Serialized Form


Package com.compomics.software.dialogs

Class com.compomics.software.dialogs.PeptideShakerSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

java.lang.String lastSelectedFolder
The selected folder.


backgroundPanel

javax.swing.JPanel backgroundPanel

browseButton

javax.swing.JButton browseButton

cancelButton

javax.swing.JButton cancelButton

jLabel2

javax.swing.JLabel jLabel2

okButton

javax.swing.JButton okButton

peptideShakerButton

javax.swing.JButton peptideShakerButton

peptideShakerDownloadLinkLabel

javax.swing.JLabel peptideShakerDownloadLinkLabel

peptideShakerDownloadPanel

javax.swing.JPanel peptideShakerDownloadPanel

peptideShakerInfoLabel

javax.swing.JLabel peptideShakerInfoLabel

peptideShakerInstallationPanel

javax.swing.JPanel peptideShakerInstallationPanel

peptideShakerJarFileHelpLabel

javax.swing.JLabel peptideShakerJarFileHelpLabel

peptideShakernstallationJTextField

javax.swing.JTextField peptideShakernstallationJTextField

Class com.compomics.software.dialogs.RelimsSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

java.lang.String lastSelectedFolder
The selected folder.


backgroundPanel

javax.swing.JPanel backgroundPanel

browseButton

javax.swing.JButton browseButton

cancelButton

javax.swing.JButton cancelButton

jLabel2

javax.swing.JLabel jLabel2

okButton

javax.swing.JButton okButton

relimsButton

javax.swing.JButton relimsButton

relimsDownloadLinkLabel

javax.swing.JLabel relimsDownloadLinkLabel

relimsDownloadPanel

javax.swing.JPanel relimsDownloadPanel

relimsInfoLabel

javax.swing.JLabel relimsInfoLabel

relimsInstallationJTextField

javax.swing.JTextField relimsInstallationJTextField

relimsInstallationPanel

javax.swing.JPanel relimsInstallationPanel

relimsJarFileHelpLabel

javax.swing.JLabel relimsJarFileHelpLabel

Class com.compomics.software.dialogs.ReporterSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

java.lang.String lastSelectedFolder
The selected folder.


backgroundPanel

javax.swing.JPanel backgroundPanel

browseButton

javax.swing.JButton browseButton

cancelButton

javax.swing.JButton cancelButton

jLabel2

javax.swing.JLabel jLabel2

okButton

javax.swing.JButton okButton

reporterButton

javax.swing.JButton reporterButton

reporterDownloadLinkLabel

javax.swing.JLabel reporterDownloadLinkLabel

reporterDownloadPanel

javax.swing.JPanel reporterDownloadPanel

reporterInfoLabel

javax.swing.JLabel reporterInfoLabel

reporterInstallationJTextField

javax.swing.JTextField reporterInstallationJTextField

reporterInstallationPanel

javax.swing.JPanel reporterInstallationPanel

reporterJarFileHelpLabel

javax.swing.JLabel reporterJarFileHelpLabel

Class com.compomics.software.dialogs.SearchGuiSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

java.lang.String lastSelectedFolder
The selected folder.


backgroundPanel

javax.swing.JPanel backgroundPanel

browseButton

javax.swing.JButton browseButton

cancelButton

javax.swing.JButton cancelButton

jLabel2

javax.swing.JLabel jLabel2

okButton

javax.swing.JButton okButton

searchGuiButton

javax.swing.JButton searchGuiButton

searchGuiDownloadLinkLabel

javax.swing.JLabel searchGuiDownloadLinkLabel

searchGuiDownloadPanel

javax.swing.JPanel searchGuiDownloadPanel

searchGuiInfoLabel

javax.swing.JLabel searchGuiInfoLabel

searchGuiInstallationJTextField

javax.swing.JTextField searchGuiInstallationJTextField

searchGuiInstallationPanel

javax.swing.JPanel searchGuiInstallationPanel

searchGuiJarFileHelpLabel

javax.swing.JLabel searchGuiJarFileHelpLabel

Package com.compomics.util

Class com.compomics.util.AlternateRowColoursJTable extends javax.swing.JTable implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iEvenRowColor

java.awt.Color iEvenRowColor
The background colour for the even rows. A value of 'null' means use the default background colour for JTable.


iUnevenRowColor

java.awt.Color iUnevenRowColor
The background colour for the uneven rows. A value of 'null' (default here) means use the default background colour for JTable.


Package com.compomics.util.db

Class com.compomics.util.db.DBResultSet extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iColCount

int iColCount
The number of columns in this resultset.


iRowCount

int iRowCount
The number of rows in this resultset.


iColNames

java.lang.String[] iColNames
The column names in this resultset.


iData

java.lang.Object[][] iData
The data.

Class com.compomics.util.db.GeneratorException extends java.lang.Exception implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iNested

java.lang.Exception iNested
The nested exception.

Class com.compomics.util.db.ObjectsDB extends java.lang.Object implements Serializable

serialVersionUID: -8595805180622832745L

Serialized Fields

dbName

java.lang.String dbName
The name of the database.


dbConnection

java.sql.Connection dbConnection
The connection, shall not be accessed outside this class. Don't be lazy, implement the dedicated methods here.


longKeys

java.util.ArrayList<E> longKeys
List of keys too long to create a table.


objectsCache

ObjectsCache objectsCache
The cache to be used for the objects


debugSpeedWriter

java.io.BufferedWriter debugSpeedWriter
The writer used to send the output to file.


debugContentWriter

java.io.BufferedWriter debugContentWriter
The writer used to send the output to file.


debugFolder

java.io.File debugFolder
The debug folder.


debugSpeed

boolean debugSpeed
Debug, if true will output a table containing statistics on the speed of the objects I/O.


debugContent

boolean debugContent
Debug, if true will output a table containing details on the objects stored.


debugInteractions

boolean debugInteractions
Debug, if true, all interaction with the database will be logged in the System.out stream.


Package com.compomics.util.examples

Class com.compomics.util.examples.HelpWindow extends javax.swing.JFrame implements Serializable

Serialized Fields

closeJButton

javax.swing.JButton closeJButton

jScrollPane1

javax.swing.JScrollPane jScrollPane1

textJEditorPane

javax.swing.JEditorPane textJEditorPane

Class com.compomics.util.examples.UtilitiesDemo extends javax.swing.JFrame implements Serializable

Serialized Fields

peffAnnotationsColorMap

java.util.HashMap<K,V> peffAnnotationsColorMap
The PEFF annotations color map.


peffAnnotationsTooltipMap

java.util.HashMap<K,V> peffAnnotationsTooltipMap
The PEFF annotations tooltip map.


peffFormat

boolean peffFormat
If true, the format shown is PEFF, if false FASTA is assumed.


keyValuePairs

java.util.TreeMap<K,V> keyValuePairs
The map of the PEFF key value pairs.


currentSequenceFile

java.io.File currentSequenceFile
The current PEFF (or FASTA) sequence file.


currentPeffBufferedReader

java.io.BufferedReader currentPeffBufferedReader
The current PEFF (or FASTA) buffered reader.


currentSequence

java.lang.String currentSequence
The current PEFF (or FASTA) sequence.


currentSequenceLine

java.lang.String currentSequenceLine
The current PEFF (or FASTA) sequence line.


linkedSpectrumPanels

java.util.HashMap<K,V> linkedSpectrumPanels
A hashmap of both the linked spectra.


allAnnotations

java.util.HashMap<K,V> allAnnotations
A hashmap of all spectrum panel annotations.


spectrumAPanel

SpectrumPanel spectrumAPanel
The first spectrum panel.


spectrumBPanel

SpectrumPanel spectrumBPanel
The second spectrum panel


spectrumPanelMaxPadding

int spectrumPanelMaxPadding
The maximum padding allowed in the spectrum panels. Increase if font size on the y-axis becomes too small.


chromatogramPanelMaxPadding

int chromatogramPanelMaxPadding
The maximum padding allowed in the chromatogram panels. Increase if font size on the y-axis becomes too small.


mascotEnzymeReader

MascotEnzymeReader mascotEnzymeReader
Used to read the enzyme details from file.


cleanProteinSequence

java.lang.String cleanProteinSequence
Used for the in silico digestion example.


selectedAnnotationTypes

java.util.HashMap<K,V> selectedAnnotationTypes
The tag colors for PEFF formatting.


sequenceAnnotationColumnHeaderTooltips

java.util.ArrayList<E> sequenceAnnotationColumnHeaderTooltips
Sequence annotation column header tooltips.


sparklineColor

java.awt.Color sparklineColor
The color used for the sparkline bar chart plots.


H2OIonsJCheckBox

javax.swing.JCheckBox H2OIonsJCheckBox

NH3IonsJCheckBox

javax.swing.JCheckBox NH3IonsJCheckBox

aIonsJCheckBox

javax.swing.JCheckBox aIonsJCheckBox

allPeaksJCheckBox

javax.swing.JCheckBox allPeaksJCheckBox

bIonsJCheckBox

javax.swing.JCheckBox bIonsJCheckBox

browseJButton

javax.swing.JButton browseJButton

cIonsJCheckBox

javax.swing.JCheckBox cIonsJCheckBox

chargeOneJCheckBox

javax.swing.JCheckBox chargeOneJCheckBox

chargeOverTwoJCheckBox

javax.swing.JCheckBox chargeOverTwoJCheckBox

chargePeptideAJSpinner

javax.swing.JSpinner chargePeptideAJSpinner

chargePeptideBJSpinner

javax.swing.JSpinner chargePeptideBJSpinner

chargeTwoJCheckBox

javax.swing.JCheckBox chargeTwoJCheckBox

chromatogramAJPanel

javax.swing.JPanel chromatogramAJPanel

chromatogramJPanel

javax.swing.JPanel chromatogramJPanel

chromatogramPanelHelpJLabel

javax.swing.JLabel chromatogramPanelHelpJLabel

chromatogramPanelInfoJLabel

javax.swing.JLabel chromatogramPanelInfoJLabel

enzymesJComboBox

javax.swing.JComboBox enzymesJComboBox

exportJButton

javax.swing.JButton exportJButton

inSilicoDigestionHelpJLabel

javax.swing.JLabel inSilicoDigestionHelpJLabel

informationJEditorPane

javax.swing.JEditorPane informationJEditorPane

informationJPanel

javax.swing.JPanel informationJPanel

informationJScrollPane

javax.swing.JScrollPane informationJScrollPane

inhibitorsJTextField

javax.swing.JTextField inhibitorsJTextField

ionSelectionJPanel

javax.swing.JPanel ionSelectionJPanel

isotopicDistributionAJPanel

javax.swing.JPanel isotopicDistributionAJPanel

isotopicDistributionCalculatorHelpJLabel

javax.swing.JLabel isotopicDistributionCalculatorHelpJLabel

isotopicDistributionCalculatorInfoJLabel

javax.swing.JLabel isotopicDistributionCalculatorInfoJLabel

isotopicDistributionJPanel

javax.swing.JPanel isotopicDistributionJPanel

jLabel1

javax.swing.JLabel jLabel1

jLabel10

javax.swing.JLabel jLabel10

jLabel11

javax.swing.JLabel jLabel11

jLabel12

javax.swing.JLabel jLabel12

jLabel13

javax.swing.JLabel jLabel13

jLabel14

javax.swing.JLabel jLabel14

jLabel15

javax.swing.JLabel jLabel15

jLabel16

javax.swing.JLabel jLabel16

jLabel17

javax.swing.JLabel jLabel17

jLabel18

javax.swing.JLabel jLabel18

jLabel19

javax.swing.JLabel jLabel19

jLabel2

javax.swing.JLabel jLabel2

jLabel20

javax.swing.JLabel jLabel20

jLabel21

javax.swing.JLabel jLabel21

jLabel24

javax.swing.JLabel jLabel24

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jLabel5

javax.swing.JLabel jLabel5

jLabel6

javax.swing.JLabel jLabel6

jLabel7

javax.swing.JLabel jLabel7

jLabel8

javax.swing.JLabel jLabel8

jLabel9

javax.swing.JLabel jLabel9

jPanel1

javax.swing.JPanel jPanel1

jPanel10

javax.swing.JPanel jPanel10

jPanel11

javax.swing.JPanel jPanel11

jPanel12

javax.swing.JPanel jPanel12

jPanel2

javax.swing.JPanel jPanel2

jPanel3

javax.swing.JPanel jPanel3

jPanel4

javax.swing.JPanel jPanel4

jPanel5

javax.swing.JPanel jPanel5

jPanel6

javax.swing.JPanel jPanel6

jPanel7

javax.swing.JPanel jPanel7

jPanel8

javax.swing.JPanel jPanel8

jPanel9

javax.swing.JPanel jPanel9

jRadioButton1

javax.swing.JRadioButton jRadioButton1

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jScrollPane2

javax.swing.JScrollPane jScrollPane2

jScrollPane3

javax.swing.JScrollPane jScrollPane3

jSeparator1

javax.swing.JSeparator jSeparator1

jSeparator2

javax.swing.JSeparator jSeparator2

jSeparator3

javax.swing.JSeparator jSeparator3

jSeparator4

javax.swing.JSeparator jSeparator4

jSeparator5

javax.swing.JSeparator jSeparator5

jSeparator6

javax.swing.JSeparator jSeparator6

jSeparator9

javax.swing.JSeparator jSeparator9

jTabbedPane

javax.swing.JTabbedPane jTabbedPane

linkedSpectraJCheckBox

javax.swing.JCheckBox linkedSpectraJCheckBox

lowerMassJSpinner

javax.swing.JSpinner lowerMassJSpinner

missedCleavagesJSpinner

javax.swing.JSpinner missedCleavagesJSpinner

nextJButton

javax.swing.JButton nextJButton

otherIonsJCheckBox

javax.swing.JCheckBox otherIonsJCheckBox

peffAnnotationsJTable

javax.swing.JTable peffAnnotationsJTable

peffHeaderJTable

javax.swing.JTable peffHeaderJTable

peptideAColorJPanel

javax.swing.JPanel peptideAColorJPanel

peptideACompositionJTextField

javax.swing.JTextField peptideACompositionJTextField

peptideAJScrollPane

javax.swing.JScrollPane peptideAJScrollPane

peptideAJXTable

org.jdesktop.swingx.JXTable peptideAJXTable

peptideAMzJTextField

javax.swing.JTextField peptideAMzJTextField

peptideBColorJPanel

javax.swing.JPanel peptideBColorJPanel

peptideBCompositionJTextField

javax.swing.JTextField peptideBCompositionJTextField

peptideBJScrollPane

javax.swing.JScrollPane peptideBJScrollPane

peptideBJXTable

org.jdesktop.swingx.JXTable peptideBJXTable

peptideBMzJTextField

javax.swing.JTextField peptideBMzJTextField

peptideSequenceAJTextField

javax.swing.JTextField peptideSequenceAJTextField

peptideSequenceBJTextField

javax.swing.JTextField peptideSequenceBJTextField

peptidesJPanel

javax.swing.JPanel peptidesJPanel

peptidesJTable

javax.swing.JTable peptidesJTable

peptidesScrollPane

javax.swing.JScrollPane peptidesScrollPane

positionJTextField

javax.swing.JTextField positionJTextField

profileSpectrumJCheckBox

javax.swing.JCheckBox profileSpectrumJCheckBox

proteinCoverageJScrollPane

javax.swing.JScrollPane proteinCoverageJScrollPane

proteinDigestionJLabel

javax.swing.JLabel proteinDigestionJLabel

proteinDigestionJPanel

javax.swing.JPanel proteinDigestionJPanel

proteinHeaderJTable

javax.swing.JTable proteinHeaderJTable

proteinSequenceCoverageJEditorPane

javax.swing.JEditorPane proteinSequenceCoverageJEditorPane

sequenceCoverageJPanel

javax.swing.JPanel sequenceCoverageJPanel

sequenceFileJTextField

javax.swing.JTextField sequenceFileJTextField

sequenceJTabbedPane

javax.swing.JTabbedPane sequenceJTabbedPane

silacLabelPeptideAJComboBox

javax.swing.JComboBox silacLabelPeptideAJComboBox

silacLabelPeptideBJComboBox

javax.swing.JComboBox silacLabelPeptideBJComboBox

siteJTextField

javax.swing.JTextField siteJTextField

spectraJPanel

javax.swing.JPanel spectraJPanel

spectrumAJPanel

javax.swing.JPanel spectrumAJPanel

spectrumBJPanel

javax.swing.JPanel spectrumBJPanel

spectrumJPanel

javax.swing.JPanel spectrumJPanel

spectrumPanelHelpJLabel

javax.swing.JLabel spectrumPanelHelpJLabel

spectrumPanelInfoJLabel

javax.swing.JLabel spectrumPanelInfoJLabel

upperMassJSpinner

javax.swing.JSpinner upperMassJSpinner

xIonsJCheckBox

javax.swing.JCheckBox xIonsJCheckBox

yIonsJCheckBox

javax.swing.JCheckBox yIonsJCheckBox

zIonsJCheckBox

javax.swing.JCheckBox zIonsJCheckBox

Package com.compomics.util.experiment

Class com.compomics.util.experiment.MsExperiment extends ExperimentObject implements Serializable

serialVersionUID: 4330394623824512352L

Serialized Fields

reference

java.lang.String reference
reference of the experiment


samples

java.util.HashMap<K,V> samples
the samples analyzed


analysis

java.util.HashMap<K,V> analysis
the analysis

Class com.compomics.util.experiment.ProteomicAnalysis extends ExperimentObject implements Serializable

serialVersionUID: -6738411343333889777L

Serialized Fields

index

int index
the analysis index


quantification

java.util.HashMap<K,V> quantification
Quantification results indexed by the method used


identification

java.util.HashMap<K,V> identification
Identification results

Class com.compomics.util.experiment.SampleAnalysisSet extends ExperimentObject implements Serializable

serialVersionUID: -5399187779025810060L

Serialized Fields

sample

Sample sample
The reference sample


analysis

java.util.HashMap<K,V> analysis
The various analysis indexed by replicates indexes


Package com.compomics.util.experiment.biology

Class com.compomics.util.experiment.biology.AminoAcid extends java.lang.Object implements Serializable

serialVersionUID: -3158896310928354857L

Serialized Fields

singleLetterCode

java.lang.String singleLetterCode
Single letter code of the amino acid.


threeLetterCode

java.lang.String threeLetterCode
Three letter code of the amino acid.


name

java.lang.String name
Name of the amino acid.


averageMass

double averageMass
Average mass of the amino acid.


monoisotopicMass

double monoisotopicMass
Monoisotopic mass of the amino acid.

Class com.compomics.util.experiment.biology.AminoAcidPattern extends java.lang.Object implements Serializable

serialVersionUID: -2823716418631089876L

Serialized Fields

target

java.lang.Integer target
The index of the amino acid of interest if there is one. Can be a modification site or a cleavage site. For trypsin: 0.


aaTargeted

java.util.HashMap<K,V> aaTargeted
The list of targeted amino acids at a given index. For trypsin: 0 -> {R, K} 1 -> {}


aaExcluded

java.util.HashMap<K,V> aaExcluded
The list of excluded amino acids at a given index For trypsin: 0 -> {} 1 -> {P}

Class com.compomics.util.experiment.biology.Atom extends ExperimentObject implements Serializable

Serialized Fields

mass

double mass

name

java.lang.String name

letter

java.lang.String letter

Class com.compomics.util.experiment.biology.Enzyme extends ExperimentObject implements Serializable

serialVersionUID: -1852087173903613377L

Serialized Fields

id

int id

name

java.lang.String name

aminoAcidBefore

java.util.ArrayList<E> aminoAcidBefore

aminoAcidAfter

java.util.ArrayList<E> aminoAcidAfter

restrictionBefore

java.util.ArrayList<E> restrictionBefore

restrictionAfter

java.util.ArrayList<E> restrictionAfter

Class com.compomics.util.experiment.biology.Ion extends ExperimentObject implements Serializable

Serialized Fields

type

Ion.IonType type
Type of ion.


theoreticMass

double theoreticMass

Class com.compomics.util.experiment.biology.NeutralLoss extends ExperimentObject implements Serializable

serialVersionUID: 5540846193082177391L

Serialized Fields

mass

double mass
The mass lost


name

java.lang.String name
The name of the neutral loss


fixed

java.lang.Boolean fixed
boolean indicating whether the neutral loss will always be accounted for

Class com.compomics.util.experiment.biology.Peptide extends ExperimentObject implements Serializable

serialVersionUID: 5632064601627536034L

Serialized Fields

sequence

java.lang.String sequence
The peptide sequence.


mass

java.lang.Double mass
The peptide mass.


parentProteins

java.util.ArrayList<E> parentProteins
The parent proteins.


modifications

java.util.ArrayList<E> modifications
The modifications carried by the peptide.

Class com.compomics.util.experiment.biology.Protein extends ExperimentObject implements Serializable

serialVersionUID: 1987224639519365761L

Serialized Fields

accession

java.lang.String accession
The protein accession


decoy

boolean decoy
Boolean indicating if the protein is not existing (decoy protein for instance)


sequence

java.lang.String sequence
The protein sequence


databaseType

Header.DatabaseType databaseType
The protein database type.

Class com.compomics.util.experiment.biology.PTM extends ExperimentObject implements Serializable

serialVersionUID: -545472596243822505L

Serialized Fields

type

int type
The modification type according to static field.


residuesArray

java.util.ArrayList<E> residuesArray
Deprecated. use amino-acid pattern instead
The residues affected by this modification. '[' denotes N-term and ']' C-term.


name

java.lang.String name
Name of the modification.


shortName

java.lang.String shortName
Short name of the modification.


mass

double mass
Mass difference produced by this modification.


neutralLosses

java.util.ArrayList<E> neutralLosses
List of known neutral losses for this modification.


reporterIons

java.util.ArrayList<E> reporterIons
List of known reporter ions for this modification.


pattern

AminoAcidPattern pattern
The amino acid pattern targeted by this modification (can be set using the AminoAcidPatternDialog).

Class com.compomics.util.experiment.biology.PTMFactory extends java.lang.Object implements Serializable

serialVersionUID: 7935264190312934466L

Serialized Fields

ptmMap

java.util.HashMap<K,V> ptmMap
A map linking indexes with modifications.


defaultMods

java.util.ArrayList<E> defaultMods
List of the indexes of default modifications.


userMods

java.util.ArrayList<E> userMods
List of the indexes of user modifications.


userColors

java.util.HashMap<K,V> userColors
Mapping of the expected modification names to the color used.


shortNames

java.util.HashMap<K,V> shortNames
Map of the short names.


defaultOmssaIndexes

java.util.HashMap<K,V> defaultOmssaIndexes
Map of omssa indexes for default modifications.

Class com.compomics.util.experiment.biology.Sample extends ExperimentObject implements Serializable

serialVersionUID: 303393644914835325L

Serialized Fields

reference

java.lang.String reference
sample reference


Package com.compomics.util.experiment.biology.aminoacids

Class com.compomics.util.experiment.biology.aminoacids.Alanine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Arginine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Asparagine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.AsparticAcid extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.B extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Cysteine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Glutamine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Glycine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Histidine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Isoleucine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.J extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Leucine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Lysine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Methionine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Phenylalanine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Proline extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Pyrrolysine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Selenocysteine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Serine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Threonine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Tryptophan extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Tyrosine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Valine extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.X extends AminoAcid implements Serializable

Class com.compomics.util.experiment.biology.aminoacids.Z extends AminoAcid implements Serializable


Package com.compomics.util.experiment.biology.atoms

Class com.compomics.util.experiment.biology.atoms.Carbon extends Atom implements Serializable

Class com.compomics.util.experiment.biology.atoms.Hydrogen extends Atom implements Serializable

Class com.compomics.util.experiment.biology.atoms.Nitrogen extends Atom implements Serializable

Class com.compomics.util.experiment.biology.atoms.Oxygen extends Atom implements Serializable

Class com.compomics.util.experiment.biology.atoms.Phosphorus extends Atom implements Serializable

Class com.compomics.util.experiment.biology.atoms.Sulfur extends Atom implements Serializable


Package com.compomics.util.experiment.biology.ions

Class com.compomics.util.experiment.biology.ions.ElementaryIon extends Ion implements Serializable

serialVersionUID: -1578136397635015592L

Serialized Fields

name

java.lang.String name
The name of the ion


subType

int subType
The subtype identifier

Class com.compomics.util.experiment.biology.ions.Glycon extends Ion implements Serializable

serialVersionUID: -2278483206647518565L

Serialized Fields

theoreticMasses

java.util.HashMap<K,V> theoreticMasses
Masses of this glycon.


name

java.lang.String name
The glycon short name which can be displayed on a spectrum.


longName

java.lang.String longName
The glycon full name.

Class com.compomics.util.experiment.biology.ions.ImmoniumIon extends Ion implements Serializable

serialVersionUID: -3403620196563864756L

Serialized Fields

subType

int subType
Subtype of immonium ion.

Class com.compomics.util.experiment.biology.ions.PeptideFragmentIon extends Ion implements Serializable

serialVersionUID: 8283809283803740651L

Serialized Fields

neutralLosses

java.util.ArrayList<E> neutralLosses
The neutral losses found on the ion.


number

int number
Position of the ion in the peptide for peptide ions.


subType

int subType
The type of fragment.

Class com.compomics.util.experiment.biology.ions.PrecursorIon extends Ion implements Serializable

serialVersionUID: -2630586959372309153L

Serialized Fields

neutralLosses

java.util.ArrayList<E> neutralLosses
the neutral losses found on the ion.

Class com.compomics.util.experiment.biology.ions.ReporterIon extends Ion implements Serializable

serialVersionUID: 1109011048958734120L

Serialized Fields

name

java.lang.String name
ion name for user defined ions.


subtype

int subtype
The ion subtype.


Package com.compomics.util.experiment.filters.massspectrometry

Class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name
The name of the filter.


Package com.compomics.util.experiment.filters.massspectrometry.spectrumfilters

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.And extends SpectrumFilter implements Serializable

serialVersionUID: -1518927119775419822L

Serialized Fields

filters

java.util.ArrayList<E> filters
List of filters on which we will do an 'and'.

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.CombFilter extends SpectrumFilter implements Serializable

serialVersionUID: -2943615250048987546L

Serialized Fields

filter

And filter
The actual filter, an and of m/z filters.

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.FingerprintPattern extends SpectrumFilter implements Serializable

serialVersionUID: 5759594763549860798L

Serialized Fields

filter

And filter
The actual filter, an and of peak filters.

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter extends SpectrumFilter implements Serializable

serialVersionUID: 7463874851796836587L

Serialized Fields

mz

double mz
The m/z to look for.


mzTolerance

double mzTolerance
The m/z to tolerance to use.


isPpm

boolean isPpm
A boolean indicating whether the m/z tolerance is in ppm.


intensityQuantile

double intensityQuantile
The intensity quantile to look into.


brotherFilter

MzFilter brotherFilter
Filter with similar properties.


mzArray

java.util.ArrayList<E> mzArray
array of m/z to be inspected.


spectrumKey

java.lang.String spectrumKey
The key of the inspected spectrum.

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.Or extends SpectrumFilter implements Serializable

serialVersionUID: 7845873802508736561L

Serialized Fields

filters

java.util.ArrayList<E> filters
List of filters on which we will do an 'or'.

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.PeakFilter extends SpectrumFilter implements Serializable

serialVersionUID: 1751883115257153259L

Serialized Fields

mz

double mz
The m/z to look for.


mzTolerance

double mzTolerance
The m/z to tolerance to use.


isPpm

boolean isPpm
A boolean indicating whether the m/z tolerance is in ppm.


intensity

double intensity
The intensity to look for.


intensityTolerance

double intensityTolerance
The intensity tolerance to look for.


Package com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.CombDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

spectrumFilter

SpectrumFilter spectrumFilter
The created filter.


mzArray

java.util.ArrayList<E> mzArray
List of the desired m/z to filter.


addButton

javax.swing.JButton addButton

cancelButton

javax.swing.JButton cancelButton

intTxt

javax.swing.JTextField intTxt

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jSeparator1

javax.swing.JSeparator jSeparator1

mzTable

javax.swing.JTable mzTable

mzTolTxt

javax.swing.JTextField mzTolTxt

okButtonButton

javax.swing.JButton okButtonButton

ppmCmb

javax.swing.JComboBox ppmCmb

removeButton

javax.swing.JButton removeButton

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.FingerprintDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

spectrumFilter

SpectrumFilter spectrumFilter
The created filter.


mzArray

java.util.ArrayList<E> mzArray
List of the desired m/z to filter.


intArray

java.util.ArrayList<E> intArray
List of the desired intensities to filter.


addButton

javax.swing.JButton addButton

cancelButton

javax.swing.JButton cancelButton

intTxt

javax.swing.JTextField intTxt

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jSeparator1

javax.swing.JSeparator jSeparator1

mzTable

javax.swing.JTable mzTable

mzTolTxt

javax.swing.JTextField mzTolTxt

okButton

javax.swing.JButton okButton

ppmCmb

javax.swing.JComboBox ppmCmb

removeButton

javax.swing.JButton removeButton

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.MzDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

spectrumFilter

SpectrumFilter spectrumFilter
The created filter.


cancelButton

javax.swing.JButton cancelButton

intTxt

javax.swing.JTextField intTxt

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jSeparator1

javax.swing.JSeparator jSeparator1

mzTolTxt

javax.swing.JTextField mzTolTxt

mzTxt

javax.swing.JTextField mzTxt

okButton

javax.swing.JButton okButton

ppmCmb

javax.swing.JComboBox ppmCmb

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.PeakDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

spectrumFilter

SpectrumFilter spectrumFilter
The created filter.


cancelButton

javax.swing.JButton cancelButton

intTolTxt

javax.swing.JTextField intTolTxt

intTxt

javax.swing.JTextField intTxt

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jLabel5

javax.swing.JLabel jLabel5

jSeparator1

javax.swing.JSeparator jSeparator1

mzTolTxt

javax.swing.JTextField mzTolTxt

mzTxt

javax.swing.JTextField mzTxt

okButton

javax.swing.JButton okButton

ppmCmb

javax.swing.JComboBox ppmCmb

Class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.TypeSelection extends javax.swing.JDialog implements Serializable

Serialized Fields

selection

int selection
The selected type.


jLabel1

javax.swing.JLabel jLabel1

okButton

javax.swing.JButton okButton

typeCmb

javax.swing.JComboBox typeCmb

Package com.compomics.util.experiment.identification

Class com.compomics.util.experiment.identification.FastaIndex extends ExperimentObject implements Serializable

Serialized Fields

indexes

java.util.HashMap<K,V> indexes
The indexes of the inspected FASTA file.


fileName

java.lang.String fileName
The FASTA file name.


isDecoy

boolean isDecoy
Boolean indicating whether the database contains decoy sequences.


nTarget

int nTarget
Number of target sequences found in the database.

Class com.compomics.util.experiment.identification.Identification extends ExperimentObject implements Serializable

serialVersionUID: -2551700699384242554L

Serialized Fields

proteinIdentification

java.util.ArrayList<E> proteinIdentification
List of the keys of all imported proteins.


peptideIdentification

java.util.ArrayList<E> peptideIdentification
List of the keys of all imported peptides.


spectrumIdentificationMap

java.util.HashMap<K,V> spectrumIdentificationMap
List of all imported psms indexed by mgf file name.


spectrumIdentification

java.util.ArrayList<E> spectrumIdentification
Deprecated. use file specific mapping instead
List of the keys of all imported psms.


proteinMap

java.util.HashMap<K,V> proteinMap
A map linking protein accessions to all their protein matches keys.


methodUsed

int methodUsed
The method used.


serializationDirectory

java.lang.String serializationDirectory
The directory where matches will be serialized/the database stored.


urParameters

java.util.HashMap<K,V> urParameters
Deprecated. use the database instead
Map of the user's parameters.


longKeys

java.util.ArrayList<E> longKeys
Deprecated. use the database instead @TODO implement this for db keys
Map of long keys (>100 characters) which will be referenced by their index for file creation/database storage.


isDB

java.lang.Boolean isDB
Boolean indicating whether the matches should be stored in a database (default) or in serialized files.


identificationDB

IdentificationDB identificationDB
The identificationDB object interacting with the database.


reference

java.lang.String reference
The reference of the identification.


orderedSpectrumFileNames

java.util.ArrayList<E> orderedSpectrumFileNames
The ordered list of spectrum file names.

Class com.compomics.util.experiment.identification.IdentificationDB extends java.lang.Object implements Serializable

serialVersionUID: 691986038787590646L

Serialized Fields

dbName

java.lang.String dbName
The name which will be used for the database.


proteinTableName

java.lang.String proteinTableName
The name of the protein table.


proteinParametersTableSuffix

java.lang.String proteinParametersTableSuffix
The suffix for protein parameters tables.


peptideTableName

java.lang.String peptideTableName
The name of the peptide table.


peptideParametersTableSuffix

java.lang.String peptideParametersTableSuffix
The suffix for a peptide parameters table.


psmTableSuffix

java.lang.String psmTableSuffix
The suffix for a PSM table.


psmParametersTableSuffix

java.lang.String psmParametersTableSuffix
The suffix for a PSM parameters table.


parametersSuffix

java.lang.String parametersSuffix
Deprecated. use match specific mapping instead
The suffix for a generic parameter table.


psmTables

java.util.ArrayList<E> psmTables
List of all psms tables.


psmParametersTables

java.util.ArrayList<E> psmParametersTables
List of all psm parameters tables.


peptideParametersTables

java.util.ArrayList<E> peptideParametersTables
List of all peptide parameters tables.


proteinParametersTables

java.util.ArrayList<E> proteinParametersTables
List of all proteins parameters tables.


matchParametersTables

java.util.ArrayList<E> matchParametersTables
Deprecated. use match specific mapping instead
List of all match parameters tables.


objectsDB

ObjectsDB objectsDB
The database which will contain the objects.

Class com.compomics.util.experiment.identification.IdentificationMatch extends ExperimentObject implements Serializable

serialVersionUID: -9132138792119651421L

Class com.compomics.util.experiment.identification.IdentificationMethod extends ExperimentObject implements Serializable

serialVersionUID: 4601179275244591663L

Serialized Fields

index

int index
index of the method

Class com.compomics.util.experiment.identification.NeutralLossesMap extends java.lang.Object implements Serializable

serialVersionUID: -4690159937753713106L

Serialized Fields

bBoundaries

java.util.HashMap<K,V> bBoundaries
Map indicating for each neutral loss when they should start being accounted for the forward ions (b ions for instance).


yBoundaries

java.util.HashMap<K,V> yBoundaries
Map indicating for each neutral loss when they should start being accounted for the reverse ions (y ions for instance).

Class com.compomics.util.experiment.identification.PeptideAssumption extends ExperimentObject implements Serializable

serialVersionUID: 3606509518581203063L

Serialized Fields

rank

int rank
The rank of the peptide assumption for the concerned spectrum.


peptide

Peptide peptide
The theoretic peptide.


advocate

int advocate
The advocate.


identificationCharge

Charge identificationCharge
The charge used for identification.


eValue

double eValue
The e-value.


file

java.lang.String file
the corresponding file.


isDecoy

java.lang.Boolean isDecoy
Is it a decoy identification?

Class com.compomics.util.experiment.identification.SearchParameters extends java.lang.Object implements Serializable

serialVersionUID: -2773993307168773763L

Serialized Fields

currentPrecursorAccuracyType

SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType
The precursor accuracy type. Default is ppm.


precursorTolerance

java.lang.Double precursorTolerance
The precursor mass tolerance.


fragmentIonMZTolerance

java.lang.Double fragmentIonMZTolerance
The ms2 ion tolerance.


utilitiesModificationProfile

ModificationProfile utilitiesModificationProfile
The expected modifications. Modified peptides will be grouped and displayed according to this classification.


enzyme

Enzyme enzyme
The enzyme used for digestion.


nMissedCleavages

java.lang.Integer nMissedCleavages
The allowed number of missed cleavages.


fastaFile

java.io.File fastaFile
The sequence database file used for identification.


parametersFile

java.io.File parametersFile
The corresponding searchGUI file.


fractionMolecularWeights

java.util.HashMap<K,V> fractionMolecularWeights
The list of fraction molecular weights. The key is the fraction file path.


forwardIon

java.lang.Integer forwardIon
The first kind of ions searched for (typically a, b or c).


rewindIon

java.lang.Integer rewindIon
The second kind of ions searched for (typically x, y or z).


minChargeSearched

Charge minChargeSearched
The minimal charge searched (in absolute value).


maxChargeSearched

Charge maxChargeSearched
The minimal charge searched (in absolute value).


maxEValue

java.lang.Double maxEValue
Maximal e-value cut-off.


hitListLength

java.lang.Integer hitListLength
The maximal hitlist length (OMSSA setting).


minimalChargeForMultipleChargedFragments

Charge minimalChargeForMultipleChargedFragments
The minimal charge to be considered for multiple fragment charges for OMSSA.


minPeptideLength

java.lang.Integer minPeptideLength
The minimum peptide length.


maxPeptideLength

java.lang.Integer maxPeptideLength
The maximal peptide length.


removePrecursor

java.lang.Boolean removePrecursor
Indicates whether the precursor removal option of OMSSA is used.


scalePrecursor

java.lang.Boolean scalePrecursor
Indicates whether the precursor scaling option of OMSSA is used.


estimateCharge

java.lang.Boolean estimateCharge
Indicates whether the precursor charge estimation option of OMSSA is used.


Package com.compomics.util.experiment.identification.advocates

Class com.compomics.util.experiment.identification.advocates.PostProcessor extends ExperimentObject implements Serializable

serialVersionUID: 1892975432623296983L

Serialized Fields

id

int id
index of the post-processor

Class com.compomics.util.experiment.identification.advocates.SearchEngine extends ExperimentObject implements Serializable

serialVersionUID: 9162799394758139976L

Serialized Fields

id

int id
index of the search engine


Package com.compomics.util.experiment.identification.identifications

Class com.compomics.util.experiment.identification.identifications.Ms2Identification extends Identification implements Serializable

serialVersionUID: -7242302146506873391L


Package com.compomics.util.experiment.identification.matches

Class com.compomics.util.experiment.identification.matches.IonMatch extends ExperimentObject implements Serializable

serialVersionUID: 5753142782728884464L

Serialized Fields

peak

Peak peak
The matched peak.


ion

Ion ion
The matching ion.


charge

Charge charge
The supposed charge of the ion.

Class com.compomics.util.experiment.identification.matches.ModificationMatch extends ExperimentObject implements Serializable

serialVersionUID: 7129515983284796207L

Serialized Fields

theoreticPtm

java.lang.String theoreticPtm
The theoretic modiffication name. The modification can be accessed via the PTM factory.


variable

boolean variable
Is the modification variable?


modifiedSite

int modifiedSite
The location in the peptide sequence, 1 is the first residue.


confident

boolean confident
A boolean indicating whether the modification is confidently localized onto the sequence. Not applicable to fixed or terminal modifications.


inferred

boolean inferred
A boolean indicating whether the modification is inferred from another peptide. Not applicable to fixed or terminal modifications.

Class com.compomics.util.experiment.identification.matches.PeptideMatch extends IdentificationMatch implements Serializable

serialVersionUID: 7195830246336841081L

Serialized Fields

theoreticPeptide

Peptide theoreticPeptide
The theoretic peptide mathing.


mainMatchKey

java.lang.String mainMatchKey
The key of the main match, typically of the highest score.


spectrumMatches

java.util.ArrayList<E> spectrumMatches
All spectrum matches indexed by spectrum id: FILE_TITLE.


isDecoy

java.lang.Boolean isDecoy
Is the peptide match a decoy hit?

Class com.compomics.util.experiment.identification.matches.ProteinMatch extends IdentificationMatch implements Serializable

serialVersionUID: -6061842447053092696L

Serialized Fields

theoreticProtein

java.util.ArrayList<E> theoreticProtein
The matching protein(s) accessions.


mainMatch

java.lang.String mainMatch
The accession of the retained protein after protein inference resolution.


peptideMatches

java.util.ArrayList<E> peptideMatches
The corresponding peptide match keys.

Class com.compomics.util.experiment.identification.matches.SpectrumMatch extends IdentificationMatch implements Serializable

serialVersionUID: 3227760855215444318L

Serialized Fields

spectrumKey

java.lang.String spectrumKey
The index of the matched spectrum.


assumptions

java.util.HashMap<K,V> assumptions
The corresponding peptide assumptions indexed by search engine and e-value.


bestAssumption

PeptideAssumption bestAssumption
The best assumption.


firstHits

java.util.HashMap<K,V> firstHits
Map containing the first hits indexed by the Advocate index.


advocates

java.util.ArrayList<E> advocates
All advocates used.


spectrumNumber

java.lang.Integer spectrumNumber
The spectrum number in the mgf file. Will be used in case the spectrum title does not match


Package com.compomics.util.experiment.io.identifications.idfilereaders

Class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader extends ExperimentObject implements Serializable

Serialized Fields

index

java.util.HashMap<K,V> index
A map of all spectrum titles and the associated index in the random access file.


bufferedRandomAccessFile

uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
Andromeda result file in random access.


fileName

java.lang.String fileName
The name of the Andromeda result file.


Package com.compomics.util.experiment.io.massspectrometry

Class com.compomics.util.experiment.io.massspectrometry.MgfIndex extends ExperimentObject implements Serializable

serialVersionUID: -5591103342266964263L

Serialized Fields

indexMap

java.util.HashMap<K,V> indexMap
The map of all indexes: spectrum title -> index in the file.


spectrumTitles

java.util.ArrayList<E> spectrumTitles
List of all spectra


fileName

java.lang.String fileName
The name of the indexed file.


maxRT

java.lang.Double maxRT
The maximum RT found in the spectra.


minRT

java.lang.Double minRT
The minimum RT found in the spectra.


maxMz

java.lang.Double maxMz
The maximal m/z in all precursors of the file.


maxIntensity

java.lang.Double maxIntensity
The maximal precursor intensity of the file.


Package com.compomics.util.experiment.massspectrometry

Class com.compomics.util.experiment.massspectrometry.Charge extends ExperimentObject implements Serializable

serialVersionUID: -7119215126058492261L

Serialized Fields

sign

int sign
Sign of the charge according to the static fields.


value

int value
Value of the charge.

Class com.compomics.util.experiment.massspectrometry.MS1Spectrum extends Spectrum implements Serializable

serialVersionUID: -7328539274222920271L

Class com.compomics.util.experiment.massspectrometry.MSnSpectrum extends Spectrum implements Serializable

serialVersionUID: -7144961253807359274L

Serialized Fields

precursor

Precursor precursor
The precursor.

Class com.compomics.util.experiment.massspectrometry.Peak extends ExperimentObject implements Serializable

serialVersionUID: -7425947046833405676L

Serialized Fields

mz

double mz
The mass over charge ratio of the peak.


rt

double rt
The retention time when the peak was recorded.


intensity

double intensity
The intensity of the peak.

Class com.compomics.util.experiment.massspectrometry.Precursor extends ExperimentObject implements Serializable

serialVersionUID: -2711244157697138296L

Serialized Fields

rt

double rt
The retention time when the precursor was isolated.


rtMin

java.lang.Double rtMin
In case an rt window is given, the minimum.


rtMax

java.lang.Double rtMax
In case an rt window is given, the maximum.


mz

double mz
The measured m/z of the precursor.


intensity

double intensity
The measured intensity of the precursor.


possibleCharges

java.util.ArrayList<E> possibleCharges
The charge of the precursor.

Class com.compomics.util.experiment.massspectrometry.Spectrum extends ExperimentObject implements Serializable

serialVersionUID: 7152424141470431489L

Serialized Fields

spectrumTitle

java.lang.String spectrumTitle
Spectrum title.


fileName

java.lang.String fileName
Spectrum file name.


level

int level
The MS level.


peakList

java.util.HashMap<K,V> peakList
Peak list.


scanNumber

java.lang.String scanNumber
Scan number or range.


scanStartTime

double scanStartTime
The timepoint when the spectrum was recorded (scan start time in mzML files).


Package com.compomics.util.experiment.personalization

Class com.compomics.util.experiment.personalization.ExperimentObject extends java.lang.Object implements Serializable

serialVersionUID: 1929697552061121072L

Serialized Fields

urParams

java.util.HashMap<K,V> urParams
Map containing user refinement parameters.


Package com.compomics.util.experiment.quantification

Class com.compomics.util.experiment.quantification.Quantification extends ExperimentObject implements Serializable

Serialized Fields

methodUsed

Quantification.QuantificationMethod methodUsed
The quantification method used


proteinQuantification

java.util.ArrayList<E> proteinQuantification
The protein quantification


peptideQuantification

java.util.ArrayList<E> peptideQuantification
The peptide quantification


modifiedPeptidesQuantification

java.util.HashMap<K,V> modifiedPeptidesQuantification
The modified peptides quantification


psmIDentificationToQuantification

java.util.HashMap<K,V> psmIDentificationToQuantification
A convenience map indicating all psm quantifying an identified PSM


quantificationDB

QuantificationDB quantificationDB
the quantificationDB object interacting with the database

Class com.compomics.util.experiment.quantification.QuantificationDB extends java.lang.Object implements Serializable

serialVersionUID: 4600091320219653637L

Serialized Fields

dbName

java.lang.String dbName
The name which will be used for the database.


proteinTableName

java.lang.String proteinTableName
The name of the protein table.


proteinParametersTableSuffix

java.lang.String proteinParametersTableSuffix
The suffix for protein parameters tables.


peptideTableName

java.lang.String peptideTableName
The suffix of a peptide table.


peptideParametersTableSuffix

java.lang.String peptideParametersTableSuffix
The suffix for a peptide parameters table.


psmTableSuffix

java.lang.String psmTableSuffix
The suffix for a PSM table.


psmParametersTableSuffix

java.lang.String psmParametersTableSuffix
The suffix for a PSM parameters table.


psmTables

java.util.ArrayList<E> psmTables
List of all psms tables.


psmParametersTables

java.util.ArrayList<E> psmParametersTables
List of all psm parameters tables.


peptideParametersTables

java.util.ArrayList<E> peptideParametersTables
List of all peptide parameters tables.


proteinParametersTables

java.util.ArrayList<E> proteinParametersTables
List of all proteins parameters tables.


objectsDB

ObjectsDB objectsDB
The database which will contain the objects.

Class com.compomics.util.experiment.quantification.QuantificationMatch extends ExperimentObject implements Serializable

Serialized Fields

ratios

java.util.HashMap<K,V> ratios
The estimated ratios.

Class com.compomics.util.experiment.quantification.Ratio extends ExperimentObject implements Serializable

Serialized Fields

measureLabel

int measureLabel
the measured label indexed by its corresponding reporter ion index


ratio

double ratio
the corresponding ratio


Package com.compomics.util.experiment.quantification.matches

Class com.compomics.util.experiment.quantification.matches.PeptideQuantification extends QuantificationMatch implements Serializable

Serialized Fields

peptideKey

java.lang.String peptideKey
The identification peptide match


psmQuantification

java.util.ArrayList<E> psmQuantification
The corresponding spectrum quantification

Class com.compomics.util.experiment.quantification.matches.ProteinQuantification extends QuantificationMatch implements Serializable

Serialized Fields

proteinKey

java.lang.String proteinKey
The identification protein match key


peptideQuantification

java.util.ArrayList<E> peptideQuantification
The peptide quantification corresponding

Class com.compomics.util.experiment.quantification.matches.PsmQuantification extends QuantificationMatch implements Serializable

Serialized Fields

spectrumKey

java.lang.String spectrumKey
The corresponding spectrum key


spectrumMatchKey

java.lang.String spectrumMatchKey
The key of the spectrum match


reporterMatches

java.util.HashMap<K,V> reporterMatches
The matches of the reporter ions


deisotopedIntensities

java.util.HashMap<K,V> deisotopedIntensities
The deisotoped intensities


referenceIntensity

double referenceIntensity
The reference intensity taken to estimate the ratios


Package com.compomics.util.experiment.quantification.reporterion

Class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification extends Quantification implements Serializable

Serialized Fields

sampleAssignement

java.util.HashMap<K,V> sampleAssignement
The sample assignement to the various ions indexed by their static indexes.


reporterMethod

ReporterMethod reporterMethod
The reporter method.

Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable


Package com.compomics.util.experiment.refinementparameters

Class com.compomics.util.experiment.refinementparameters.MascotScore extends java.lang.Object implements Serializable

serialVersionUID: 1781298332459022056L

Serialized Fields

score

double score
The Mascot score


Package com.compomics.util.general

Class com.compomics.util.general.UnknownElementMassException extends java.lang.Exception implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

element

java.lang.String element
The element symbol that was not recognized.


Package com.compomics.util.general.servlet

Class com.compomics.util.general.servlet.MassCalcServlet extends javax.servlet.http.HttpServlet implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Package com.compomics.util.gui

Class com.compomics.util.gui.AminoAcidPatternDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

pattern

AminoAcidPattern pattern
The pattern displayed


editable

boolean editable
A boolean indicating whether the pattern can be edited


cancel

boolean cancel
A boolean indicating whether the used clicked the cancel button


patternDesignTableToolTips

java.util.ArrayList<E> patternDesignTableToolTips
The pattern design table column header tooltips.


exampleSequence

java.lang.String exampleSequence
The example sequence.


addJMenuItem

javax.swing.JMenuItem addJMenuItem

backgroundPanel

javax.swing.JPanel backgroundPanel

cancelButton

javax.swing.JButton cancelButton

deleteSelectedRowJMenuItem

javax.swing.JMenuItem deleteSelectedRowJMenuItem

exampleLabel

javax.swing.JLabel exampleLabel

jSeparator3

javax.swing.JSeparator jSeparator3

jSeparator4

javax.swing.JSeparator jSeparator4

moveDownJMenuItem

javax.swing.JMenuItem moveDownJMenuItem

moveUpJMenuItem

javax.swing.JMenuItem moveUpJMenuItem

okButton

javax.swing.JButton okButton

patternDesignPanel

javax.swing.JPanel patternDesignPanel

patternDesignScrollPane

javax.swing.JScrollPane patternDesignScrollPane

patternDesignTable

javax.swing.JTable patternDesignTable

patternTestEditorPane

javax.swing.JEditorPane patternTestEditorPane

patternTestJScrollPane

javax.swing.JScrollPane patternTestJScrollPane

popupJMenu

javax.swing.JPopupMenu popupJMenu

testPanel

javax.swing.JPanel testPanel

Class com.compomics.util.gui.FlamableJFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.gui.JExceptionDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iMessages

java.lang.String[] iMessages

iThrowable

java.lang.Throwable iThrowable

Class com.compomics.util.gui.JFrameForBytes extends javax.swing.JFrame implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iData

byte[] iData
This byte[] is the data that will be shown.


txtData

javax.swing.JTextArea txtData

btnUnzip

javax.swing.JButton btnUnzip

btnSave

javax.swing.JButton btnSave

Class com.compomics.util.gui.JLabelAndComponentPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.gui.JTableForDB extends AlternateRowColoursJTable implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iDateTimeFormat

java.lang.String iDateTimeFormat
This String contains the date and time format.


iFrames

java.util.Vector<E> iFrames
This Vector holds the references to all the tables that have been created during the life cycle.

Class com.compomics.util.gui.SampleSelection extends javax.swing.JDialog implements Serializable

Serialized Fields

samples

java.lang.String[] samples
The samples found.


choice

java.lang.String choice
The choice of the user.


backgroundPanel

javax.swing.JPanel backgroundPanel

comboBox

javax.swing.JComboBox comboBox

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

okButton

javax.swing.JButton okButton

titleLbl

javax.swing.JLabel titleLbl

Class com.compomics.util.gui.VisibleTableColumnsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

visibleTableColumnsDialogParent

VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
The VisibleTableColumnsDialogParent.


backgroundPanel

javax.swing.JPanel backgroundPanel

deselectAllMenuItem

javax.swing.JMenuItem deselectAllMenuItem

okButton

javax.swing.JButton okButton

selectAllMenuItem

javax.swing.JMenuItem selectAllMenuItem

selectJPopupMenu

javax.swing.JPopupMenu selectJPopupMenu

selectedColumnsTable

javax.swing.JTable selectedColumnsTable

selectedValuesTableScrollPane

javax.swing.JScrollPane selectedValuesTableScrollPane

Class com.compomics.util.gui.XYPlottingDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

progressDialog

ProgressDialogX progressDialog
The progress dialog.


tabelModel

javax.swing.table.TableModel tabelModel
The table model.


chartPanel

org.jfree.chart.ChartPanel chartPanel
The chart panel.


bubbleSize

double bubbleSize
The bubble size.


bubbleScalingFactor

double bubbleScalingFactor
The bubble scaling factor in percent. 1.0 means no scaling.


numberOfBins

int numberOfBins
The number if bins for the histograms.


userDefinedBinSize

boolean userDefinedBinSize
If true, the user defined bin size will be used instead of the automatic one.


dialogParent

java.awt.Frame dialogParent
The dialog parent.


isPlotting

boolean isPlotting
If true, the plot is currently being updated.


mouseDragged

boolean mouseDragged
If true, the mouse is currently being dragged.


dragStart

java.awt.Point dragStart
The starting location of the mouse dragging.


dragEnd

java.awt.Point dragEnd
The ending location of the mouse dragging.


selectedDataPoints

java.util.HashMap<K,V> selectedDataPoints
The currently selected data points. The keys are the series keys, while the elements are the lists of data indexes.


selectionActive

boolean selectionActive
If true, selection is currently being performed.


dataPointToRowNumber

java.util.HashMap<K,V> dataPointToRowNumber
The datapoint to model row number map.


selectedModelRows

java.util.ArrayList<E> selectedModelRows
The index of the selected rows.


cellRenderers

java.util.HashMap<K,V> cellRenderers
The cell renderers for the table.


maxColumnWidths

java.util.HashMap<K,V> maxColumnWidths
The maximum column widths for the table.


minColumnWidths

java.util.HashMap<K,V> minColumnWidths
The minmum column widths for the table.


tableToolTips

java.util.ArrayList<E> tableToolTips
The table column header tool tips.


colorGradient

no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient
The color gradient to use.


histogramColor

java.awt.Color histogramColor
The color used for the bars in the histograms.


lastSelectedFolder

java.lang.String lastSelectedFolder
The last selected folder.


normalIcon

java.awt.Image normalIcon
The normal icon for the parent dialog.


waitingIcon

java.awt.Image waitingIcon
The icon to use when busy.


allTableColumns

java.util.ArrayList<E> allTableColumns
The table columns.


visibleColumns

java.util.HashMap<K,V> visibleColumns
Boolean indicators of which columns to show.


useGradientColorCoding

boolean useGradientColorCoding
If true, gradient color coding is used.


showRegressionLine

boolean showRegressionLine
If true, the regression line is shown.


backgroundPanel

javax.swing.JPanel backgroundPanel

binSizeSpinner

javax.swing.JSpinner binSizeSpinner

binsLabel

javax.swing.JLabel binsLabel

bubbleSizeComboBox

javax.swing.JComboBox bubbleSizeComboBox

bubbleSizeLabel

javax.swing.JLabel bubbleSizeLabel

colorLabel

javax.swing.JLabel colorLabel

colorsComboBox

javax.swing.JComboBox colorsComboBox

contextMenuPlotBackgroundPanel

javax.swing.JPanel contextMenuPlotBackgroundPanel

contextMenuSelectedValuesTableBackgroundPanel

javax.swing.JPanel contextMenuSelectedValuesTableBackgroundPanel

densityPlotRadioButton

javax.swing.JRadioButton densityPlotRadioButton

dragButtonGroup

javax.swing.ButtonGroup dragButtonGroup

dragSettingsPanel

javax.swing.JPanel dragSettingsPanel

dragToSelectRadioButton

javax.swing.JRadioButton dragToSelectRadioButton

dragToZoomRadioButton

javax.swing.JRadioButton dragToZoomRadioButton

exportPlotMenuItem

javax.swing.JMenuItem exportPlotMenuItem

exportSelectedValuesMenuItem

javax.swing.JMenuItem exportSelectedValuesMenuItem

hideColumnsMenuItem

javax.swing.JMenuItem hideColumnsMenuItem

histogramRadioButton

javax.swing.JRadioButton histogramRadioButton

logAcisPanel

javax.swing.JPanel logAcisPanel

plotHelpJButton

javax.swing.JButton plotHelpJButton

plotLayeredPane

javax.swing.JLayeredPane plotLayeredPane

plotOptionsJButton

javax.swing.JButton plotOptionsJButton

plotPanel

javax.swing.JPanel plotPanel

plotPopupMenu

javax.swing.JPopupMenu plotPopupMenu

plotTypeButtonGroup

javax.swing.ButtonGroup plotTypeButtonGroup

plotTypePanel

javax.swing.JPanel plotTypePanel

regressionLineCheckBoxMenuItem

javax.swing.JCheckBoxMenuItem regressionLineCheckBoxMenuItem

selectedValuesLayeredPane

javax.swing.JLayeredPane selectedValuesLayeredPane

selectedValuesPanel

javax.swing.JPanel selectedValuesPanel

selectedValuesScrollPane

javax.swing.JScrollPane selectedValuesScrollPane

selectedValuesTable

javax.swing.JTable selectedValuesTable

selectedValuesTableHelpJButton

javax.swing.JButton selectedValuesTableHelpJButton

selectedValuesTableOptionsJButton

javax.swing.JButton selectedValuesTableOptionsJButton

selectedValuesTablePopupMenu

javax.swing.JPopupMenu selectedValuesTablePopupMenu

sizeLogCheckBox

javax.swing.JCheckBox sizeLogCheckBox

xAxisComboBox

javax.swing.JComboBox xAxisComboBox

xAxisLabel

javax.swing.JLabel xAxisLabel

xAxisLogCheckBox

javax.swing.JCheckBox xAxisLogCheckBox

xAxisPanel

javax.swing.JPanel xAxisPanel

xyPlotPanel

javax.swing.JPanel xyPlotPanel

xyPlotRadioButton

javax.swing.JRadioButton xyPlotRadioButton

yAxisComboBox

javax.swing.JComboBox yAxisComboBox

yAxisLabel

javax.swing.JLabel yAxisLabel

yAxisLogCheckBox

javax.swing.JCheckBox yAxisLogCheckBox

Package com.compomics.util.gui.error_handlers

Class com.compomics.util.gui.error_handlers.BugReport extends javax.swing.JDialog implements Serializable

Serialized Fields

selectionFolder

java.lang.String selectionFolder
The folder to open in the file selection dialog.


toolName

java.lang.String toolName
The name of the tool to get the bug report for, e.g., "PeptideShaker"


googleCodeToolName

java.lang.String googleCodeToolName
The google code name of the tool, e.g., "peptide-shaker"


toolVersion

java.lang.String toolVersion
The version number of the tool the log files belongs to.


logFile

java.io.File logFile
The log file to display.


backgroundPanel

javax.swing.JPanel backgroundPanel

clearJButton

javax.swing.JButton clearJButton

exitButton

javax.swing.JButton exitButton

infoJEditorPane

javax.swing.JEditorPane infoJEditorPane

infoJPanel

javax.swing.JPanel infoJPanel

infoJScrollPane

javax.swing.JScrollPane infoJScrollPane

logJPanel

javax.swing.JPanel logJPanel

logJScrollPane

javax.swing.JScrollPane logJScrollPane

logTxt

javax.swing.JTextArea logTxt

saveJButton

javax.swing.JButton saveJButton

Class com.compomics.util.gui.error_handlers.HelpDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

windowWidth

int windowWidth
The default width of the frame.


windowHeightReduction

int windowHeightReduction
The default height reduction relative to the parent frame.


frameParent

java.awt.Frame frameParent
The parent of the parent is a Frame.


dialogParent

javax.swing.JDialog dialogParent
The parent of the parent is a JDialog.


aboutIcon

java.awt.Image aboutIcon
The icon to use for the about pages.


helpIcon

java.awt.Image helpIcon
The icon to use for the help pages.


backgroundPanel

javax.swing.JPanel backgroundPanel

closeJButton

javax.swing.JButton closeJButton

jScrollPane1

javax.swing.JScrollPane jScrollPane1

textJEditorPane

javax.swing.JEditorPane textJEditorPane

Package com.compomics.util.gui.export_graphics

Class com.compomics.util.gui.export_graphics.ExportGraphicsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

chartPanel

org.jfree.chart.ChartPanel chartPanel
The chart panel to export.


graphicsPanel

java.awt.Component graphicsPanel
The panel to export.


progressDialog

ProgressDialogX progressDialog
The progress dialog.


exportGraphicsDialogParent

ExportGraphicsDialogParent exportGraphicsDialogParent
The export graphics dialog parent.


frame

javax.swing.JFrame frame
The parent frame.


backgroundPanel

javax.swing.JPanel backgroundPanel

buttonGroup

javax.swing.ButtonGroup buttonGroup

cancelJButton

javax.swing.JButton cancelJButton

exportJButton

javax.swing.JButton exportJButton

pdfJRadioButton

javax.swing.JRadioButton pdfJRadioButton

plottingTypeJPanel

javax.swing.JPanel plottingTypeJPanel

pngJRadioButton

javax.swing.JRadioButton pngJRadioButton

svgJRadioButton

javax.swing.JRadioButton svgJRadioButton

tiffJRadioButton

javax.swing.JRadioButton tiffJRadioButton

Package com.compomics.util.gui.filehandling

Class com.compomics.util.gui.filehandling.FileSelectionDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

fileMap

java.util.HashMap<K,V> fileMap
A map of the parameter files indexed by their name.


canceled

boolean canceled
boolean indicating whether the user pushed the cancel button


cancelButton

javax.swing.JButton cancelButton

fileList

javax.swing.JList fileList

jScrollPane1

javax.swing.JScrollPane jScrollPane1

okButton

javax.swing.JButton okButton

txtLabel

javax.swing.JLabel txtLabel

Package com.compomics.util.gui.isotopic_calculator

Class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui extends javax.swing.JFrame implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

txtSequence

javax.swing.JTextArea txtSequence

lblComp

javax.swing.JLabel lblComp

lblMass

javax.swing.JLabel lblMass

calculateButton

javax.swing.JButton calculateButton

table1

AlternateRowColoursJTable table1

jpanContent

javax.swing.JPanel jpanContent

headerTable

javax.swing.JPanel headerTable

spectrumPanel

javax.swing.JPanel spectrumPanel

spinCharge

javax.swing.JSpinner spinCharge

lblPeptide

javax.swing.JLabel lblPeptide

iSequence

AASequenceImpl iSequence
The amino acid sequence


iElements

java.util.HashMap<K,V> iElements
HashMap with the molecular formula for all the aminoacids


iCharge

double iCharge
The charge


Package com.compomics.util.gui.protein

Class com.compomics.util.gui.protein.SequenceModificationPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

fragmentIonRectangles

java.util.HashMap<K,V> fragmentIonRectangles
A map of the rectangles used to draw each profile peak. This map is later used for the tooltip for each peak.


iSequenceComponents

java.lang.String[] iSequenceComponents
Elementary data for composing the Panel.


profiles

java.util.ArrayList<E> profiles
The list of modification profiles.


iBaseFont

java.awt.Font iBaseFont
The font to use.


iMaxBarHeight

double iMaxBarHeight
The maximum bar height.


iBarWidth

int iBarWidth
The width of the bars.


iHorizontalSpace

int iHorizontalSpace
The horizontal space.


iXStart

int iXStart
The x-axis start position.


iYStart

int iYStart
The y-axis start position.


isModifiedSequence

boolean isModifiedSequence
This boolean holds whether or not the given sequence is a modified sequence or a normal peptide sequence. Normal: KENNY Modified: NH2-KENNY-COOH


Package com.compomics.util.gui.ptm

Class com.compomics.util.gui.ptm.ModificationsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ptmFactory

PTMFactory ptmFactory
The post translational modifications factory.


ptmDialogParent

PtmDialogParent ptmDialogParent
The dialog parent.


ptmToPrideMap

PtmToPrideMap ptmToPrideMap
The PSI-MOD mappings.


sparklineColor

java.awt.Color sparklineColor
The color used for the sparkline bar chart plots.


selectedRowHtmlTagFontColor

java.lang.String selectedRowHtmlTagFontColor
The color to use for the HTML tags for the selected rows, in HTML color code.


notSelectedRowHtmlTagFontColor

java.lang.String notSelectedRowHtmlTagFontColor
The color to use for the HTML tags for the rows that are not selected, in HTML color code.


defaultModsTableToolTips

java.util.ArrayList<E> defaultModsTableToolTips
The default mods table column header tooltips.


userModsTableToolTips

java.util.ArrayList<E> userModsTableToolTips
The user mods table column header tooltips.


searchPossibilities

java.util.ArrayList<E> searchPossibilities
The lines of the ptms concerned by the search


searchCurrentSelection

int searchCurrentSelection
The search current selection.


searchWelcomeText

java.lang.String searchWelcomeText
The search text to display by default.


addUserPTM

javax.swing.JButton addUserPTM

defaultModificationsTable

javax.swing.JTable defaultModificationsTable

defaultModsPanel

javax.swing.JPanel defaultModsPanel

defaultModsScrollPane

javax.swing.JScrollPane defaultModsScrollPane

defaultPtmPopupMenu

javax.swing.JPopupMenu defaultPtmPopupMenu

deleteUserPTM

javax.swing.JButton deleteUserPTM

editDefaultPtmJMenuItem

javax.swing.JMenuItem editDefaultPtmJMenuItem

editUserPTM

javax.swing.JButton editUserPTM

editUserPtmJMenuItem

javax.swing.JMenuItem editUserPtmJMenuItem

findJLabel

javax.swing.JLabel findJLabel

modificationsEditorPanel

javax.swing.JPanel modificationsEditorPanel

modificationsHelpJButton

javax.swing.JButton modificationsHelpJButton

modificationsSplitPane

javax.swing.JSplitPane modificationsSplitPane

okButton

javax.swing.JButton okButton

searchIndexLabel

javax.swing.JLabel searchIndexLabel

searchInputTxt

javax.swing.JTextField searchInputTxt

searchNextButton

javax.swing.JButton searchNextButton

searchPreviousButton

javax.swing.JButton searchPreviousButton

userModificationsTable

javax.swing.JTable userModificationsTable

userModsPanel

javax.swing.JPanel userModsPanel

userModsScrollPane

javax.swing.JScrollPane userModsScrollPane

userPtmPopupMenu

javax.swing.JPopupMenu userPtmPopupMenu

Class com.compomics.util.gui.ptm.PtmDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ptmDialogParent

PtmDialogParent ptmDialogParent
The PtmDialog parent.


ptmFactory

PTMFactory ptmFactory
The post translational modifications factory.


currentPtm

PTM currentPtm
The edited ptm.


neutralLosses

java.util.ArrayList<E> neutralLosses
The neutral losses.


reporterIons

java.util.ArrayList<E> reporterIons
The reporter ions.


ptmToPrideMap

PtmToPrideMap ptmToPrideMap
The ptm to pride map.


cvTerm

CvTerm cvTerm
The modification cv term.


editable

boolean editable
Boolean indicating wheter the user can edit the ptm or not.


pattern

AminoAcidPattern pattern
The amino acid pattern of the modification


addNeutralLoss

javax.swing.JButton addNeutralLoss

addReporterIon

javax.swing.JButton addReporterIon

backgroundPanel

javax.swing.JPanel backgroundPanel

cancelButton

javax.swing.JButton cancelButton

detailsPanel

javax.swing.JPanel detailsPanel

helpJButton

javax.swing.JButton helpJButton

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel5

javax.swing.JLabel jLabel5

jPanel1

javax.swing.JPanel jPanel1

massTxt

javax.swing.JTextField massTxt

nameTxt

javax.swing.JTextField nameTxt

neutralLossesAndReporterIonsPanel

javax.swing.JPanel neutralLossesAndReporterIonsPanel

neutralLossesJScrollPane

javax.swing.JScrollPane neutralLossesJScrollPane

neutralLossesTable

javax.swing.JTable neutralLossesTable

okButton

javax.swing.JButton okButton

olsJButton

javax.swing.JButton olsJButton

psiModMappingJTextField

javax.swing.JTextField psiModMappingJTextField

psiModMappingPanel

javax.swing.JPanel psiModMappingPanel

removeNeutralLoss

javax.swing.JButton removeNeutralLoss

removerReporterIon

javax.swing.JButton removerReporterIon

reporterIonsJScrollPane

javax.swing.JScrollPane reporterIonsJScrollPane

reporterIonsTable

javax.swing.JTable reporterIonsTable

residuesTxt

javax.swing.JTextField residuesTxt

typeCmb

javax.swing.JComboBox typeCmb

Package com.compomics.util.gui.renderers

Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends javax.swing.DefaultListCellRenderer implements Serializable

Serialized Fields

align

int align
One of the following constants defined in SwingConstants: LEFT, CENTER (the default for image-only labels), RIGHT, LEADING (the default for text-only labels) or TRAILING.

Class com.compomics.util.gui.renderers.ByteArrayRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iData

byte[] iData
This byte[] is the actual data cached by the renderer.

Class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer extends javax.swing.JLabel implements Serializable

Serialized Fields

minXAxisValue

double minXAxisValue
The minimum x-axis value.


maxXAxisValue

double maxXAxisValue
The maxium x-axis value.


delegate

javax.swing.table.TableCellRenderer delegate
A reference to a standard table cell renderer.

Class com.compomics.util.gui.renderers.TimestampRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends javax.swing.plaf.basic.BasicComboBoxRenderer implements Serializable

Serialized Fields

tooltips

java.util.Vector<E> tooltips
The tooltips for each element in the list.


align

int align
The horizontal alignment of the text.


MAX_TOOLTIP_WIDTH

int MAX_TOOLTIP_WIDTH
The maxium width of a tool tip (in number of characters). Tooltips longer than the maximum will be split into multiple lines.


Package com.compomics.util.gui.spectrum

Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable

Serialized Fields

iChromatogramColor

java.awt.Color iChromatogramColor
Color in which the chromatogram polyline is rendered. Defaults to gray.


iChromatogramPointColor

java.awt.Color iChromatogramPointColor
Color in which the data points and peaks are rendered. Defaults to black.

Class com.compomics.util.gui.spectrum.FragmentIonTable extends javax.swing.JTable implements Serializable

Serialized Fields

currentFragmentIonTypes

java.util.ArrayList<E> currentFragmentIonTypes
The list of currently selected fragment ion types.


neutralLosses

NeutralLossesMap neutralLosses
The list of the currently selected neutral loss types.


singleCharge

boolean singleCharge
If true, singly charge ions are included in the table.


twoCharges

boolean twoCharges
If true, doubly charged ions are included in the table.


tooltips

java.util.ArrayList<E> tooltips
The table tooltips.


currentPeptide

Peptide currentPeptide
The current peptide.


peptideSequence

java.lang.String peptideSequence
The current peptide sequence.


allAnnotations

java.util.ArrayList<E> allAnnotations
The spectrum annotations map.


allSpectra

java.util.ArrayList<E> allSpectra
The list of spectra. Needed for intensity normalization.

Class com.compomics.util.gui.spectrum.GraphicsPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

peakWidth

float peakWidth
The width used for the annotated peaks.


backgroundPeakWidth

float backgroundPeakWidth
The width used for the bcakground peaks.


subscriptAnnotationNumbers

boolean subscriptAnnotationNumbers
If true, all numbers in peak annotations are subscripted.


peakWaterMarkColor

java.awt.Color peakWaterMarkColor
The color to use for the non-annotated peaks when only the annotated peaks are to be shown.


scientificXAxis

boolean scientificXAxis
If true the x-axis will be drawn using the scientific annotation. The pattern i set in the "scientificPattern" field.


scientificYAxis

boolean scientificYAxis
If true the y-axis will be drawn using the scientific annotation. The pattern i set in the "scientificPattern" field.


scientificPattern

java.lang.String scientificPattern
The number format pattern for scientific annotation.


referenceAreasXAxis

java.util.HashMap<K,V> referenceAreasXAxis
A hashmap of the current x-axis reference areas. Key is the name of the reference area.


referenceAreasYAxis

java.util.HashMap<K,V> referenceAreasYAxis
A hashmap of the current y-axis reference areas. Key is the name of the reference area.


miniature

boolean miniature
If set to true, the y-axis is removed, the y- and x-axis tags are removed, and any annotations are hidden. All to make the graphics panel look better in a smaller version, e.g., when put into a table cell. When turning miniature mode one it is also recommended to reduce the max padding. Note that miniature and reduced max padding is set automatically by the GraphicsPanelTableCellRenderer.


yDataIsPositive

boolean yDataIsPositive
If set to true, all y data is assumed to be positive. This adds a white polygon under the y-axis hiding any polygon data lines that crosses (slightly) below the y-axis.


alphaLevel

float alphaLevel
The opacity of the spectra. 0 means completely see-through, 1 means opaque.


useMassDeltaCombinations

boolean useMassDeltaCombinations
If true, pairs of delta mass annotations are used when doing de novo sequencing. If false, only single delta masses are annotated.


deltaMassWindow

double deltaMassWindow
The size of the window to use when searcing for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.


iXAxisLabel

java.lang.String iXAxisLabel
The label (and unit between brackets, if available) for the x-axis. Defaults to "m/z".


iYAxisLabel

java.lang.String iYAxisLabel
The label (and unit between brackets, if available) for the y-axis. Defaults to "Int".


iFilenameColor

java.awt.Color iFilenameColor
This is the color the filename should be presented in.


iDataPointAndLineColor

java.util.ArrayList<E> iDataPointAndLineColor
Colors in which the data points and peaks are rendered. Indexed by dataset.


iAreaUnderCurveColor

java.util.ArrayList<E> iAreaUnderCurveColor
Colors in which the chromatogram polyline is rendered. Indexed by dataset.


iPointSize

java.lang.Integer iPointSize
Size for the point on a polygon.


iFilename

java.lang.String iFilename
The spectrum or chromatogram filename.


iSpecPanelListeners

java.util.ArrayList<E> iSpecPanelListeners
The list of SpectrumPanelListeners.


iPointDetectionTolerance

int iPointDetectionTolerance
The deviation (both left and right) allowed for point highlighting detection.


iStartXLoc

int iStartXLoc
When the mouse is dragged, this represents the X-coordinate of the starting location.


iStartYLoc

int iStartYLoc
When the mouse is dragged, this represents the Y-coordinate of the starting location.


iEndXLoc

int iEndXLoc
When the mouse is dragged, this represents the X-coordinate of the ending location.


xAxisZoomRangeLowerValue

double xAxisZoomRangeLowerValue
The lower range for the current zoom range.


xAxisZoomRangeUpperValue

double xAxisZoomRangeUpperValue
The upper range for the current zoom range.


iDragXLoc

int iDragXLoc
The current dragging location.


iXScaleUnit

double iXScaleUnit
Scale unit for the X axis


iYScaleUnit

double iYScaleUnit
Scale unit for the Y axis


iXUnit

int iXUnit
Graphical unit for the X axis


iYUnit

int iYUnit
Graphical unit for the Y axis


iXPadding

int iXPadding
Effective distance from the x-axis to the panel border.


iTopPadding

int iTopPadding
Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark).


iXAxisStartAtZero

boolean iXAxisStartAtZero
This boolean is set to 'true' if the x-axis should start at zero.


iDragged

boolean iDragged
This boolean is set to 'true' when dragging is performed.


xTagCount

int xTagCount
The number of X-axis tags.


yTagCount

int yTagCount
The number of Y-axis tags.


padding

int padding
The padding (distance between the axes and the border of the panel).


currentPadding

int currentPadding
The current padding (distance between the axes and the border of the panel).


maxPadding

int maxPadding
The maximum padding (distance between the axes and the border of the panel). Increase if font size on the y-axis becomes too small.


showFileName

boolean showFileName
The boolean is set to 'true' if the file name is to be shown in the panel.


showPrecursorDetails

boolean showPrecursorDetails
The boolean is set to 'true' if the precursor details is to be shown in the panel.


showResolution

boolean showResolution
The boolean is set to 'true' if the resolution is to be shown in the panel.


iXAxisData

java.util.ArrayList<E> iXAxisData
All the x-axis data points. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.


iXAxisMin

double iXAxisMin
The minimum x-axis value to display.


iXAxisMax

double iXAxisMax
The maximum x-axis value to display.


iYAxisMin

double iYAxisMin
The minimum y-axis value to display.


iYAxisMax

double iYAxisMax
The maximum y-axis value to display.


iAnnotationYAxisThreshold

double iAnnotationYAxisThreshold
The procentual non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation. Default is '0.0'.


iYAxisData

java.util.ArrayList<E> iYAxisData
All the y-axis values. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis valuea are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.


iPrecursorMZ

double iPrecursorMZ
This variable holds the precursor M/Z.


iPrecursorCharge

java.lang.String iPrecursorCharge
This String holds the charge for the precursor.


iXAxisDataInPixels

java.util.ArrayList<E> iXAxisDataInPixels
This array will hold the x-coordinates in pixels for all the x-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).


iYAxisDataInPixels

java.util.ArrayList<E> iYAxisDataInPixels
This array will hold the y-coordinates in pixels for all the y-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).


iHighLight

boolean iHighLight
Boolean that will be 'true' when a point needs highlighting.


iHighLightIndex

int iHighLightIndex
Index of the point that needs to be highlighted.


iHighLightDatasetIndex

int iHighLightDatasetIndex
Index of the dataset containing the point that needs to be highlighted.


iClicked

boolean iClicked
Boolean that indicates whether a point has been marked by clicking.


iClickedIndex

int iClickedIndex
Int that indicates which point was clicked.


iClickedDataSetIndex

int iClickedDataSetIndex
Int that indicates which dataset contains the clicked point.


iClickedList

java.util.Vector<E> iClickedList
The Vector that holds all points clicked up to now.


iClickedListDatasetIndices

java.util.Vector<E> iClickedListDatasetIndices
The Vector that holds the dataset indices of all points clicked up to now.


iStoredSequence

java.util.Vector<E> iStoredSequence
The Vector that holds a set of stored points from a previously established list.


iStoredSequenceDatasetIndices

java.util.Vector<E> iStoredSequenceDatasetIndices
The Vector that holds the dataset indices of stored points from a previously established list.


iAnnotations

java.util.Vector<E> iAnnotations
The Vector that holds a set of Annotation instances.


iMinDrag

int iMinDrag
Minimal dragging distance in pixels.


iDrawStyle

int iDrawStyle
This variable holds the drawing style.


iDotRadius

int iDotRadius
This variable holds the dot radius; only used when drawing style is DOTS style.


iMSLevel

int iMSLevel
The ms level of the current spectrum. O is assumed to mean no ms level given.


showAllPeaks

boolean showAllPeaks
If false, only the annotated peaks will be shown. Note that this setting is ignored in profile mode!


yAxisZoomExcludesBackgroundPeaks

boolean yAxisZoomExcludesBackgroundPeaks
If true, the automatic y-axis zoom excludes the background peaks. False includes all peaks in the zoom.


currentGraphicsPanelType

GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
Sets the current GraphicsPanel type, default to centroid spectrum.

Class com.compomics.util.gui.spectrum.IntensityHistogram extends javax.swing.JPanel implements Serializable

Serialized Fields

chartPanel

org.jfree.chart.ChartPanel chartPanel
The chart panel for external access.

Class com.compomics.util.gui.spectrum.IonLabelColorTableModel extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

ionMap

java.util.HashMap<K,V> ionMap
The list of ions.


keys

java.util.ArrayList<E> keys
The keys.

Class com.compomics.util.gui.spectrum.IsotopicDistributionPanel extends GraphicsPanel implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

aSpectrumPeakColor

java.awt.Color aSpectrumPeakColor
The color used for the peaks. Default to red.


aSpectrumProfileModeLineColor

java.awt.Color aSpectrumProfileModeLineColor
The color used for the area under the curve. Defaults to pink.


peptideSequences

java.util.ArrayList<E> peptideSequences
The peptide sequences to display the isotopic distribution for.


peptideCharges

java.util.ArrayList<E> peptideCharges
The charges of the peptides. Indexed by dataset.


iElements

java.util.HashMap<K,V> iElements
HashMap with the molecular formula for all the aminoacids

Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends javax.swing.JPanel implements Serializable

Serialized Fields

useRelativeError

boolean useRelativeError
If true the relative error (ppm) is used instead of the absolute error (Da).


currentFragmentIons

java.util.ArrayList<E> currentFragmentIons
The currently selected fragment ion types.


includeSinglyCharge

boolean includeSinglyCharge
If singly charged fragment ions are to be included.


includeDoublyCharge

boolean includeDoublyCharge
If doubly charged fragment ions are to be included.


includeMoreThanTwoCharges

boolean includeMoreThanTwoCharges
If fragment ions with more than two charges are to be included.


currentlyUsedIonMatches

java.util.ArrayList<E> currentlyUsedIonMatches
The list of currently used ions.


chartPanel

org.jfree.chart.ChartPanel chartPanel
The chart panel.

Class com.compomics.util.gui.spectrum.MassErrorPlot extends javax.swing.JPanel implements Serializable

Serialized Fields

annotations

java.util.ArrayList<E> annotations
The complete list of possible spectrum annotations.


currentFragmentIons

java.util.ArrayList<E> currentFragmentIons
The currently selected fragment ion types.


includeSinglyCharge

boolean includeSinglyCharge
If singly charged fragment ions are to be included.


includeDoublyCharge

boolean includeDoublyCharge
If doubly charged fragment ions are to be included.


includeMoreThanTwoCharges

boolean includeMoreThanTwoCharges
If fragment ions with more than two charges are to be included.


currentlyUsedIonMatches

java.util.ArrayList<E> currentlyUsedIonMatches
The list of currently used ions.


chartPanel

org.jfree.chart.ChartPanel chartPanel
The chart panel.


useRelativeError

boolean useRelativeError
If true the relative error (ppm) is used instead of the absolute error (Da).

Class com.compomics.util.gui.spectrum.SequenceFragmentationPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

tooltipRectangles

java.util.HashMap<K,V> tooltipRectangles
A map of the rectangles that have tooltips, i.e., the fragement ion peaks and the PTM highlighting.


iSequenceComponents

java.lang.String[] iSequenceComponents
Elementary data for composing the Panel.


iIonMatches

java.util.ArrayList<E> iIonMatches
The list of fragment ion matches.


bIons

double[] bIons
Double array on b-ions for the sequence components. If '0', no corresponding ions were given for the component. Otherwise, a double between [0:1] is stored in the array that is relative with the intensity of the most intense fragmention.


yIons

double[] yIons
Double array on y-ions for the sequence components. If '0', no corresponding ions were given for the component. Otherwise, a double between [0:1] is stored in the array that is relative with the intensity of the most intense fragmention.


iBaseFont

java.awt.Font iBaseFont
The font to use.


iMaxBarHeight

double iMaxBarHeight
The maximum bar height.


iBarWidth

int iBarWidth
The width of the bars.


iHorizontalSpace

int iHorizontalSpace
The horizontal space.


iXStart

int iXStart
The x-axis start position.


isModifiedSequence

boolean isModifiedSequence
This boolean holds whether or not the given sequence is a modified sequence or a normal peptide sequence. Normal: KENNY Modified: NH2-K<Ace>ENNY-COOH


iHighlightModifications

boolean iHighlightModifications
If true the modification are highlighted with a background color.


modificationProfile

ModificationProfile modificationProfile
The modification profile.


forwardIon

int forwardIon
the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields


rewindIon

int rewindIon
the rewind ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields


forwardColor

java.awt.Color forwardColor
Color for the forward ion


rewindColor

java.awt.Color rewindColor
Color for the rewind ion

Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable

Serialized Fields

aSpectrumPeakColor

java.awt.Color aSpectrumPeakColor
The color used for the peaks. Default to red.


aSpectrumProfileModeLineColor

java.awt.Color aSpectrumProfileModeLineColor
The color used for the profile mode spectra. Defaults to pink.


Package com.compomics.util.gui.utils

Class com.compomics.util.gui.utils.ConnectionDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iConnections

java.util.ArrayList<E> iConnections
ArrayList that holds all the preconfigured connections. Note that when this list holds only 0 or 1 elements, it changes the behaviour of the GUI.


cmbConfigurations

javax.swing.JComboBox cmbConfigurations

txtDriver

javax.swing.JTextField txtDriver

txtUrl

javax.swing.JTextField txtUrl

txtUser

javax.swing.JTextField txtUser

txtPassword

javax.swing.JPasswordField txtPassword

btnOK

javax.swing.JButton btnOK

btnCancel

javax.swing.JButton btnCancel

iTarget

Connectable iTarget

iPropsFile

java.lang.String iPropsFile

iLastInitiatedConfiguration

java.lang.String iLastInitiatedConfiguration

Class com.compomics.util.gui.utils.DateChooser extends javax.swing.JDialog implements Serializable

Serialized Fields

iSelectedCalendar

java.util.Calendar iSelectedCalendar

iShownCalendar

java.util.Calendar iShownCalendar

iSelectedDayIndex

int iSelectedDayIndex

lblDayNames

javax.swing.JLabel[] lblDayNames

lblDays

javax.swing.JLabel[] lblDays

iDays

java.lang.Integer[] iDays

lblCurrentMonthYear

javax.swing.JLabel lblCurrentMonthYear

Package com.compomics.util.gui.waiting

Class com.compomics.util.gui.waiting.ProgressDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iProgress

javax.swing.JProgressBar iProgress

Package com.compomics.util.gui.waiting.waitinghandlers

Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX extends javax.swing.JDialog implements Serializable

Serialized Fields

doNothingOnClose

boolean doNothingOnClose
If set to true, trying to close the progess bar will be ignored. Use this option if the process being monitored can not be stopped.
Note: replaced by unstoppable.


unstoppable

boolean unstoppable
Set this to true of the process the progress bar is used for is not possible to stop, or not possble to stop nicely. If the user still tries to close the progress bar the a warning message is first shown were the user has to confirm that he/she still wants to close the progress bar.


canceled

boolean canceled
Boolean indicating whether the process has been canceled.


finished

boolean finished
Boolean indicating wheter the process has been completed.


waitingIcon

java.awt.Image waitingIcon
The dialog/frame icon to use when waiting.


normalIcon

java.awt.Image normalIcon
The dialog/frame icon to use when done.


waitingHandlerParentFrame

java.awt.Frame waitingHandlerParentFrame
The waitingHandlerParent frame.


waitingHandlerParentDialog

javax.swing.JDialog waitingHandlerParentDialog
The waitingHandlerParent dialog.


progressBar

javax.swing.JProgressBar progressBar

Class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

dialog

javax.swing.JDialog dialog
Needed for the shaking feature.


naturalLocation

java.awt.Point naturalLocation
Used in the shaking feature.


shakeTimer

javax.swing.Timer shakeTimer
Timer for the shaking feature.


runFinished

boolean runFinished
Boolean indicating whether the process is finished.


runCanceled

boolean runCanceled
Boolean indicating whether the process is canceled.


tips

java.util.ArrayList<E> tips
An array list of the tip of the day.


currentTipIndex

int currentTipIndex
The current tip index.


lastSelectedFolder

java.lang.String lastSelectedFolder
The last selected folder


waitingIcon

java.awt.Image waitingIcon
The dialog/frame icon to use when waiting.


normalIcon

java.awt.Image normalIcon
The dialog/frame icon to use when done.


waitingHandlerParent

java.awt.Frame waitingHandlerParent
The waitingHandlerParent.


shakeWhenFinished

boolean shakeWhenFinished
If true, the dialog will shake when completed. Mainly a PeptideShaker feature.


processName

java.lang.String processName
The name of the process we are waiting for, e.g., 'Import Data' or 'Search'.


toolName

java.lang.String toolName
The name of the tool using the waiting dialog. Used for the report.


toolVersion

java.lang.String toolVersion
The version number of the tool using the waiting dialog. Used for the report.


backgroundPanel

javax.swing.JPanel backgroundPanel

closeDialogWhenImportCompletesCheckBox

javax.swing.JCheckBox closeDialogWhenImportCompletesCheckBox

closeJButton

javax.swing.JButton closeJButton

layeredPane

javax.swing.JLayeredPane layeredPane

nextJButton

javax.swing.JButton nextJButton

okButton

javax.swing.JButton okButton

processProgressPanel

javax.swing.JPanel processProgressPanel

progressBar

javax.swing.JProgressBar progressBar

reportArea

javax.swing.JTextArea reportArea

reportAreaScrollPane

javax.swing.JScrollPane reportAreaScrollPane

saveReportLabel

javax.swing.JLabel saveReportLabel

secondaryJProgressBar

javax.swing.JProgressBar secondaryJProgressBar

secondaryProgressBarSplitPane

javax.swing.JSplitPane secondaryProgressBarSplitPane

showTipOfTheDayCheckBox

javax.swing.JCheckBox showTipOfTheDayCheckBox

tempJProgressBar

javax.swing.JProgressBar tempJProgressBar

tipOfTheDayEditorPane

javax.swing.JEditorPane tipOfTheDayEditorPane

tipOfTheDayJPanel

javax.swing.JPanel tipOfTheDayJPanel

tipOfTheDayLayeredPane

javax.swing.JLayeredPane tipOfTheDayLayeredPane

tipOfTheDayScrollPane

javax.swing.JScrollPane tipOfTheDayScrollPane

Package com.compomics.util.io

Class com.compomics.util.io.FtpConnectionException extends FtpProtocolException implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.io.FtpLoginException extends FtpProtocolException implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.io.FtpProtocolException extends java.io.IOException implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Package com.compomics.util.preferences

Class com.compomics.util.preferences.AnnotationPreferences extends java.lang.Object implements Serializable

serialVersionUID: -524156803097913546L

Serialized Fields

yAxisZoomExcludesBackgroundPeaks

boolean yAxisZoomExcludesBackgroundPeaks
If true, the automatic y-axis zoom excludes background peaks. False includes all peaks in the auto zoom.


intensityIonTable

boolean intensityIonTable
If true, the ion table is shown as an intensity versionm, false displays the standard Mascot version.


showBars

boolean showBars
If true, bars are shown in the bubble plot highlighting the ions.


showAllPeaks

boolean showAllPeaks
If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.


intensityLimit

double intensityLimit
The intensity limit used when only the most intense peaks are to be annotated.


automaticAnnotation

boolean automaticAnnotation
Shall PeptideShaker use automatic annotation.


selectedIons

java.util.HashMap<K,V> selectedIons
The types of ions to annotate.


neutralLossesMap

NeutralLossesMap neutralLossesMap
The neutral losses searched for.


neutralLossesSequenceDependant

boolean neutralLossesSequenceDependant
Shall neutral losses be only considered for ions containing amino acids of interest?


selectedCharges

java.util.ArrayList<E> selectedCharges
The maximum fragment charge to be searched for.


fragmentIonAccuracy

double fragmentIonAccuracy
Fragment ion accuracy used for peak matching.


currentPeptide

Peptide currentPeptide
The currently inspected peptide.


currentPrecursorCharge

int currentPrecursorCharge
The charge of the currently inspected precursor.


showForwardIonDeNovoTags

boolean showForwardIonDeNovoTags
If true, the automatic forward ion de novo tags are shown.


showRewindIonDeNovoTags

boolean showRewindIonDeNovoTags
If true, the automatic rewind ion de novo tags are shown.


deNovoCharge

int deNovoCharge
The charge for the fragment ions in the de novo sequencing.

Class com.compomics.util.preferences.ModificationProfile extends java.lang.Object implements Serializable

serialVersionUID: 342611308111304721L

Serialized Fields

modificationNames

java.util.HashMap<K,V> modificationNames
Deprecated. use the expected variable modification lists
Mapping of the utilities modification names to the PeptideShaker names.


fixedModifications

java.util.ArrayList<E> fixedModifications
List of the expected fixed modifications.


variableModifications

java.util.ArrayList<E> variableModifications
List of the expected variable modifications


refinementModifications

java.util.ArrayList<E> refinementModifications
List of modifications searched during the second pass search


omssaIndexes

java.util.HashMap<K,V> omssaIndexes
Map of the omssa indexes used for user modifications in this search


colors

java.util.HashMap<K,V> colors
Mapping of the expected modification names to the color used.


backUp

java.util.HashMap<K,V> backUp
Back-up mapping of the PTMs for portability.

Class com.compomics.util.preferences.UtilitiesUserPreferences extends java.lang.Object implements Serializable

serialVersionUID: -4343570286224891504L

Serialized Fields

spectrumAnnotatedPeakWidth

java.lang.Float spectrumAnnotatedPeakWidth
The width to use for the annotated peaks.


spectrumBackgroundPeakWidth

java.lang.Float spectrumBackgroundPeakWidth
The width to use for the background peaks.


spectrumAnnotatedPeakColor

java.awt.Color spectrumAnnotatedPeakColor
The color to use for the annotated peaks.


spectrumBackgroundPeakColor

java.awt.Color spectrumBackgroundPeakColor
The color to use for the background peaks.


sparklineColorValidated

java.awt.Color sparklineColorValidated
The color used for the sparkline bar chart plots.


sparklineColorNonValidated

java.awt.Color sparklineColorNonValidated
The color used for the non-validated sparkline bar chart plots.


sparklineColorNotFound

java.awt.Color sparklineColorNotFound
The color used for the not found sparkline bar chart plots.


sparklineColorPossible

java.awt.Color sparklineColorPossible
The color used for the possible values sparkline bar chart plots.


peptideSelected

java.awt.Color peptideSelected
The color of the selected peptide.


memoryPreference

int memoryPreference
The memory to use by PeptideShaker.


searchGuiPath

java.lang.String searchGuiPath
The path to the SearchGUI installation (if any). Makes it possible to start SearchGUI directly from PeptideShaker. Set to null if no path is provided.


peptideShakerPath

java.lang.String peptideShakerPath
The path to the PeptideShaker installation (if any). Set to null if no path is provided.


reporterPath

java.lang.String reporterPath
The path to the Reporter installation (if any). Set to null if no path is provided.


relimsPath

java.lang.String relimsPath
The path to the Relims installation (if any). Set to null if no path is provided.


localPrideFolder

java.lang.String localPrideFolder
The local PRIDE projects folder.


Package com.compomics.util.pride

Class com.compomics.util.pride.CvTerm extends java.lang.Object implements Serializable

serialVersionUID: -2890434198335005181L

Serialized Fields

ontology

java.lang.String ontology
The ontology.


accession

java.lang.String accession
The accession number.


name

java.lang.String name
The name/term.


value

java.lang.String value
The value for the given term.

Class com.compomics.util.pride.PtmToPrideMap extends java.lang.Object implements Serializable

serialVersionUID: 7368502853292052566L

Serialized Fields

modToCvMap

java.util.HashMap<K,V> modToCvMap
Map of the cv terms indexed by modification user name.


Package com.compomics.util.pride.prideobjects

Class com.compomics.util.pride.prideobjects.Contact extends java.lang.Object implements Serializable

serialVersionUID: -9182316910747747823L

Serialized Fields

name

java.lang.String name
The contact's name.


eMail

java.lang.String eMail
The contact's e-mail.


institution

java.lang.String institution
The contact's institution.

Class com.compomics.util.pride.prideobjects.ContactGroup extends java.lang.Object implements Serializable

serialVersionUID: -9182316910747747823L

Serialized Fields

contacts

java.util.ArrayList<E> contacts
The contacts.


groupName

java.lang.String groupName
The contact group name.

Class com.compomics.util.pride.prideobjects.Instrument extends java.lang.Object implements Serializable

serialVersionUID: -8802861658166703745L

Serialized Fields

name

java.lang.String name
The instrument name.


cvTerms

java.util.ArrayList<E> cvTerms
The list of analyzer CV terms.


source

CvTerm source
The instrument source.


detector

CvTerm detector
The instrument detector.

Class com.compomics.util.pride.prideobjects.Protocol extends java.lang.Object implements Serializable

serialVersionUID: -9045298216154032632L

Serialized Fields

name

java.lang.String name
The protcol name.


cvTerms

java.util.ArrayList<E> cvTerms
The list of CV terms.

Class com.compomics.util.pride.prideobjects.Reference extends java.lang.Object implements Serializable

serialVersionUID: -5449836209751629549L

Serialized Fields

reference

java.lang.String reference
The reference text.


pmid

java.lang.String pmid
The PubMed ID.


doi

java.lang.String doi
The Digital Object Identifier.

Class com.compomics.util.pride.prideobjects.ReferenceGroup extends java.lang.Object implements Serializable

serialVersionUID: -9182316910747747823L

Serialized Fields

references

java.util.ArrayList<E> references
The references.


groupName

java.lang.String groupName
The reference group name.

Class com.compomics.util.pride.prideobjects.Sample extends java.lang.Object implements Serializable

serialVersionUID: -7142471175737857227L

Serialized Fields

name

java.lang.String name
The sample name.


cvTerms

java.util.ArrayList<E> cvTerms
The list of CV terms.


Package com.compomics.util.protein

Class com.compomics.util.protein.Header extends java.lang.Object implements Serializable

serialVersionUID: 7665784733371863163L

Serialized Fields

iID

java.lang.String iID
The ID String corresponds to the String that is present as the first element following the opening '>'. It is most notably 'sw' for SwissProt, and 'gi' for NCBI.
ID is the first element in the abbreviated header String.


iForeignID

java.lang.String iForeignID
The foreign ID is the ID of another database this entry is orignally from. Most notably used for SwissProt entries in NCBI.
The foreign ID String is an addendum to the accession String in the abbreviated header String.


iAccession

java.lang.String iAccession
The accession String is the unique identifier for the sequence in the respective database. Note that for NCBI, the accession number also defines a unique moment in time.
Accession String is the second element in the abbreviated header String.


databaseType

Header.DatabaseType databaseType
Extracted database name. As there are no standard database names, this is only an internally consistent naming scheme included to be able to later separate the databases. For example when linking to the online version of the database. The links themselves are not included as these might change outside the control of the compomics-utilties library. Note that the type is set to unknown by default, and is set to the correct type during the parsing of the header.


iForeignAccession

java.lang.String iForeignAccession
The foreign accession String is an accession String in another database of significance. Most notably used for SwissProt accessions that are kept in the NCBI database.
The foreign accession String is an addendum to the foreign ID String in the abbreviated header String.


iDescription

java.lang.String iDescription
The description is a more or less elaborate description of the protein in question.
The description is the third element (and final) in the abbreviated header String.


iGeneName

java.lang.String iGeneName
The name of the gene the protein comes from. Note that this is only available for UniProt-based databases.


iProteinEvidence

java.lang.String iProteinEvidence
The protein evidence for the protein. Note that this is only available for UniProt-based databases.


iTaxonomy

java.lang.String iTaxonomy
The name of the taxonomy the protein comes from. Note that this is only available for UniProt-based databases.


iForeignDescription

java.lang.String iForeignDescription
The foreign Description is a description for an entry in another DB. Most notably, the SwissProt short description for an entry that is found within NCBI.
The foreign description is an addendum to the foreign accession String in the abbreviated header String.


iRest

java.lang.String iRest
This variable holds all unidentified parts for the Header. If the String was not (recognized as) a standard SwissProt or NCBI header, this variable holds the entire header.


iAddenda

java.lang.StringBuffer iAddenda
This StringBuffer holds all the addenda for this header.


iStart

int iStart
This variable holds a possible startindex for the associated sequence


iEnd

int iEnd
This variable holds a possible endindex for the associated sequence

Class com.compomics.util.protein.ModificationImplementation extends java.lang.Object implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

iTemplate

ModificationTemplate iTemplate
The ModificationTemplate which holds all the shared information for a modification. It is to be considered a singleton and it is immutable.


iLocation

int iLocation
The location for the modification in the parent sequence.


Package com.compomics.util.sun

Class com.compomics.util.sun.TableMap extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

model

javax.swing.table.TableModel model

Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

indexes

int[] indexes

sortingColumns

java.util.Vector<E> sortingColumns

ascending

boolean ascending

compares

int compares

listMouseListener

java.awt.event.MouseAdapter listMouseListener



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