinner
javax.swing.JSpinner missedCleavagesJSpinner
javax.swing.JButton nextJButton
javax.swing.JCheckBox otherIonsJCheckBox
javax.swing.JTable peffAnnotationsJTable
javax.swing.JTable peffHeaderJTable
javax.swing.JPanel peptideAColorJPanel
javax.swing.JTextField peptideACompositionJTextField
javax.swing.JScrollPane peptideAJScrollPane
org.jdesktop.swingx.JXTable peptideAJXTable
javax.swing.JTextField peptideAMzJTextField
javax.swing.JPanel peptideBColorJPanel
javax.swing.JTextField peptideBCompositionJTextField
javax.swing.JScrollPane peptideBJScrollPane
org.jdesktop.swingx.JXTable peptideBJXTable
javax.swing.JTextField peptideBMzJTextField
javax.swing.JTextField peptideSequenceAJTextField
javax.swing.JTextField peptideSequenceBJTextField
javax.swing.JPanel peptidesJPanel
javax.swing.JTable peptidesJTable
javax.swing.JScrollPane peptidesScrollPane
javax.swing.JTextField positionJTextField
javax.swing.JCheckBox profileSpectrumJCheckBox
javax.swing.JScrollPane proteinCoverageJScrollPane
javax.swing.JLabel proteinDigestionJLabel
javax.swing.JPanel proteinDigestionJPanel
javax.swing.JTable proteinHeaderJTable
javax.swing.JEditorPane proteinSequenceCoverageJEditorPane
javax.swing.JPanel sequenceCoverageJPanel
javax.swing.JTextField sequenceFileJTextField
javax.swing.JTabbedPane sequenceJTabbedPane
javax.swing.JComboBox silacLabelPeptideAJComboBox
javax.swing.JComboBox silacLabelPeptideBJComboBox
javax.swing.JTextField siteJTextField
javax.swing.JPanel spectraJPanel
javax.swing.JPanel spectrumAJPanel
javax.swing.JPanel spectrumBJPanel
javax.swing.JPanel spectrumJPanel
javax.swing.JLabel spectrumPanelHelpJLabel
javax.swing.JLabel spectrumPanelInfoJLabel
javax.swing.JSpinner upperMassJSpinner
javax.swing.JCheckBox xIonsJCheckBox
javax.swing.JCheckBox yIonsJCheckBox
javax.swing.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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java.lang.String reference
java.util.HashMap<K,V> samples
java.util.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
java.util.HashMap<K,V> quantification
java.util.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
java.util.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
java.lang.String name
java.lang.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
java.lang.String name
java.util.ArrayList<E> aminoAcidBefore
java.util.ArrayList<E> aminoAcidAfter
java.util.ArrayList<E> restrictionBefore
java.util.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
java.lang.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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java.lang.String sequence
java.lang.Double mass
java.util.ArrayList<E> parentProteins
java.util.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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java.lang.String accession
boolean decoy
java.lang.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
java.util.ArrayList<E> residuesArray
java.lang.String name
java.lang.String shortName
double mass
java.util.ArrayList<E> neutralLosses
java.util.ArrayList<E> reporterIons
Class com.compomics.util.experiment.biology.PTMFactory extends java.lang.Object implements Serializable |
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serialVersionUID: 7935264190312934466L
Serialized Fields |
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java.util.HashMap<K,V> ptmMap
java.util.ArrayList<E> defaultMods
java.util.ArrayList<E> userMods
java.util.HashMap<K,V> omssaIndexes
Class com.compomics.util.experiment.biology.Sample extends ExperimentObject implements Serializable |
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serialVersionUID: 303393644914835325L
Serialized Fields |
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java.lang.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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java.util.HashMap<K,V> theoreticMasses
java.lang.String name
java.lang.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
java.util.ArrayList<E> neutralLosses
int number
java.lang.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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java.lang.String name
Package com.compomics.util.experiment.identification |
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Class com.compomics.util.experiment.identification.AAStats extends java.lang.Object implements Serializable |
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serialVersionUID: 4600458866001677754L
Serialized Fields |
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java.util.HashMap<K,V> aaOccurences
int totalAA
java.util.HashMap<K,V> aaAfter
java.util.HashMap<K,V> totalAAAfter
java.util.HashMap<K,V> aaBefore
java.util.HashMap<K,V> totalAABefore
java.util.ArrayList<E> implementedAa
Class com.compomics.util.experiment.identification.FastaIndex extends ExperimentObject implements Serializable |
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Serialized Fields |
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java.util.HashMap<K,V> indexes
java.lang.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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java.util.ArrayList<E> proteinIdentification
java.util.ArrayList<E> peptideIdentification
java.util.ArrayList<E> spectrumIdentification
java.util.HashMap<K,V> proteinMap
int methodUsed
int cacheSize
java.lang.String serializationDirectory
boolean inMemory
boolean automatedMemoryManagement
java.util.HashMap<K,V> loadedMatchesMap
java.util.ArrayList<E> loadedMatches
java.util.HashMap<K,V> modifiedMatches
java.util.HashMap<K,V> urParameters
java.util.ArrayList<E> longKeys
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 java.lang.Object implements Serializable |
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serialVersionUID: -4690159937753713106L
Serialized Fields |
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java.util.HashMap<K,V> bBoundaries
java.util.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
java.lang.String file
java.lang.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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java.lang.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
java.lang.String mainMatchKey
java.util.ArrayList<E> spectrumMatches
java.lang.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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java.util.ArrayList<E> theoreticProtein
java.lang.String mainMatch
java.util.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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java.lang.String spectrumKey
java.util.HashMap<K,V> assumptions
PeptideAssumption bestAssumption
java.util.HashMap<K,V> firstHits
java.util.ArrayList<E> advocates
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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java.util.HashMap<K,V> index
java.io.RandomAccessFile randomAccessFile
java.lang.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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java.io.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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java.io.File identificationFile
java.io.File modsFile
java.io.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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java.util.HashMap<K,V> indexMap
java.util.ArrayList<E> spectrumTitles
java.lang.String fileName
java.lang.Double maxRT
java.lang.Double minRT
java.lang.Double maxMz
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
java.util.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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java.lang.String spectrumTitle
java.lang.String fileName
int level
java.util.HashMap<K,V> peakList
java.lang.String scanNumber
double scanStartTime
Package com.compomics.util.experiment.personalization |
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Class com.compomics.util.experiment.personalization.ExperimentObject extends java.lang.Object implements Serializable |
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serialVersionUID: 1929697552061121072L
Serialized Fields |
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java.util.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
int cacheSize
java.lang.String serializationDirectory
boolean inMemory
boolean automatedMemoryManagement
java.util.HashMap<K,V> loadedMatchesMap
java.util.ArrayList<E> loadedMatches
java.util.HashMap<K,V> modifiedMatches
java.util.HashMap<K,V> urParameters
java.util.ArrayList<E> longKeys
java.util.ArrayList<E> proteinQuantification
java.util.ArrayList<E> peptideQuantification
java.util.HashMap<K,V> psmIDentificationToQuantification
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.QuantificationMatch extends ExperimentObject implements Serializable |
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Serialized Fields |
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java.util.HashMap<K,V> ratios
Class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification extends Quantification implements Serializable |
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Serialized Fields |
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java.util.HashMap<K,V> sampleAssignement
int referenceLabel
ReporterIonQuantification.ReporterIonMethod reporterMethod
Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable |
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Serialized Fields |
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java.util.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 QuantificationMatch implements Serializable |
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Serialized Fields |
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java.lang.String peptideKey
java.util.ArrayList<E> psmQuantification
Class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification extends QuantificationMatch implements Serializable |
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Serialized Fields |
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java.lang.String proteinKey
java.util.ArrayList<E> peptideQuantification
Class com.compomics.util.experiment.quantification.reporterion.quantification.PsmQuantification extends QuantificationMatch implements Serializable |
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Serialized Fields |
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java.lang.String spectrumKey
java.lang.String spectrumMatchKey
java.util.HashMap<K,V> reporterMatches
java.util.HashMap<K,V> deisotopedIntensities
Package com.compomics.util.experiment.refinementparameters |
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Class com.compomics.util.experiment.refinementparameters.MascotScore extends java.lang.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 java.lang.Exception implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
java.lang.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 javax.swing.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 javax.swing.JDialog implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
java.lang.String[] iMessages
java.lang.Throwable iThrowable
Class com.compomics.util.gui.JFrameForBytes extends javax.swing.JFrame implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
byte[] iData
javax.swing.JTextArea txtData
javax.swing.JButton btnUnzip
javax.swing.JButton btnSave
Class com.compomics.util.gui.JLabelAndComponentPanel extends javax.swing.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
java.lang.String iDateTimeFormat
java.util.Vector<E> iFrames
Package com.compomics.util.gui.dialogs |
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Class com.compomics.util.gui.dialogs.ConnectionDialog extends javax.swing.JDialog implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
java.util.ArrayList<E> iConnections
javax.swing.JComboBox cmbConfigurations
javax.swing.JTextField txtDriver
javax.swing.JTextField txtUrl
javax.swing.JTextField txtUser
javax.swing.JPasswordField txtPassword
javax.swing.JButton btnOK
javax.swing.JButton btnCancel
Connectable iTarget
java.lang.String iPropsFile
java.lang.String iLastInitiatedConfiguration
Class com.compomics.util.gui.dialogs.DateChooser extends javax.swing.JDialog implements Serializable |
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Serialized Fields |
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java.util.Calendar iSelectedCalendar
java.util.Calendar iShownCalendar
int iSelectedDayIndex
javax.swing.JLabel[] lblDayNames
javax.swing.JLabel[] lblDays
java.lang.Integer[] iDays
javax.swing.JLabel lblCurrentMonthYear
Class com.compomics.util.gui.dialogs.ProgressDialog extends javax.swing.JDialog implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
javax.swing.JProgressBar iProgress
Class com.compomics.util.gui.dialogs.ProgressDialogX extends javax.swing.JDialog implements Serializable |
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Serialized Fields |
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ProgressDialogParent progressDialogFrame
boolean doNothingOnClose
javax.swing.JProgressBar progressBar
Package com.compomics.util.gui.isotopic_calculator |
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Class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui extends javax.swing.JFrame implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
javax.swing.JTextArea txtSequence
javax.swing.JLabel lblComp
javax.swing.JLabel lblMass
javax.swing.JButton calculateButton
AlternateRowColoursJTable table1
javax.swing.JPanel jpanContent
javax.swing.JPanel headerTable
javax.swing.JPanel spectrumPanel
javax.swing.JSpinner spinCharge
javax.swing.JLabel lblPeptide
AASequenceImpl iSequence
java.util.HashMap<K,V> iElements
double iCharge
Package com.compomics.util.gui.protein |
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Class com.compomics.util.gui.protein.SequenceModificationPanel extends javax.swing.JPanel implements Serializable |
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Serialized Fields |
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java.util.HashMap<K,V> fragmentIonRectangles
java.lang.String[] iSequenceComponents
java.util.ArrayList<E> profiles
java.awt.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 javax.swing.DefaultListCellRenderer implements Serializable |
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Serialized Fields |
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int align
Class com.compomics.util.gui.renderers.ByteArrayRenderer extends javax.swing.table.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 javax.swing.JLabel implements Serializable |
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Serialized Fields |
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double minXAxisValue
double maxXAxisValue
javax.swing.table.TableCellRenderer delegate
Class com.compomics.util.gui.renderers.TimestampRenderer extends javax.swing.table.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 javax.swing.plaf.basic.BasicComboBoxRenderer implements Serializable |
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Serialized Fields |
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java.util.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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java.awt.Color iChromatogramColor
java.awt.Color iChromatogramPointColor
Class com.compomics.util.gui.spectrum.FragmentIonTable extends javax.swing.JTable implements Serializable |
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Serialized Fields |
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java.util.ArrayList<E> currentFragmentIonTypes
NeutralLossesMap neutralLosses
boolean singleCharge
boolean twoCharges
java.util.ArrayList<E> tooltips
Peptide currentPeptide
java.lang.String peptideSequence
java.util.ArrayList<E> allAnnotations
java.util.ArrayList<E> annotations
java.util.ArrayList<E> allSpectra
Class com.compomics.util.gui.spectrum.GraphicsPanel extends javax.swing.JPanel implements Serializable |
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Serialized Fields |
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boolean subscriptAnnotationNumbers
java.awt.Color peakWaterMarkColor
boolean scientificXAxis
boolean scientificYAxis
java.lang.String scientificPattern
java.util.HashMap<K,V> referenceAreasXAxis
java.util.HashMap<K,V> referenceAreasYAxis
boolean miniature
boolean yDataIsPositive
float alphaLevel
double deltaMassWindow
java.lang.String iXAxisLabel
java.lang.String iYAxisLabel
java.awt.Color iFilenameColor
java.util.ArrayList<E> iDataPointAndLineColor
java.util.ArrayList<E> iAreaUnderCurveColor
java.lang.Integer iPointSize
java.lang.String iFilename
java.util.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
java.util.ArrayList<E> iXAxisData
double iXAxisMin
double iXAxisMax
double iYAxisMin
double iYAxisMax
double iAnnotationYAxisThreshold
java.util.ArrayList<E> iYAxisData
double iPrecursorMZ
java.lang.String iPrecursorCharge
java.util.ArrayList<E> iXAxisDataInPixels
java.util.ArrayList<E> iYAxisDataInPixels
boolean iHighLight
int iHighLightIndex
int iHighLightDatasetIndex
boolean iClicked
int iClickedIndex
int iClickedDataSetIndex
java.util.Vector<E> iClickedList
java.util.Vector<E> iClickedListDatasetIndices
java.util.Vector<E> iStoredSequence
java.util.Vector<E> iStoredSequenceDatasetIndices
java.util.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 javax.swing.JPanel implements Serializable |
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Serialized Fields |
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org.jfree.chart.ChartPanel chartPanel
Class com.compomics.util.gui.spectrum.IsotopicDistributionPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
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org.apache.log4j.Logger logger
java.awt.Color aSpectrumPeakColor
java.awt.Color aSpectrumProfileModeLineColor
java.util.ArrayList<E> peptideSequences
java.util.ArrayList<E> peptideCharges
java.util.HashMap<K,V> iElements
Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends javax.swing.JPanel implements Serializable |
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Serialized Fields |
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boolean useRelativeError
java.util.ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
java.util.ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
Class com.compomics.util.gui.spectrum.MassErrorPlot extends javax.swing.JPanel implements Serializable |
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Serialized Fields |
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java.util.ArrayList<E> annotations
java.util.ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
java.util.ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
boolean useRelativeError
Class com.compomics.util.gui.spectrum.SequenceFragmentationPanel extends javax.swing.JPanel implements Serializable |
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Serialized Fields |
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java.util.HashMap<K,V> tooltipRectangles
java.lang.String[] iSequenceComponents
java.util.ArrayList<E> iIonMatches
double[] bIons
double[] yIons
java.awt.Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
boolean isModifiedSequence
boolean iHighlightModifications
java.util.HashMap<K,V> iModificationColors
, etc.
java.util.HashMap<K,V> iModificationNames
Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable |
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Serialized Fields |
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java.awt.Color aSpectrumPeakColor
java.awt.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 |
---|
org.apache.log4j.Logger logger
Class com.compomics.util.io.FtpLoginException extends FtpProtocolException implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
Class com.compomics.util.io.FtpProtocolException extends java.io.IOException implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
Package com.compomics.util.pride |
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Class com.compomics.util.pride.CvTerm extends java.lang.Object implements Serializable |
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serialVersionUID: -2890434198335005181L
Serialized Fields |
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java.lang.String ontology
java.lang.String accession
java.lang.String name
java.lang.String value
Class com.compomics.util.pride.PtmToPrideMap extends java.lang.Object implements Serializable |
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serialVersionUID: 7368502853292052566L
Serialized Fields |
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java.util.HashMap<K,V> modToCvMap
Package com.compomics.util.pride.prideobjects |
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Class com.compomics.util.pride.prideobjects.Contact extends java.lang.Object implements Serializable |
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serialVersionUID: -9182316910747747823L
Serialized Fields |
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java.lang.String name
java.lang.String eMail
java.lang.String institution
Class com.compomics.util.pride.prideobjects.Instrument extends java.lang.Object implements Serializable |
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serialVersionUID: -8802861658166703745L
Serialized Fields |
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java.lang.String name
java.util.ArrayList<E> cvTerms
CvTerm source
CvTerm detector
Class com.compomics.util.pride.prideobjects.Protocol extends java.lang.Object implements Serializable |
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serialVersionUID: -9045298216154032632L
Serialized Fields |
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java.lang.String name
java.util.ArrayList<E> cvTerms
Class com.compomics.util.pride.prideobjects.Reference extends java.lang.Object implements Serializable |
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serialVersionUID: -5449836209751629549L
Serialized Fields |
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java.lang.String reference
java.lang.String pmid
java.lang.String doi
Class com.compomics.util.pride.prideobjects.Sample extends java.lang.Object implements Serializable |
---|
serialVersionUID: -7142471175737857227L
Serialized Fields |
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java.lang.String name
java.util.ArrayList<E> cvTerms
Package com.compomics.util.protein |
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Class com.compomics.util.protein.Header extends java.lang.Object implements Serializable |
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serialVersionUID: 7665784733371863163L
Serialized Fields |
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java.lang.String iID
java.lang.String iForeignID
java.lang.String iAccession
Header.DatabaseType databaseType
java.lang.String iForeignAccession
java.lang.String iDescription
java.lang.String iForeignDescription
java.lang.String iRest
java.lang.StringBuffer iAddenda
int iStart
int iEnd
Class com.compomics.util.protein.ModificationImplementation extends java.lang.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 javax.swing.table.AbstractTableModel implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
javax.swing.table.TableModel model
Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable |
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Serialized Fields |
---|
org.apache.log4j.Logger logger
int[] indexes
java.util.Vector<E> sortingColumns
boolean ascending
int compares
java.awt.event.MouseAdapter listMouseListener
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