Serialized Form


Package com.compomics.software.dialogs

Class com.compomics.software.dialogs.JavaOptionsDialog extends JDialog implements Serializable

Serialized Fields

javaOptionsDialogParent

JavaOptionsDialogParent javaOptionsDialogParent
The main instance of the GUI.


welcomeDialog

JDialog welcomeDialog
A reference to the Welcome Dialog.


toolName

String toolName
The name of the tool, e.g., PeptideShaker.


backgroundPanel

JPanel backgroundPanel

cancelButton

JButton cancelButton

javaOptionsHelpJButton

JButton javaOptionsHelpJButton

mbLabel

JLabel mbLabel

memoryLimitLabel

JLabel memoryLimitLabel

memoryTxt

JTextField memoryTxt

okButton

JButton okButton

settingsPanel

JPanel settingsPanel

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

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

String lastSelectedFolder
The selected folder.


dialogCanceled

boolean dialogCanceled
Set to true if the dialog was canceled.


backgroundPanel

JPanel backgroundPanel

browseButton

JButton browseButton

cancelButton

JButton cancelButton

jLabel2

JLabel jLabel2

okButton

JButton okButton

peptideShakerButton

JButton peptideShakerButton

peptideShakerDownloadLinkLabel

JLabel peptideShakerDownloadLinkLabel

peptideShakerDownloadPanel

JPanel peptideShakerDownloadPanel

peptideShakerInfoLabel

JLabel peptideShakerInfoLabel

peptideShakerInstallationPanel

JPanel peptideShakerInstallationPanel

peptideShakerJarFileHelpLabel

JLabel peptideShakerJarFileHelpLabel

peptideShakernstallationJTextField

JTextField peptideShakernstallationJTextField

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

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
Deprecated. 
The utilities preferences.


lastSelectedFolder

String lastSelectedFolder
Deprecated. 
The selected folder.


backgroundPanel

JPanel backgroundPanel
Deprecated. 

browseButton

JButton browseButton
Deprecated. 

cancelButton

JButton cancelButton
Deprecated. 

jLabel2

JLabel jLabel2
Deprecated. 

okButton

JButton okButton
Deprecated. 

relimsButton

JButton relimsButton
Deprecated. 

relimsDownloadLinkLabel

JLabel relimsDownloadLinkLabel
Deprecated. 

relimsDownloadPanel

JPanel relimsDownloadPanel
Deprecated. 

relimsInfoLabel

JLabel relimsInfoLabel
Deprecated. 

relimsInstallationJTextField

JTextField relimsInstallationJTextField
Deprecated. 

relimsInstallationPanel

JPanel relimsInstallationPanel
Deprecated. 

relimsJarFileHelpLabel

JLabel relimsJarFileHelpLabel
Deprecated. 

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

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

String lastSelectedFolder
The selected folder.


dialogCanceled

boolean dialogCanceled
Set to true if the dialog was canceled.


backgroundPanel

JPanel backgroundPanel

browseButton

JButton browseButton

cancelButton

JButton cancelButton

jLabel2

JLabel jLabel2

okButton

JButton okButton

reporterButton

JButton reporterButton

reporterDownloadLinkLabel

JLabel reporterDownloadLinkLabel

reporterDownloadPanel

JPanel reporterDownloadPanel

reporterInfoLabel

JLabel reporterInfoLabel

reporterInstallationJTextField

JTextField reporterInstallationJTextField

reporterInstallationPanel

JPanel reporterInstallationPanel

reporterJarFileHelpLabel

JLabel reporterJarFileHelpLabel

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

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities preferences.


lastSelectedFolder

String lastSelectedFolder
The selected folder.


dialogCanceled

boolean dialogCanceled
Set to true if the dialog was canceled.


backgroundPanel

JPanel backgroundPanel

browseButton

JButton browseButton

cancelButton

JButton cancelButton

jLabel2

JLabel jLabel2

okButton

JButton okButton

searchGuiButton

JButton searchGuiButton

searchGuiDownloadLinkLabel

JLabel searchGuiDownloadLinkLabel

searchGuiDownloadPanel

JPanel searchGuiDownloadPanel

searchGuiInfoLabel

JLabel searchGuiInfoLabel

searchGuiInstallationJTextField

JTextField searchGuiInstallationJTextField

searchGuiInstallationPanel

JPanel searchGuiInstallationPanel

searchGuiJarFileHelpLabel

JLabel searchGuiJarFileHelpLabel

Package com.compomics.util

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iEvenRowColor

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


iUnevenRowColor

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 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

String[] iColNames
The column names in this resultset.


iData

Object[][] iData
The data.

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iNested

Exception iNested
The nested exception.

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

serialVersionUID: -8595805180622832745L

Serialized Fields

dbName

String dbName
The name of the database.


dbConnection

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


longKeys

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


objectsCache

ObjectsCache objectsCache
The cache to be used for the objects


debugSpeedWriter

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


debugContentWriter

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


debugFolder

File debugFolder
The debug folder.


busy

boolean busy
A boolean indicating whether the database is being queried.


tableQueueUpdating

String tableQueueUpdating
The name of the table currently updating in the queue.


tableQueue

ArrayList<E> tableQueue
A queue of entire tables to load.


contentQueue

HashMap<K,V> contentQueue
A queue of table components to load.


contentTableQueue

ArrayList<E> contentTableQueue
A queue of tables of content to load.


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.


useSQLite

boolean useSQLite
If true, SQLite is used as the database, if false Derby is used.


Package com.compomics.util.denovo

Class com.compomics.util.denovo.PeptideAssumptionDetails extends Object implements Serializable

Serialized Fields

nTermGap

double nTermGap
The mass gap from the N-terminal to the start of the PepNovo sequence.


cTermGap

double cTermGap
The mass gap from the C-terminal to the end of the PepNovo sequence.


rankScore

double rankScore
The PepNovo rank score.


mH

double mH
The PepNovo M+H.


Package com.compomics.util.examples

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

Serialized Fields

closeJButton

JButton closeJButton

jScrollPane1

JScrollPane jScrollPane1

textJEditorPane

JEditorPane textJEditorPane

Class com.compomics.util.examples.MirroredSpectraTestDialog extends JDialog implements Serializable

Serialized Fields

backgroundPanel

JPanel backgroundPanel

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

Serialized Fields

peffAnnotationsColorMap

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


peffAnnotationsTooltipMap

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

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


currentSequenceFile

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


currentPeffBufferedReader

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


currentSequence

String currentSequence
The current PEFF (or FASTA) sequence.


currentSequenceLine

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


linkedSpectrumPanels

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


allAnnotations

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

String cleanProteinSequence
Used for the in silico digestion example.


selectedAnnotationTypes

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


sequenceAnnotationColumnHeaderTooltips

ArrayList<E> sequenceAnnotationColumnHeaderTooltips
Sequence annotation column header tooltips.


sparklineColor

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


H2OIonsJCheckBox

JCheckBox H2OIonsJCheckBox

NH3IonsJCheckBox

JCheckBox NH3IonsJCheckBox

aIonsJCheckBox

JCheckBox aIonsJCheckBox

allPeaksJCheckBox

JCheckBox allPeaksJCheckBox

bIonsJCheckBox

JCheckBox bIonsJCheckBox

browseJButton

JButton browseJButton

cIonsJCheckBox

JCheckBox cIonsJCheckBox

chargeOneJCheckBox

JCheckBox chargeOneJCheckBox

chargeOverTwoJCheckBox

JCheckBox chargeOverTwoJCheckBox

chargePeptideAJSpinner

JSpinner chargePeptideAJSpinner

chargePeptideBJSpinner

JSpinner chargePeptideBJSpinner

chargeTwoJCheckBox

JCheckBox chargeTwoJCheckBox

chromatogramAJPanel

JPanel chromatogramAJPanel

chromatogramJPanel

JPanel chromatogramJPanel

chromatogramPanelHelpJLabel

JLabel chromatogramPanelHelpJLabel

chromatogramPanelInfoJLabel

JLabel chromatogramPanelInfoJLabel

enzymesJComboBox

JComboBox enzymesJComboBox

exportJButton

JButton exportJButton

inSilicoDigestionHelpJLabel

JLabel inSilicoDigestionHelpJLabel

informationJEditorPane

JEditorPane informationJEditorPane

informationJPanel

JPanel informationJPanel

informationJScrollPane

JScrollPane informationJScrollPane

inhibitorsJTextField

JTextField inhibitorsJTextField

ionSelectionJPanel

JPanel ionSelectionJPanel

isotopicDistributionAJPanel

JPanel isotopicDistributionAJPanel

isotopicDistributionCalculatorHelpJLabel

JLabel isotopicDistributionCalculatorHelpJLabel

isotopicDistributionCalculatorInfoJLabel

JLabel isotopicDistributionCalculatorInfoJLabel

isotopicDistributionJPanel

JPanel isotopicDistributionJPanel

jLabel1

JLabel jLabel1

jLabel10

JLabel jLabel10

jLabel11

JLabel jLabel11

jLabel12

JLabel jLabel12

jLabel13

JLabel jLabel13

jLabel14

JLabel jLabel14

jLabel15

JLabel jLabel15

jLabel16

JLabel jLabel16

jLabel17

JLabel jLabel17

jLabel18

JLabel jLabel18

jLabel19

JLabel jLabel19

jLabel2

JLabel jLabel2

jLabel20

JLabel jLabel20

jLabel21

JLabel jLabel21

jLabel24

JLabel jLabel24

jLabel3

JLabel jLabel3

jLabel4

JLabel jLabel4

jLabel5

JLabel jLabel5

jLabel6

JLabel jLabel6

jLabel7

JLabel jLabel7

jLabel8

JLabel jLabel8

jLabel9

JLabel jLabel9

jPanel1

JPanel jPanel1

jPanel10

JPanel jPanel10

jPanel11

JPanel jPanel11

jPanel12

JPanel jPanel12

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jPanel4

JPanel jPanel4

jPanel5

JPanel jPanel5

jPanel6

JPanel jPanel6

jPanel7

JPanel jPanel7

jPanel8

JPanel jPanel8

jPanel9

JPanel jPanel9

jRadioButton1

JRadioButton jRadioButton1

jScrollPane1

JScrollPane jScrollPane1

jScrollPane2

JScrollPane jScrollPane2

jScrollPane3

JScrollPane jScrollPane3

jSeparator1

JSeparator jSeparator1

jSeparator2

JSeparator jSeparator2

jSeparator3

JSeparator jSeparator3

jSeparator4

JSeparator jSeparator4

jSeparator5

JSeparator jSeparator5

jSeparator6

JSeparator jSeparator6

jSeparator9

JSeparator jSeparator9

jTabbedPane

JTabbedPane jTabbedPane

linkedSpectraJCheckBox

JCheckBox linkedSpectraJCheckBox

lowerMassJSpinner

JSpinner lowerMassJSpinner

missedCleavagesJSpinner

JSpinner missedCleavagesJSpinner

nextJButton

JButton nextJButton

otherIonsJCheckBox

JCheckBox otherIonsJCheckBox

peffAnnotationsJTable

JTable peffAnnotationsJTable

peffHeaderJTable

JTable peffHeaderJTable

peptideAColorJPanel

JPanel peptideAColorJPanel

peptideACompositionJTextField

JTextField peptideACompositionJTextField

peptideAJScrollPane

JScrollPane peptideAJScrollPane

peptideAJXTable

org.jdesktop.swingx.JXTable peptideAJXTable

peptideAMzJTextField

JTextField peptideAMzJTextField

peptideBColorJPanel

JPanel peptideBColorJPanel

peptideBCompositionJTextField

JTextField peptideBCompositionJTextField

peptideBJScrollPane

JScrollPane peptideBJScrollPane

peptideBJXTable

org.jdesktop.swingx.JXTable peptideBJXTable

peptideBMzJTextField

JTextField peptideBMzJTextField

peptideSequenceAJTextField

JTextField peptideSequenceAJTextField

peptideSequenceBJTextField

JTextField peptideSequenceBJTextField

peptidesJPanel

JPanel peptidesJPanel

peptidesJTable

JTable peptidesJTable

peptidesScrollPane

JScrollPane peptidesScrollPane

positionJTextField

JTextField positionJTextField

profileSpectrumJCheckBox

JCheckBox profileSpectrumJCheckBox

proteinCoverageJScrollPane

JScrollPane proteinCoverageJScrollPane

proteinDigestionJLabel

JLabel proteinDigestionJLabel

proteinDigestionJPanel

JPanel proteinDigestionJPanel

proteinHeaderJTable

JTable proteinHeaderJTable

proteinSequenceCoverageJEditorPane

JEditorPane proteinSequenceCoverageJEditorPane

sequenceCoverageJPanel

JPanel sequenceCoverageJPanel

sequenceFileJTextField

JTextField sequenceFileJTextField

sequenceJTabbedPane

JTabbedPane sequenceJTabbedPane

silacLabelPeptideAJComboBox

JComboBox silacLabelPeptideAJComboBox

silacLabelPeptideBJComboBox

JComboBox silacLabelPeptideBJComboBox

siteJTextField

JTextField siteJTextField

spectraJPanel

JPanel spectraJPanel

spectrumAJPanel

JPanel spectrumAJPanel

spectrumBJPanel

JPanel spectrumBJPanel

spectrumJPanel

JPanel spectrumJPanel

spectrumPanelHelpJLabel

JLabel spectrumPanelHelpJLabel

spectrumPanelInfoJLabel

JLabel spectrumPanelInfoJLabel

upperMassJSpinner

JSpinner upperMassJSpinner

xIonsJCheckBox

JCheckBox xIonsJCheckBox

yIonsJCheckBox

JCheckBox yIonsJCheckBox

zIonsJCheckBox

JCheckBox zIonsJCheckBox

Package com.compomics.util.experiment

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

serialVersionUID: 4330394623824512352L

Serialized Fields

reference

String reference
reference of the experiment


samples

HashMap<K,V> samples
the samples analyzed


analysis

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

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


identification

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

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 Object implements Serializable

serialVersionUID: -3158896310928354857L

Serialized Fields

singleLetterCode

String singleLetterCode
Single letter code of the amino acid.


threeLetterCode

String threeLetterCode
Three letter code of the amino acid.


name

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 Object implements Serializable

serialVersionUID: -2823716418631089876L

Serialized Fields

target

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

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


aaExcluded

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

String name

letter

String letter

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

serialVersionUID: -1852087173903613377L

Serialized Fields

id

int id

name

String name

aminoAcidBefore

ArrayList<E> aminoAcidBefore

aminoAcidAfter

ArrayList<E> aminoAcidAfter

restrictionBefore

ArrayList<E> restrictionBefore

restrictionAfter

ArrayList<E> restrictionAfter

isSemiSpecific

Boolean isSemiSpecific
If true, the enzyme is considered as semi-specific, meaning that only one end of the resulting peptide has to be enzymatic.

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

serialVersionUID: -1505719074403886934L

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

String name
The name of the neutral loss.


fixed

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

String sequence
The peptide sequence.


mass

Double mass
The peptide mass.


parentProteins

ArrayList<E> parentProteins
The parent proteins.


modifications

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

String accession
The protein accession.


decoy

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


sequence

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

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


name

String name
Name of the modification.


shortName

String shortName
Short name of the modification.


mass

double mass
Mass difference produced by this modification.


neutralLosses

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


reporterIons

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 Object implements Serializable

serialVersionUID: 7935264190312934466L

Serialized Fields

ptmMap

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


defaultMods

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


userMods

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


userColors

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


shortNames

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


defaultOmssaIndexes

HashMap<K,V> defaultOmssaIndexes
Map of OMSSA indexes for default modifications.


defaultModsSorted

boolean defaultModsSorted
Set to true if the default mods are sorted alphabetically.


usersModsSorted

boolean usersModsSorted
Set to true if the users mods are sorted alphabetically.

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

serialVersionUID: 303393644914835325L

Serialized Fields

reference

String reference
sample reference


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

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

serialVersionUID: 2553535668713619525L

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

serialVersionUID: -5308475190007072857L

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

serialVersionUID: 5951975489690885808L

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

serialVersionUID: -8410332876209882538L

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

serialVersionUID: -584166511231722270L

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

serialVersionUID: 9171494537928740228L

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

serialVersionUID: 6850534412637609745L

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

serialVersionUID: -1552736259723394861L

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

serialVersionUID: 2128316713069027803L

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

serialVersionUID: -669587024023052011L

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

serialVersionUID: -514676021245212886L

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

serialVersionUID: 1963175809911841522L

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

serialVersionUID: -656824121858821632L

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

serialVersionUID: 3427548228986235710L

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

serialVersionUID: 1841628592146093511L

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

serialVersionUID: -939609662176974248L

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

serialVersionUID: 3754407258673679661L

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

serialVersionUID: 8680204019988094523L

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

serialVersionUID: -2123392615229813870L

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

serialVersionUID: -2201410868329421240L

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

serialVersionUID: 172831874616867727L

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

serialVersionUID: -6773437038176247799L

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

serialVersionUID: 7542892886050340088L

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

serialVersionUID: -5155418025636472676L

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

serialVersionUID: -2618109862080991929L

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

serialVersionUID: -7714841171012071337L


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

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

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


name

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


longName

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

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

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

String name
ion name for user defined ions.


subtype

int subtype
The ion subtype.


Package com.compomics.util.experiment.identification

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

Serialized Fields

indexes

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


fileName

String fileName
The FASTA file name.


name

String name
The name of the database.


lastModified

Long lastModified
The last time the indexed file was modified.


isDefaultReversed

boolean isDefaultReversed
In case decoy hits are found, check whether these are reversed versions of the target with default accession suffix.


nTarget

int nTarget
Number of target sequences found in the database.


databaseType

Header.DatabaseType databaseType
The database type.


version

String version
The version of the database.


concatenatedTargetDecoy

boolean concatenatedTargetDecoy
Indicates whether the database is a concatenated target/decoy.


decoyTag

String decoyTag
The tag used for decoy sequences.

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

serialVersionUID: -2551700699384242554L

Serialized Fields

proteinIdentification

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


peptideIdentification

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


spectrumIdentificationMap

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


spectrumIdentification

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


proteinMap

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


methodUsed

int methodUsed
The method used.


serializationDirectory

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


urParameters

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


longKeys

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


isDB

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

String reference
The reference of the identification.


orderedSpectrumFileNames

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

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

serialVersionUID: 691986038787590646L

Serialized Fields

dbName

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


proteinTableName

String proteinTableName
The name of the protein table.


proteinParametersTableSuffix

String proteinParametersTableSuffix
The suffix for protein parameters tables.


peptideTableName

String peptideTableName
The name of the peptide table.


peptideParametersTableSuffix

String peptideParametersTableSuffix
The suffix for a peptide parameters table.


psmTableSuffix

String psmTableSuffix
The suffix for a PSM table.


psmParametersTableSuffix

String psmParametersTableSuffix
The suffix for a PSM parameters table.


parametersSuffix

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


psmTables

ArrayList<E> psmTables
List of all psms tables.


psmParametersTables

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


peptideParametersTables

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


proteinParametersTables

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


matchParametersTables

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 Object implements Serializable

serialVersionUID: -4690159937753713106L

Serialized Fields

bBoundaries

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

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 score, the lower the better. Ought to be renamed but kept for backward compatibility


file

String file
the corresponding file.

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

serialVersionUID: -2773993307168773763L

Serialized Fields

currentPrecursorAccuracyType

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


precursorTolerance

Double precursorTolerance
The precursor mass tolerance.


fragmentIonMZTolerance

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

Integer nMissedCleavages
The allowed number of missed cleavages.


fastaFile

File fastaFile
The sequence database file used for identification.


parametersFile

File parametersFile
The corresponding searchGUI file.


fractionMolecularWeights

HashMap<K,V> fractionMolecularWeights
Deprecated. use fractionMolecularWeightRanges instead
The list of fraction molecular weights. The key is the fraction file path.


fractionMolecularWeightRanges

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


forwardIon

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


rewindIon

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

Double maxEValue
Maximal e-value cut-off. (OMSSA and X!Tandem only)


hitListLength

Integer hitListLength
The maximal hit list length (OMSSA setting only).


hitListLengthDeNovo

Integer hitListLengthDeNovo
The maximal hit list length for PepNovo+.


minimalChargeForMultipleChargedFragments

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


minPeptideLength

Integer minPeptideLength
The minimum peptide length (for semi and non tryptic searches with OMSSA).


maxPeptideLength

Integer maxPeptideLength
The maximal peptide length (for semi and non tryptic searches with OMSSA).


removePrecursor

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


scalePrecursor

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


estimateCharge

Boolean estimateCharge
Indicates whether the precursor charge estimation option (OMSSA and DeNovoGUI).


correctPrecursorMass

Boolean correctPrecursorMass
Indicates whether the precursor mass shall be corrected (DeNovoGUI setting).


discardLowQualitySpectra

Boolean discardLowQualitySpectra
Indicates whether the low quality spectra shall be discarded (DeNovoGUI setting).


fragmentationModel

String fragmentationModel
DeNovoGUI fragmentation model.


generateQuery

Boolean generateQuery
Indicates whether a blast query shall be generated (DeNovoGUI setting).


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

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 match.


mainMatchKey

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


spectrumMatches

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


isDecoy

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

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


mainMatch

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


peptideMatches

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

String spectrumKey
The index of the matched spectrum.


assumptions

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


bestAssumption

PeptideAssumption bestAssumption
The best assumption.


firstHits

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


advocates

ArrayList<E> advocates
All advocates used.


spectrumNumber

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.identification.protein_inference.proteintree

Class com.compomics.util.experiment.identification.protein_inference.proteintree.Node extends Object implements Serializable

serialVersionUID: 8936868785405252371L

Serialized Fields

depth

int depth
The depth of the node in the tree.


accessions

HashMap<K,V> accessions
List of accessions contained in this node.


termini

HashMap<K,V> termini
In case of splitting, the terminal mappings are put here.


subtree

HashMap<K,V> subtree
Subtree starting from this node.


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

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

Serialized Fields

index

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

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

Serialized Fields

indexMap

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


spectrumTitles

ArrayList<E> spectrumTitles
List of all spectra.


fileName

String fileName
The name of the indexed file.


lastModified

Long lastModified
The last time the indexed file was modified.


maxRT

Double maxRT
The maximum RT found in the spectra.


minRT

Double minRT
The minimum RT found in the spectra.


maxMz

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


maxIntensity

Double maxIntensity
The maximal precursor intensity of the file.


maxCharge

Integer maxCharge
The maximal charge.


maxPeakCount

Integer maxPeakCount
The maximal peak count.


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

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


rtMax

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

ArrayList<E> possibleCharges
The charge of the precursor.

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

serialVersionUID: 7152424141470431489L

Serialized Fields

spectrumTitle

String spectrumTitle
Spectrum title.


fileName

String fileName
Spectrum file name.


level

int level
The MS level.


peakList

HashMap<K,V> peakList
Peak list.


scanNumber

String scanNumber
Scan number or range.


scanStartTime

double scanStartTime
The time point 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 Object implements Serializable

serialVersionUID: 1929697552061121072L

Serialized Fields

urParams

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

ArrayList<E> proteinQuantification
The protein quantification


peptideQuantification

ArrayList<E> peptideQuantification
The peptide quantification


modifiedPeptidesQuantification

HashMap<K,V> modifiedPeptidesQuantification
The modified peptides quantification


psmIDentificationToQuantification

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 Object implements Serializable

serialVersionUID: 4600091320219653637L

Serialized Fields

dbName

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


proteinTableName

String proteinTableName
The name of the protein table.


proteinParametersTableSuffix

String proteinParametersTableSuffix
The suffix for protein parameters tables.


peptideTableName

String peptideTableName
The suffix of a peptide table.


peptideParametersTableSuffix

String peptideParametersTableSuffix
The suffix for a peptide parameters table.


psmTableSuffix

String psmTableSuffix
The suffix for a PSM table.


psmParametersTableSuffix

String psmParametersTableSuffix
The suffix for a PSM parameters table.


psmTables

ArrayList<E> psmTables
List of all psms tables.


psmParametersTables

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


peptideParametersTables

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


proteinParametersTables

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

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

String peptideKey
The identification peptide match.


psmQuantification

ArrayList<E> psmQuantification
The corresponding spectrum quantification

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

Serialized Fields

proteinKey

String proteinKey
The identification protein match key.


peptideQuantification

ArrayList<E> peptideQuantification
The peptide quantification corresponding.

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

Serialized Fields

spectrumKey

String spectrumKey
The corresponding spectrum key.


spectrumMatchKey

String spectrumMatchKey
The key of the spectrum match.


reporterMatches

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


deisotopedIntensities

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

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 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 Exception implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

element

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 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

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


exampleSequence

String exampleSequence
The example sequence.


addJMenuItem

JMenuItem addJMenuItem

backgroundPanel

JPanel backgroundPanel

cancelButton

JButton cancelButton

deleteSelectedRowJMenuItem

JMenuItem deleteSelectedRowJMenuItem

exampleLabel

JLabel exampleLabel

jSeparator3

JSeparator jSeparator3

jSeparator4

JSeparator jSeparator4

moveDownJMenuItem

JMenuItem moveDownJMenuItem

moveUpJMenuItem

JMenuItem moveUpJMenuItem

okButton

JButton okButton

patternDesignPanel

JPanel patternDesignPanel

patternDesignScrollPane

JScrollPane patternDesignScrollPane

patternDesignTable

JTable patternDesignTable

patternTestEditorPane

JEditorPane patternTestEditorPane

patternTestJScrollPane

JScrollPane patternTestJScrollPane

popupJMenu

JPopupMenu popupJMenu

rightClickHelpLabel

JLabel rightClickHelpLabel

testPanel

JPanel testPanel

Class com.compomics.util.gui.DummyFrame extends JFrame implements Serializable

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

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.gui.GeneDetailsDialog extends JDialog implements Serializable

Serialized Fields

goFactory

GOFactory goFactory
The GO terms factory.


geneFactory

GeneFactory geneFactory
The Gene factory.


proteinAccessions

ArrayList<E> proteinAccessions
the protein accessions of this match.


goTermDescriptions

ArrayList<E> goTermDescriptions
The GO term descriptions attached to this protein match.


selectedRowHtmlTagFontColor

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


notSelectedRowHtmlTagFontColor

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


backgroundPanel

JPanel backgroundPanel

chromosomeLabel

JLabel chromosomeLabel

chromosomeNameTxt

JTextField chromosomeNameTxt

detailsPanel

JPanel detailsPanel

ensemlbIdLabel

JLabel ensemlbIdLabel

geneIdTxt

JTextField geneIdTxt

geneNameLabel

JLabel geneNameLabel

geneNameTxt

JTextField geneNameTxt

goAnnotationLabel

JLabel goAnnotationLabel

goTable

JTable goTable

goTableScrollPane

JScrollPane goTableScrollPane

okButton

JButton okButton

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iMessages

String[] iMessages

iThrowable

Throwable iThrowable

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iData

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


txtData

JTextArea txtData

btnUnzip

JButton btnUnzip

btnSave

JButton btnSave

Class com.compomics.util.gui.JLabelAndComponentPanel extends 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

String iDateTimeFormat
This String contains the date and time format.


iFrames

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 JDialog implements Serializable

Serialized Fields

samples

String[] samples
The samples found.


choice

String choice
The choice of the user.


backgroundPanel

JPanel backgroundPanel

comboBox

JComboBox comboBox

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

okButton

JButton okButton

titleLbl

JLabel titleLbl

Class com.compomics.util.gui.VennDiagramDialog extends JDialog implements Serializable

Serialized Fields

currentVennDiagramType

VennDiagramDialog.VennDiagramType currentVennDiagramType
The current Venn diagram type.


tooltipToDatasetMap

HashMap<K,V> tooltipToDatasetMap
Map each dataset tooltip back to the given dataset.


vennDiagramResults

HashMap<K,V> vennDiagramResults
The current Venn diagram results/data.


groupNames

HashMap<K,V> groupNames
The current Venn diagram group names.


chartPanel

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


dialogParent

Frame dialogParent
The dialog parent.


lastSelectedFolder

String lastSelectedFolder
The last selected folder.


normalIcon

Image normalIcon
The normal icon for the parent dialog.


waitingIcon

Image waitingIcon
The icon to use when busy.


fontSizeValues

int fontSizeValues
The font size to use for the values.


fontSizeLegend

int fontSizeLegend
The font size to use for the legend.


showLegend

boolean showLegend
If true, the legend is shown.


legendDatasetAThreeWay

no.uib.jsparklines.data.XYDataPoint legendDatasetAThreeWay
The legend location of Dataset A in a one to three way Venn diagram.


legendDatasetBThreeWay

no.uib.jsparklines.data.XYDataPoint legendDatasetBThreeWay
The legend location of Dataset B in a one to three way Venn diagram.


legendDatasetCThreeWay

no.uib.jsparklines.data.XYDataPoint legendDatasetCThreeWay
The legend location of Dataset C in a one to three way Venn diagram.


legendDatasetAFourWay

no.uib.jsparklines.data.XYDataPoint legendDatasetAFourWay
The legend location of Dataset A in a four-way Venn diagram.


legendDatasetBFourWay

no.uib.jsparklines.data.XYDataPoint legendDatasetBFourWay
The legend location of Dataset B in a four-way Venn diagram.


legendDatasetCFourWay

no.uib.jsparklines.data.XYDataPoint legendDatasetCFourWay
The legend location of Dataset C in a four-way Venn diagram.


legendDatasetDFourWay

no.uib.jsparklines.data.XYDataPoint legendDatasetDFourWay
The legend location of Dataset D in a four-way Venn diagram.


backgroundPanel

JPanel backgroundPanel

contextMenuPlotBackgroundPanel

JPanel contextMenuPlotBackgroundPanel

dataPanel

JPanel dataPanel

datasetAColorJPanel

JPanel datasetAColorJPanel

datasetAScrollPane

JScrollPane datasetAScrollPane

datasetATextArea

JTextArea datasetATextArea

datasetATextField

JTextField datasetATextField

datasetBColorJPanel

JPanel datasetBColorJPanel

datasetBScrollPane

JScrollPane datasetBScrollPane

datasetBTextArea

JTextArea datasetBTextArea

datasetBTextField

JTextField datasetBTextField

datasetCColorJPanel

JPanel datasetCColorJPanel

datasetCScrollPane

JScrollPane datasetCScrollPane

datasetCTextArea

JTextArea datasetCTextArea

datasetCTextField

JTextField datasetCTextField

datasetDColorJPanel

JPanel datasetDColorJPanel

datasetDScrollPane

JScrollPane datasetDScrollPane

datasetDTextArea

JTextArea datasetDTextArea

datasetDTextField

JTextField datasetDTextField

exportPlotMenuItem

JMenuItem exportPlotMenuItem

fontSizeMenu

JMenu fontSizeMenu

jSeparator1

JPopupMenu.Separator jSeparator1

jSeparator2

JPopupMenu.Separator jSeparator2

legendCheckBoxMenuItem

JCheckBoxMenuItem legendCheckBoxMenuItem

legendFontSizeMenuItem

JMenuItem legendFontSizeMenuItem

legendLocationMenuItem

JMenuItem legendLocationMenuItem

plotHelpJButton

JButton plotHelpJButton

plotLayeredPane

JLayeredPane plotLayeredPane

plotOptionsJButton

JButton plotOptionsJButton

plotPanel

JPanel plotPanel

plotPopupMenu

JPopupMenu plotPopupMenu

valueFontSizeMenuItem

JMenuItem valueFontSizeMenuItem

xyPlotPanel

JPanel xyPlotPanel

Class com.compomics.util.gui.VennDiagramLegendLocationDialog extends JDialog implements Serializable

Serialized Fields

vennDiagramDialog

VennDiagramDialog vennDiagramDialog
The VennDiagramDialog parent.


legendShiftSize

double legendShiftSize
Legend shift size.


backgroundPanel

JPanel backgroundPanel

datasetALabel

JLabel datasetALabel

datasetBLabel

JLabel datasetBLabel

datasetCLabel

JLabel datasetCLabel

datasetDLabel

JLabel datasetDLabel

downDatasetAButton

JButton downDatasetAButton

downDatasetBButton

JButton downDatasetBButton

downDatasetCButton

JButton downDatasetCButton

downDatasetDButton

JButton downDatasetDButton

leftDatasetAButton

JButton leftDatasetAButton

leftDatasetBButton

JButton leftDatasetBButton

leftDatasetCButton

JButton leftDatasetCButton

leftDatasetDButton

JButton leftDatasetDButton

legendLocationPanel

JPanel legendLocationPanel

okButton

JButton okButton

rightDatasetAButton

JButton rightDatasetAButton

rightDatasetBButton

JButton rightDatasetBButton

rightDatasetCButton

JButton rightDatasetCButton

rightDatasetDButton

JButton rightDatasetDButton

shiftSizeLabel

JLabel shiftSizeLabel

shiftSizeSpinner

JSpinner shiftSizeSpinner

upDatasetAButton

JButton upDatasetAButton

upDatasetBButton

JButton upDatasetBButton

upDatasetCButton

JButton upDatasetCButton

upDatasetDButton

JButton upDatasetDButton

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

Serialized Fields

visibleTableColumnsDialogParent

VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
The VisibleTableColumnsDialogParent.


backgroundPanel

JPanel backgroundPanel

deselectAllMenuItem

JMenuItem deselectAllMenuItem

okButton

JButton okButton

selectAllMenuItem

JMenuItem selectAllMenuItem

selectJPopupMenu

JPopupMenu selectJPopupMenu

selectedColumnsTable

JTable selectedColumnsTable

selectedValuesTableScrollPane

JScrollPane selectedValuesTableScrollPane

Class com.compomics.util.gui.XYPlotFiltersDialog extends JDialog implements Serializable

Serialized Fields

xyPlottingDialog

XYPlottingDialog xyPlottingDialog
The XYPlottingDialog parent.


backgroundPanel

JPanel backgroundPanel

cancelButton

JButton cancelButton

filterTypesLabel

JLabel filterTypesLabel

filtersScrollPane

JScrollPane filtersScrollPane

filtersTable

JTable filtersTable

okButton

JButton okButton

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

Serialized Fields

progressDialog

ProgressDialogX progressDialog
The progress dialog.


tableModel

TableModel tableModel
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

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

Point dragStart
The starting location of the mouse dragging.


dragEnd

Point dragEnd
The ending location of the mouse dragging.


selectedDataPoints

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

HashMap<K,V> dataPointToRowNumber
The data point to model row number map.


selectedModelRows

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


cellRenderers

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


maxColumnWidths

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


minColumnWidths

HashMap<K,V> minColumnWidths
The minimum column widths for the table.


tableToolTips

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


colorGradient

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


histogramColor

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


lastSelectedFolder

String lastSelectedFolder
The last selected folder.


normalIcon

Image normalIcon
The normal icon for the parent dialog.


waitingIcon

Image waitingIcon
The icon to use when busy.


allTableColumns

ArrayList<E> allTableColumns
The table columns.


visibleColumns

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.


filters

HashMap<K,V> filters
The data filters.


colummnNames

Vector<E> colummnNames
The column names.


rowsAfterDataFiltering

ArrayList<E> rowsAfterDataFiltering
The rows remaining after applying the data filters.


backgroundPanel

JPanel backgroundPanel

binSizeSpinner

JSpinner binSizeSpinner

binsLabel

JLabel binsLabel

bubbleSizeComboBox

JComboBox bubbleSizeComboBox

bubbleSizeLabel

JLabel bubbleSizeLabel

colorLabel

JLabel colorLabel

colorsComboBox

JComboBox colorsComboBox

contextMenuPlotBackgroundPanel

JPanel contextMenuPlotBackgroundPanel

contextMenuSelectedValuesTableBackgroundPanel

JPanel contextMenuSelectedValuesTableBackgroundPanel

densityPlotRadioButton

JRadioButton densityPlotRadioButton

dragButtonGroup

ButtonGroup dragButtonGroup

dragSettingsPanel

JPanel dragSettingsPanel

dragToSelectRadioButton

JRadioButton dragToSelectRadioButton

dragToZoomRadioButton

JRadioButton dragToZoomRadioButton

editFiltersButton

JButton editFiltersButton

exportPlotMenuItem

JMenuItem exportPlotMenuItem

exportSelectedValuesMenuItem

JMenuItem exportSelectedValuesMenuItem

filterPanel

JPanel filterPanel

hideColumnsMenuItem

JMenuItem hideColumnsMenuItem

histogramRadioButton

JRadioButton histogramRadioButton

logAcisPanel

JPanel logAcisPanel

plotHelpJButton

JButton plotHelpJButton

plotLayeredPane

JLayeredPane plotLayeredPane

plotOptionsJButton

JButton plotOptionsJButton

plotPanel

JPanel plotPanel

plotPopupMenu

JPopupMenu plotPopupMenu

plotTypeButtonGroup

ButtonGroup plotTypeButtonGroup

plotTypePanel

JPanel plotTypePanel

regressionLineCheckBoxMenuItem

JCheckBoxMenuItem regressionLineCheckBoxMenuItem

selectedValuesLayeredPane

JLayeredPane selectedValuesLayeredPane

selectedValuesPanel

JPanel selectedValuesPanel

selectedValuesScrollPane

JScrollPane selectedValuesScrollPane

selectedValuesTable

JTable selectedValuesTable

selectedValuesTableHelpJButton

JButton selectedValuesTableHelpJButton

selectedValuesTableOptionsJButton

JButton selectedValuesTableOptionsJButton

selectedValuesTablePopupMenu

JPopupMenu selectedValuesTablePopupMenu

sizeLogCheckBox

JCheckBox sizeLogCheckBox

xAxisComboBox

JComboBox xAxisComboBox

xAxisLabel

JLabel xAxisLabel

xAxisLogCheckBox

JCheckBox xAxisLogCheckBox

xAxisPanel

JPanel xAxisPanel

xyPlotPanel

JPanel xyPlotPanel

xyPlotRadioButton

JRadioButton xyPlotRadioButton

yAxisComboBox

JComboBox yAxisComboBox

yAxisLabel

JLabel yAxisLabel

yAxisLogCheckBox

JCheckBox yAxisLogCheckBox

Package com.compomics.util.gui.error_handlers

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

Serialized Fields

selectionFolder

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


toolName

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


googleCodeToolName

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


toolVersion

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


logFile

File logFile
The log file to display.


backgroundPanel

JPanel backgroundPanel

clearJButton

JButton clearJButton

exitButton

JButton exitButton

infoJEditorPane

JEditorPane infoJEditorPane

infoJPanel

JPanel infoJPanel

infoJScrollPane

JScrollPane infoJScrollPane

logJPanel

JPanel logJPanel

logJScrollPane

JScrollPane logJScrollPane

logTxt

JTextArea logTxt

saveJButton

JButton saveJButton

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

Serialized Fields

frameParent

Frame frameParent
The parent of the parent is a Frame.


dialogParent

JDialog dialogParent
The parent of the parent is a JDialog.


backgroundPanel

JPanel backgroundPanel

closeJButton

JButton closeJButton

jScrollPane1

JScrollPane jScrollPane1

textJEditorPane

JEditorPane textJEditorPane

Package com.compomics.util.gui.export_graphics

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

Serialized Fields

chartPanel

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


graphicsPanel

Component graphicsPanel
The panel to export.


progressDialog

ProgressDialogX progressDialog
The progress dialog.


exportGraphicsDialogParent

ExportGraphicsDialogParent exportGraphicsDialogParent
The export graphics dialog parent.


frame

JFrame frame
The parent frame.


backgroundPanel

JPanel backgroundPanel

buttonGroup

ButtonGroup buttonGroup

cancelJButton

JButton cancelJButton

exportJButton

JButton exportJButton

pdfJRadioButton

JRadioButton pdfJRadioButton

plottingTypeJPanel

JPanel plottingTypeJPanel

pngJRadioButton

JRadioButton pngJRadioButton

svgJRadioButton

JRadioButton svgJRadioButton

tiffJRadioButton

JRadioButton tiffJRadioButton

Package com.compomics.util.gui.filehandling

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

Serialized Fields

fileMap

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

JButton cancelButton

fileList

JList fileList

fileListScrollPane

JScrollPane fileListScrollPane

helpLabel

JLabel helpLabel

okButton

JButton okButton

Package com.compomics.util.gui.gene_mapping

Class com.compomics.util.gui.gene_mapping.SpeciesDialog extends JDialog implements Serializable

Serialized Fields

goFactory

GOFactory goFactory
The GO factory.


geneFactory

GeneFactory geneFactory
The gene factory.


progressDialog

ProgressDialogX progressDialog
The progress dialog.


frameParent

JFrame frameParent
The frame parent, if any.


dialogParent

JDialog dialogParent
The dialog parent, if any.


waitingImage

Image waitingImage
The icon to display when waiting


normalImage

Image normalImage
The icon to display when processing is finished


genePreferences

GenePreferences genePreferences
The gene preferences


backgroundPanel

JPanel backgroundPanel

ensemblCategoryJComboBox

JComboBox ensemblCategoryJComboBox

ensemblVersionLabel

JLabel ensemblVersionLabel

jPanel1

JPanel jPanel1

okButton

JButton okButton

speciesJComboBox

JComboBox speciesJComboBox

unknownSpeciesLabel

JLabel unknownSpeciesLabel

updateMappingsButton

JButton updateMappingsButton

Package com.compomics.util.gui.isotopic_calculator

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

Serialized Fields

logger

org.apache.log4j.Logger logger

txtSequence

JTextArea txtSequence

lblComp

JLabel lblComp

lblMass

JLabel lblMass

calculateButton

JButton calculateButton

table1

AlternateRowColoursJTable table1

jpanContent

JPanel jpanContent

headerTable

JPanel headerTable

spectrumPanel

JPanel spectrumPanel

spinCharge

JSpinner spinCharge

lblPeptide

JLabel lblPeptide

iSequence

AASequenceImpl iSequence
The amino acid sequence


iElements

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.SequenceDbDetailsDialog extends JDialog implements Serializable

Serialized Fields

sequenceFactory

SequenceFactory sequenceFactory
The sequence factory.


lastSelectedFolder

String lastSelectedFolder
The last selected folder.


dbEditable

boolean dbEditable
boolean indicating whether the db can be changed.


waitingImage

Image waitingImage
The icon to display when waiting.


normalImange

Image normalImange
The normal icon.


parentFrame

Frame parentFrame
The parent frame.


utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences
The utilities user preferences.


accessionsSpinner

JSpinner accessionsSpinner

backgroundPanel

JPanel backgroundPanel

browseButton

JButton browseButton

cancelButton

JButton cancelButton

databaseHelpSettingsJLabel

JLabel databaseHelpSettingsJLabel

databaseInformationPanel

JPanel databaseInformationPanel

dbNameTxt

JTextField dbNameTxt

decoyButton

JButton decoyButton

decoyFlagTxt

JTextField decoyFlagTxt

decoyTagLabel

JLabel decoyTagLabel

fileTxt

JTextField fileTxt

jLabel1

JLabel jLabel1

lastModifiedLabel

JLabel lastModifiedLabel

lastModifiedTxt

JTextField lastModifiedTxt

nameLabel

JLabel nameLabel

okButton

JButton okButton

previewPanel

JPanel previewPanel

proteinLabel

JLabel proteinLabel

proteinTxt

JTextArea proteinTxt

proteinYxtScrollPane

JScrollPane proteinYxtScrollPane

sizeLabel

JLabel sizeLabel

sizeTxt

JTextField sizeTxt

targetDecoyTxt

JLabel targetDecoyTxt

typeCmb

JComboBox typeCmb

typeLabel

JLabel typeLabel

versionLabel

JLabel versionLabel

versionTxt

JTextField versionTxt

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

Serialized Fields

fragmentIonRectangles

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

String[] iSequenceComponents
Elementary data for composing the Panel.


profiles

ArrayList<E> profiles
The list of modification profiles.


iBaseFont

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 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

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


selectedRowHtmlTagFontColor

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


notSelectedRowHtmlTagFontColor

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


defaultModsTableToolTips

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


userModsTableToolTips

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


searchPossibilities

ArrayList<E> searchPossibilities
The lines of the PTMs concerned by the search.


searchCurrentSelection

int searchCurrentSelection
The search current selection.


searchWelcomeText

String searchWelcomeText
The search text to display by default.


addUserPTM

JButton addUserPTM

defaultModificationsTable

JTable defaultModificationsTable

defaultModsPanel

JPanel defaultModsPanel

defaultModsScrollPane

JScrollPane defaultModsScrollPane

defaultPtmPopupMenu

JPopupMenu defaultPtmPopupMenu

deleteUserPTM

JButton deleteUserPTM

editDefaultPtmJMenuItem

JMenuItem editDefaultPtmJMenuItem

editUserPTM

JButton editUserPTM

editUserPtmJMenuItem

JMenuItem editUserPtmJMenuItem

findJLabel

JLabel findJLabel

modificationsEditorPanel

JPanel modificationsEditorPanel

modificationsHelpJButton

JButton modificationsHelpJButton

modificationsSplitPane

JSplitPane modificationsSplitPane

okButton

JButton okButton

searchIndexLabel

JLabel searchIndexLabel

searchInputTxt

JTextField searchInputTxt

searchNextButton

JButton searchNextButton

searchPreviousButton

JButton searchPreviousButton

userModificationsTable

JTable userModificationsTable

userModsPanel

JPanel userModsPanel

userModsScrollPane

JScrollPane userModsScrollPane

userPtmPopupMenu

JPopupMenu userPtmPopupMenu

Class com.compomics.util.gui.ptm.PtmDialog extends 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

ArrayList<E> neutralLosses
The neutral losses.


reporterIons

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 whether the user can edit the PTM or not.


pattern

AminoAcidPattern pattern
The amino acid pattern of the modification


addNeutralLoss

JButton addNeutralLoss

addReporterIon

JButton addReporterIon

backgroundPanel

JPanel backgroundPanel

cancelButton

JButton cancelButton

detailsPanel

JPanel detailsPanel

helpJButton

JButton helpJButton

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

massLabel

JLabel massLabel

massTxt

JTextField massTxt

nameLabel

JLabel nameLabel

nameShortLabel

JLabel nameShortLabel

nameShortTxt

JTextField nameShortTxt

nameTxt

JTextField nameTxt

neutralLossesAndReporterIonsPanel

JPanel neutralLossesAndReporterIonsPanel

neutralLossesJScrollPane

JScrollPane neutralLossesJScrollPane

neutralLossesTable

JTable neutralLossesTable

okButton

JButton okButton

olsJButton

JButton olsJButton

patternLabel

JLabel patternLabel

psiModMappingJTextField

JTextField psiModMappingJTextField

psiModMappingPanel

JPanel psiModMappingPanel

removeNeutralLoss

JButton removeNeutralLoss

removerReporterIon

JButton removerReporterIon

reporterIonsJScrollPane

JScrollPane reporterIonsJScrollPane

reporterIonsTable

JTable reporterIonsTable

residuesTxt

JTextField residuesTxt

typeCmb

JComboBox typeCmb

Package com.compomics.util.gui.renderers

Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends 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 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 JLabel implements Serializable

Serialized Fields

minXAxisValue

double minXAxisValue
The minimum x-axis value.


maxXAxisValue

double maxXAxisValue
The maxium x-axis value.


delegate

TableCellRenderer delegate
A reference to a standard table cell renderer.

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

Serialized Fields

logger

org.apache.log4j.Logger logger

Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends BasicComboBoxRenderer implements Serializable

Serialized Fields

tooltips

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 maximum 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.searchsettings

Class com.compomics.util.gui.searchsettings.EnzymeSelectionDialog extends JDialog implements Serializable

Serialized Fields

enzymeFactory

EnzymeFactory enzymeFactory
The enzyme factory.


selectionCanceled

boolean selectionCanceled
True of the enzyme selection was canceled by the user.


backgroundPanel

JPanel backgroundPanel

cancelButton

JButton cancelButton

enzymeLabel

JLabel enzymeLabel

enzymesCmb

JComboBox enzymesCmb

mappingPanel

JPanel mappingPanel

okButton

JButton okButton

prideEnzymeNameLabel

JLabel prideEnzymeNameLabel

prideEnzymeNameTextField

JTextField prideEnzymeNameTextField

Class com.compomics.util.gui.searchsettings.SearchSettingsDialog extends JDialog implements Serializable

Serialized Fields

sequenceFactory

SequenceFactory sequenceFactory
The sequence factory.


enzymeFactory

EnzymeFactory enzymeFactory
The enzyme factory.


forwardIons

String[] forwardIons
Convenience array for forward ion type selection.


rewindIons

String[] rewindIons
Convenience array for rewind ion type selection.


ptmFactory

PTMFactory ptmFactory
The post translational modifications factory.


parametersFile

File parametersFile
The parameter file.


searchSettingsDialogParent

SearchSettingsDialogParent searchSettingsDialogParent
The SearchSettingsDialogParent.


searchParameters

SearchParameters searchParameters

modificationTableToolTips

ArrayList<E> modificationTableToolTips
The modification table column header tooltips.


parentFrame

JFrame parentFrame
The dialog parent frame.


normalIcon

Image normalIcon
The normal dialog icon.


waitingIcon

Image waitingIcon
The waiting dialog icon.


addFixedModification

JButton addFixedModification

addVariableModification

JButton addVariableModification

availableModsPanel

JPanel availableModsPanel

backgroundPanel

JPanel backgroundPanel

browseConfigurationButton2

JButton browseConfigurationButton2

cancelButton

JButton cancelButton

configurationFileLbl2

JLabel configurationFileLbl2

configurationFilePanelSettings

JPanel configurationFilePanelSettings

configurationFileTxt_parameters

JTextField configurationFileTxt_parameters

dataBasePanelSettings

JPanel dataBasePanelSettings

databaseSettingsLbl

JLabel databaseSettingsLbl

databaseSettingsTxt

JTextField databaseSettingsTxt

editDatabaseSettings

JButton editDatabaseSettings

enzymeLabel

JLabel enzymeLabel

enzymesCmb

JComboBox enzymesCmb

fixedModificationsLabel

JLabel fixedModificationsLabel

fixedModsJScrollPane

JScrollPane fixedModsJScrollPane

fixedModsTable

JTable fixedModsTable

fragmentIon1Cmb

JComboBox fragmentIon1Cmb

fragmentIon2Cmb

JComboBox fragmentIon2Cmb

fragmentIonAccuracyTxt

JTextField fragmentIonAccuracyTxt

fragmentIonLbl

JLabel fragmentIonLbl

fragmentIonType1Lbl

JLabel fragmentIonType1Lbl

jPanel8

JPanel jPanel8

jPanel9

JPanel jPanel9

maxMissedCleavagesLabel

JLabel maxMissedCleavagesLabel

maxPrecursorChargeTxt

JTextField maxPrecursorChargeTxt

minPrecursorChargeTxt

JTextField minPrecursorChargeTxt

missedCleavagesTxt

JTextField missedCleavagesTxt

modificationTypesSplitPane

JSplitPane modificationTypesSplitPane

modificationsJScrollPane

JScrollPane modificationsJScrollPane

modificationsLayeredPane

JLayeredPane modificationsLayeredPane

modificationsListCombo

JComboBox modificationsListCombo

modificationsPanel

JPanel modificationsPanel

modificationsTable

JTable modificationsTable

okButton

JButton okButton

openDialogHelpJButton1

JButton openDialogHelpJButton1

openModificationSettingsJButton

JButton openModificationSettingsJButton

precursorChargeLbl

JLabel precursorChargeLbl

precursorChargeRangeLabel

JLabel precursorChargeRangeLabel

precursorIonAccuracyTxt

JTextField precursorIonAccuracyTxt

precursorIonLbl

JLabel precursorIonLbl

precursorIonUnit

JComboBox precursorIonUnit

proteaseAndFragmentationPanel

JPanel proteaseAndFragmentationPanel

removeFixedModification

JButton removeFixedModification

removeVariableModification

JButton removeVariableModification

saveConfiguration

JButton saveConfiguration

saveConfigurationAs

JButton saveConfigurationAs

variableModificationsLabel

JLabel variableModificationsLabel

variableModsJScrollPane

JScrollPane variableModsJScrollPane

variableModsTable

JTable variableModsTable

Package com.compomics.util.gui.spectrum

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

Serialized Fields

iChromatogramColor

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


iChromatogramPointColor

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

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

Serialized Fields

currentFragmentIonTypes

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

ArrayList<E> tooltips
The table tooltips.


currentPeptide

Peptide currentPeptide
The current peptide.


peptideSequence

String peptideSequence
The current peptide sequence.


allAnnotations

ArrayList<E> allAnnotations
The spectrum annotations map.


allSpectra

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

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

Serialized Fields

peakWidth

float peakWidth
The width used for the annotated peaks.


backgroundPeakWidth

float backgroundPeakWidth
The width used for the background peaks.


subscriptAnnotationNumbers

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


peakWaterMarkColor

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

String scientificPattern
The number format pattern for scientific annotation.


referenceAreasXAxis

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


referenceAreasYAxis

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.


dataSetCounter

int dataSetCounter
The number of datasets currently displayed in the panel.


dataSetCounterMirroredSpectra

int dataSetCounterMirroredSpectra
The number of mirrored datasets currently displayed in the panel.


INTERACTIVE_STATUS

int INTERACTIVE_STATUS
This status indicates that no annotation will be displayed, but the user will have a fully functional interface (point clicking, selecting, sequencing etc.)


ANNOTATED_STATUS

int ANNOTATED_STATUS
This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out.


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 searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.


iXAxisLabel

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


iYAxisLabel

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


iFilenameColor

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


iDataPointAndLineColor

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


iDataPointAndLineColorMirroredSpectra

ArrayList<E> iDataPointAndLineColorMirroredSpectra
Colors in which the data points and peaks are rendered for the mirrored spectra. Indexed by dataset.


iAreaUnderCurveColor

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


iAreaUnderCurveColorMirroredSpectra

ArrayList<E> iAreaUnderCurveColorMirroredSpectra
Colors in which the chromatogram polyline is rendered for the mirrored spectra. Indexed by dataset.


iPointSize

Integer iPointSize
Size for the point on a polygon.


iFilename

String iFilename
The spectrum or chromatogram filename.


iFilenameMirrorredSpectrum

String iFilenameMirrorredSpectrum
The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.


iSpecPanelListeners

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

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.


iXAxisDataMirroredSpectrum

ArrayList<E> iXAxisDataMirroredSpectrum
All the x-axis data points for the mirrored spectrum. 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

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 values 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.


iYAxisDataMirroredSpectrum

ArrayList<E> iYAxisDataMirroredSpectrum
All the y-axis values for the mirrored spectra. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values 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.


iPrecursorMZMirroredSpectrum

double iPrecursorMZMirroredSpectrum
This variable holds the precursor M/Z for the mirrored spectrum.


iPrecursorCharge

String iPrecursorCharge
This String holds the charge for the precursor.


iPrecursorChargeMirorredSpectrum

String iPrecursorChargeMirorredSpectrum
This String holds the charge for the precursor for the mirrored spectrum.


iXAxisDataInPixels

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

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).


iXAxisDataInPixelsMirroredSpectrum

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


iYAxisDataInPixelsMirroredSpectrum

ArrayList<E> iYAxisDataInPixelsMirroredSpectrum
This array will hold the y-coordinates in pixels for all the y-axis values of the mirrored spectrum. 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

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


iClickedListDatasetIndices

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


iStoredSequence

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


iStoredSequenceDatasetIndices

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


iAnnotations

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


iMinDrag

int iMinDrag
Minimal dragging distance in pixels.


iCurrentDrawStyle

GraphicsPanel.DrawingStyle iCurrentDrawStyle
This variable holds the current 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 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 DefaultTableModel implements Serializable

Serialized Fields

ionMap

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


keys

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

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


aSpectrumProfileModeLineColor

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


peptideSequences

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


peptideCharges

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


iElements

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

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

Serialized Fields

useRelativeError

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


currentFragmentIons

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

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 JPanel implements Serializable

Serialized Fields

annotations

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


currentFragmentIons

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

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 JPanel implements Serializable

Serialized Fields

tooltipRectangles

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


iSequenceComponents

String[] iSequenceComponents
Elementary data for composing the Panel.


iIonMatches

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 fragment ion.


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 fragment ion.


iBaseFont

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

Color forwardColor
Color for the forward ion


rewindColor

Color rewindColor
Color for the rewind ion

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

Serialized Fields

spectrumPeakColor

Color spectrumPeakColor
The color used for the peaks. Default to red.


spectrumProfileModeLineColor

Color spectrumProfileModeLineColor
The color used for the profile mode spectra. Defaults to pink.


Package com.compomics.util.gui.tablemodels

Class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel extends DefaultTableModel implements Serializable

Serialized Fields

rowStartLoading

int rowStartLoading
The view start index of the rows being loaded.


rowEndLoading

int rowEndLoading
The view end index of the rows being loaded.


selfUpdating

boolean selfUpdating
If false, the table will not update automatically.


updateScheduled

boolean updateScheduled
boolean indicating whether an update was scheduled.


lastLoadingRunnable

com.compomics.util.gui.tablemodels.SelfUpdatingTableModel.LoadingRunnable lastLoadingRunnable
The last loading runnable.


viewIndexes

ArrayList<E> viewIndexes
List of view indexes.


lastColumnSorted

int lastColumnSorted
Indicates which column was last changed.


sortAscending

boolean sortAscending
If true the current sorting is ascending.


unsorted

boolean unsorted
If true the table has not yet been sorted.


progressDialog

ProgressDialogX progressDialog
A progress dialog.


Package com.compomics.util.gui.utils

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iConnections

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

JComboBox cmbConfigurations

txtDriver

JTextField txtDriver

txtUrl

JTextField txtUrl

txtUser

JTextField txtUser

txtPassword

JPasswordField txtPassword

btnOK

JButton btnOK

btnCancel

JButton btnCancel

iTarget

Connectable iTarget

iPropsFile

String iPropsFile

iLastInitiatedConfiguration

String iLastInitiatedConfiguration

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

Serialized Fields

iSelectedCalendar

Calendar iSelectedCalendar

iShownCalendar

Calendar iShownCalendar

iSelectedDayIndex

int iSelectedDayIndex

lblDayNames

JLabel[] lblDayNames

lblDays

JLabel[] lblDays

iDays

Integer[] iDays

lblCurrentMonthYear

JLabel lblCurrentMonthYear

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

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iProgress

JProgressBar iProgress

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

Serialized Fields

doNothingOnClose

boolean doNothingOnClose
If set to true, trying to close the progress 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 possible 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 whether the process has been completed.


waitingIcon

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


normalIcon

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


waitingHandlerParentFrame

Frame waitingHandlerParentFrame
The waitingHandlerParent frame.


waitingHandlerParentDialog

JDialog waitingHandlerParentDialog
The waitingHandlerParent dialog.


waitingActionListener

WaitingActionListener waitingActionListener
The waiting action listener.


progressBar

JProgressBar progressBar

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

Serialized Fields

dialog

JDialog dialog
Needed for the shaking feature.


naturalLocation

Point naturalLocation
Used in the shaking feature.


shakeTimer

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

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


currentTipIndex

int currentTipIndex
The current tip index.


lastSelectedFolder

String lastSelectedFolder
The last selected folder


waitingIcon

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


normalIcon

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


waitingHandlerParent

Frame waitingHandlerParent
The waitingHandlerParent.


shakeWhenFinished

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


processName

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


toolName

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


toolVersion

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


waitingActionListener

WaitingActionListener waitingActionListener
The waiting action listener.


backgroundPanel

JPanel backgroundPanel

closeDialogWhenImportCompletesCheckBox

JCheckBox closeDialogWhenImportCompletesCheckBox

closeJButton

JButton closeJButton

layeredPane

JLayeredPane layeredPane

nextJButton

JButton nextJButton

okButton

JButton okButton

processProgressPanel

JPanel processProgressPanel

progressBar

JProgressBar progressBar

reportArea

JTextArea reportArea

reportAreaScrollPane

JScrollPane reportAreaScrollPane

saveReportLabel

JLabel saveReportLabel

secondaryJProgressBar

JProgressBar secondaryJProgressBar

secondaryProgressBarSplitPane

JSplitPane secondaryProgressBarSplitPane

showTipOfTheDayCheckBox

JCheckBox showTipOfTheDayCheckBox

tempJProgressBar

JProgressBar tempJProgressBar

tipOfTheDayEditorPane

JEditorPane tipOfTheDayEditorPane

tipOfTheDayJPanel

JPanel tipOfTheDayJPanel

tipOfTheDayLayeredPane

JLayeredPane tipOfTheDayLayeredPane

tipOfTheDayScrollPane

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 IOException implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

Package com.compomics.util.preferences

Class com.compomics.util.preferences.AnnotationPreferences extends 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

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

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.GenePreferences extends Object implements Serializable

serialVersionUID: -1286840382594446279L

Serialized Fields

currentSpecies

String currentSpecies
The current species. Used for the gene mappings.


currentSpeciesType

String currentSpeciesType
The current species type. Used for the gene mappings.


goDomainMap

HashMap<K,V> goDomainMap
The GO domain map. e.g., key: GO term: GO:0007568, element: biological_process.


speciesMap

HashMap<K,V> speciesMap
Deprecated. use
The species map, key: latin name, element: ensembl database name, e.g., key: Homo sapiens, element: hsapiens_gene_ensembl.


allSpeciesMap

HashMap<K,V> allSpeciesMap
The species map. Main key: Ensembl type, e.g., Vertebrates or Plants. Next level: key: latin name, element: ensembl database name, e.g., key: Homo sapiens, element: hsapiens_gene_ensembl.


ensemblVersionsMap

HashMap<K,V> ensemblVersionsMap
The Ensembl versions for the downloaded species.


availableSpecies

ArrayList<E> availableSpecies
Deprecated. use allSpecies instead
The list of species.


allSpecies

HashMap<K,V> allSpecies
Map of all the species.


species

Vector<E> species
Deprecated. 
Old vector of species.

Class com.compomics.util.preferences.IdFilter extends Object implements Serializable

serialVersionUID: 8416219001106063781L

Serialized Fields

minPepLength

int minPepLength
The minimal peptide length allowed.


maxPepLength

int maxPepLength
The maximal peptide length allowed.


mascotMaxEvalue

double mascotMaxEvalue
Mascot maximal e-value allowed.


omssaMaxEvalue

double omssaMaxEvalue
OMSSA maximal e-value allowed.


xtandemMaxEvalue

double xtandemMaxEvalue
X!Tandem maximal e-value allowed.


maxMassDeviation

double maxMassDeviation
The maximal m/z deviation allowed.


isPpm

boolean isPpm
Boolean indicating the unit of the allowed m/z deviation (true: ppm, false: Da).


unknownPtm

boolean unknownPtm
Boolean indicating whether peptides presenting unknown PTMs should be ignored.

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

serialVersionUID: 342611308111304721L

Serialized Fields

modificationNames

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


fixedModifications

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


variableModifications

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


refinementModifications

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


omssaIndexes

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


colors

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


backUp

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

Class com.compomics.util.preferences.ProcessingPreferences extends Object implements Serializable

serialVersionUID: -5883143685674607162L

Serialized Fields

aScore

boolean aScore
Deprecated. use the PTM scoring preferences instead
Boolean indicating whether the A-score should be estimated.


proteinFDR

double proteinFDR
The default protein FDR.


peptideFDR

double peptideFDR
The default peptide FDR.


psmFDR

double psmFDR
The default PSM FDR.


proteinConfidenceMwPlots

Double proteinConfidenceMwPlots
The minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.

Class com.compomics.util.preferences.PTMScoringPreferences extends Object implements Serializable

serialVersionUID: -6656074270981104708L

Serialized Fields

aScoreCalculation

boolean aScoreCalculation
Boolean indicating whether the A-score should be calculated.


aScoreNeutralLosses

boolean aScoreNeutralLosses
Boolean indicating whether neutral losses shall be accounted in the calculation of the A-score.


flr

double flr
the FLR threshold in percent

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

serialVersionUID: -4343570286224891504L

Serialized Fields

spectrumAnnotatedPeakWidth

Float spectrumAnnotatedPeakWidth
The width to use for the annotated peaks.


spectrumBackgroundPeakWidth

Float spectrumBackgroundPeakWidth
The width to use for the background peaks.


spectrumAnnotatedPeakColor

Color spectrumAnnotatedPeakColor
The color to use for the annotated peaks.


spectrumBackgroundPeakColor

Color spectrumBackgroundPeakColor
The color to use for the background peaks.


sparklineColorValidated

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


sparklineColorNonValidated

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


sparklineColorNotFound

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


sparklineColorPossible

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


peptideSelected

Color peptideSelected
The color of the selected peptide.


memoryPreference

int memoryPreference
The memory to use by PeptideShaker.


searchGuiPath

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

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


reporterPath

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


relimsPath

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


localPrideFolder

String localPrideFolder
The local PRIDE projects folder.


dbFolder

File dbFolder
The user last used database folder.


favoriteDBs

ArrayList<E> favoriteDBs
The user last used databases.


Package com.compomics.util.preferences.gui

Class com.compomics.util.preferences.gui.ImportSettingsDialog extends JDialog implements Serializable

Serialized Fields

editable

boolean editable
If true the user can edit the settings.


userFilter

IdFilter userFilter
The identification filter set by the user. Null if cancel was pressed.


originalFilter

IdFilter originalFilter
The original filter


backgroundPanel

JPanel backgroundPanel

cancelButton

JButton cancelButton

filterPanel

JPanel filterPanel

helpJButton

JButton helpJButton

mascotEValueLabel

JLabel mascotEValueLabel

mascotEvalueTxt

JTextField mascotEvalueTxt

nAAmaxTxt

JTextField nAAmaxTxt

nAAminTxt

JTextField nAAminTxt

okButton

JButton okButton

omssaEValueLabel

JLabel omssaEValueLabel

omssaEvalueTxt

JTextField omssaEvalueTxt

peptideLengthLabel

JLabel peptideLengthLabel

peptideLengthRangeLabel

JLabel peptideLengthRangeLabel

precDevTxt

JTextField precDevTxt

precursorAccuracyLabel

JLabel precursorAccuracyLabel

ptmsCheck

JCheckBox ptmsCheck

unitCmb

JComboBox unitCmb

xtandemEValueLabel

JLabel xtandemEValueLabel

xtandemEvalueTxt

JTextField xtandemEvalueTxt

Class com.compomics.util.preferences.gui.ProcessingPreferencesDialog extends JDialog implements Serializable

Serialized Fields

processingPreferences

ProcessingPreferences processingPreferences
The processing preferences.


ptmScoringPreferences

PTMScoringPreferences ptmScoringPreferences
The PTM preferences. This deserves to be modifiable after import of the files as well.


aScoreLabel

JLabel aScoreLabel

ascoreCmb

JComboBox ascoreCmb

backgroundPanel

JPanel backgroundPanel

estimateAScoreLabel

JLabel estimateAScoreLabel

flrTxt

JTextField flrTxt

fractionsPanel

JPanel fractionsPanel

neutralLossesCmb

JComboBox neutralLossesCmb

neutralLossesLabel

JLabel neutralLossesLabel

okButton

JButton okButton

peptideFdrLabel

JLabel peptideFdrLabel

peptideFdrTxt

JTextField peptideFdrTxt

percentLabel

JLabel percentLabel

percentLabel1

JLabel percentLabel1

percentLabel2

JLabel percentLabel2

percentLabel3

JLabel percentLabel3

percentLabel4

JLabel percentLabel4

processingParamsPanel

JPanel processingParamsPanel

proteinConfidenceMwTxt

JTextField proteinConfidenceMwTxt

proteinFdrLabel

JLabel proteinFdrLabel

proteinFdrTxt

JTextField proteinFdrTxt

proteinMwLabel

JLabel proteinMwLabel

psmFdrLabel

JLabel psmFdrLabel

psmFdrTxt

JTextField psmFdrTxt

ptmScoringPanel

JPanel ptmScoringPanel

Package com.compomics.util.pride

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

serialVersionUID: -2890434198335005181L

Serialized Fields

ontology

String ontology
The ontology.


accession

String accession
The accession number.


name

String name
The name/term.


value

String value
The value for the given term.

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

serialVersionUID: 7368502853292052566L

Serialized Fields

modToCvMap

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 Object implements Serializable

serialVersionUID: -9182316910747747823L

Serialized Fields

name

String name
The contact's name.


eMail

String eMail
The contact's e-mail.


institution

String institution
The contact's institution.

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

serialVersionUID: -9182316910747747823L

Serialized Fields

contacts

ArrayList<E> contacts
The contacts.


groupName

String groupName
The contact group name.

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

serialVersionUID: -8802861658166703745L

Serialized Fields

name

String name
The instrument name.


cvTerms

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 Object implements Serializable

serialVersionUID: -9045298216154032632L

Serialized Fields

name

String name
The protcol name.


cvTerms

ArrayList<E> cvTerms
The list of CV terms.

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

serialVersionUID: -5449836209751629549L

Serialized Fields

reference

String reference
The reference text.


pmid

String pmid
The PubMed ID.


doi

String doi
The Digital Object Identifier.

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

serialVersionUID: -9182316910747747823L

Serialized Fields

references

ArrayList<E> references
The references.


groupName

String groupName
The reference group name.

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

serialVersionUID: -7142471175737857227L

Serialized Fields

name

String name
The sample name.


cvTerms

ArrayList<E> cvTerms
The list of CV terms.


Package com.compomics.util.protein

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

serialVersionUID: 7665784733371863163L

Serialized Fields

iID

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

String iForeignID
The foreign ID is the ID of another database this entry is originally 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

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

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

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.


iDescriptionShort

String iDescriptionShort
A short protein description, removing all but the protein description itself. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" becomes "78 kDa glucose-regulated protein".


iDescriptionProteinName

String iDescriptionProteinName
Protein name, the protein name extracted from the protein description. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" returns "GRP78_HUMAN".


iGeneName

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


iProteinEvidence

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


iTaxonomy

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


iForeignDescription

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

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

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 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 AbstractTableModel implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

model

TableModel model

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

Serialized Fields

logger

org.apache.log4j.Logger logger

indexes

int[] indexes

sortingColumns

Vector<E> sortingColumns

ascending

boolean ascending

compares

int compares

listMouseListener

MouseAdapter listMouseListener



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