Serialized Form


Package com.compomics.util

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iEvenRowColor

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


iUnevenRowColor

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


Package com.compomics.util.db

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iColCount

int iColCount
The number of columns in this resultset.


iRowCount

int iRowCount
The number of rows in this resultset.


iColNames

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


iData

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

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iNested

java.lang.Exception iNested
The nested exception.


Package com.compomics.util.examples

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

Serialized Fields

closeJButton

javax.swing.JButton closeJButton

jScrollPane1

javax.swing.JScrollPane jScrollPane1

textJEditorPane

javax.swing.JEditorPane textJEditorPane

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

Serialized Fields

peffAnnotationsColorMap

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


peffAnnotationsTooltipMap

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


peffFormat

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


keyValuePairs

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


currentSequenceFile

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


currentPeffBufferedReader

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


currentSequence

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


currentSequenceLine

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


linkedSpectrumPanels

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


allAnnotations

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


spectrumAPanel

SpectrumPanel spectrumAPanel
The first spectrum panel.


spectrumBPanel

SpectrumPanel spectrumBPanel
The second spectrum panel


spectrumPanelMaxPadding

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


chromatogramPanelMaxPadding

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


mascotEnzymeReader

MascotEnzymeReader mascotEnzymeReader
Used to read the enzyme details from file.


cleanProteinSequence

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


selectedAnnotationTypes

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


sequenceAnnotationColumnHeaderTooltips

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


sparklineColor

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


H2OIonsJCheckBox

javax.swing.JCheckBox H2OIonsJCheckBox

NH3IonsJCheckBox

javax.swing.JCheckBox NH3IonsJCheckBox

aIonsJCheckBox

javax.swing.JCheckBox aIonsJCheckBox

allPeaksJCheckBox

javax.swing.JCheckBox allPeaksJCheckBox

bIonsJCheckBox

javax.swing.JCheckBox bIonsJCheckBox

browseJButton

javax.swing.JButton browseJButton

cIonsJCheckBox

javax.swing.JCheckBox cIonsJCheckBox

chargeOneJCheckBox

javax.swing.JCheckBox chargeOneJCheckBox

chargeOverTwoJCheckBox

javax.swing.JCheckBox chargeOverTwoJCheckBox

chargePeptideAJSpinner

javax.swing.JSpinner chargePeptideAJSpinner

chargePeptideBJSpinner

javax.swing.JSpinner chargePeptideBJSpinner

chargeTwoJCheckBox

javax.swing.JCheckBox chargeTwoJCheckBox

chromatogramAJPanel

javax.swing.JPanel chromatogramAJPanel

chromatogramJPanel

javax.swing.JPanel chromatogramJPanel

chromatogramPanelHelpJLabel

javax.swing.JLabel chromatogramPanelHelpJLabel

chromatogramPanelInfoJLabel

javax.swing.JLabel chromatogramPanelInfoJLabel

enzymesJComboBox

javax.swing.JComboBox enzymesJComboBox

exportJButton

javax.swing.JButton exportJButton

inSilicoDigestionHelpJLabel

javax.swing.JLabel inSilicoDigestionHelpJLabel

informationJEditorPane

javax.swing.JEditorPane informationJEditorPane

informationJPanel

javax.swing.JPanel informationJPanel

informationJScrollPane

javax.swing.JScrollPane informationJScrollPane

inhibitorsJTextField

javax.swing.JTextField inhibitorsJTextField

ionSelectionJPanel

javax.swing.JPanel ionSelectionJPanel

isotopicDistributionAJPanel

javax.swing.JPanel isotopicDistributionAJPanel

isotopicDistributionCalculatorHelpJLabel

javax.swing.JLabel isotopicDistributionCalculatorHelpJLabel

isotopicDistributionCalculatorInfoJLabel

javax.swing.JLabel isotopicDistributionCalculatorInfoJLabel

isotopicDistributionJPanel

javax.swing.JPanel isotopicDistributionJPanel

jLabel1

javax.swing.JLabel jLabel1

jLabel10

javax.swing.JLabel jLabel10

jLabel11

javax.swing.JLabel jLabel11

jLabel12

javax.swing.JLabel jLabel12

jLabel13

javax.swing.JLabel jLabel13

jLabel14

javax.swing.JLabel jLabel14

jLabel15

javax.swing.JLabel jLabel15

jLabel16

javax.swing.JLabel jLabel16

jLabel17

javax.swing.JLabel jLabel17

jLabel18

javax.swing.JLabel jLabel18

jLabel19

javax.swing.JLabel jLabel19

jLabel2

javax.swing.JLabel jLabel2

jLabel20

javax.swing.JLabel jLabel20

jLabel21

javax.swing.JLabel jLabel21

jLabel24

javax.swing.JLabel jLabel24

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jLabel5

javax.swing.JLabel jLabel5

jLabel6

javax.swing.JLabel jLabel6

jLabel7

javax.swing.JLabel jLabel7

jLabel8

javax.swing.JLabel jLabel8

jLabel9

javax.swing.JLabel jLabel9

jPanel1

javax.swing.JPanel jPanel1

jPanel10

javax.swing.JPanel jPanel10

jPanel11

javax.swing.JPanel jPanel11

jPanel12

javax.swing.JPanel jPanel12

jPanel2

javax.swing.JPanel jPanel2

jPanel3

javax.swing.JPanel jPanel3

jPanel4

javax.swing.JPanel jPanel4

jPanel5

javax.swing.JPanel jPanel5

jPanel6

javax.swing.JPanel jPanel6

jPanel7

javax.swing.JPanel jPanel7

jPanel8

javax.swing.JPanel jPanel8

jPanel9

javax.swing.JPanel jPanel9

jRadioButton1

javax.swing.JRadioButton jRadioButton1

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jScrollPane2

javax.swing.JScrollPane jScrollPane2

jScrollPane3

javax.swing.JScrollPane jScrollPane3

jSeparator1

javax.swing.JSeparator jSeparator1

jSeparator2

javax.swing.JSeparator jSeparator2

jSeparator3

javax.swing.JSeparator jSeparator3

jSeparator4

javax.swing.JSeparator jSeparator4

jSeparator5

javax.swing.JSeparator jSeparator5

jSeparator6

javax.swing.JSeparator jSeparator6

jSeparator9

javax.swing.JSeparator jSeparator9

jTabbedPane

javax.swing.JTabbedPane jTabbedPane

linkedSpectraJCheckBox

javax.swing.JCheckBox linkedSpectraJCheckBox

lowerMassJSpinner

javax.swing.JSpinner lowerMassJSpinner

missedCleavagesJSpinner

javax.swing.JSpinner missedCleavagesJSpinner

nextJButton

javax.swing.JButton nextJButton

otherIonsJCheckBox

javax.swing.JCheckBox otherIonsJCheckBox

peffAnnotationsJTable

javax.swing.JTable peffAnnotationsJTable

peffHeaderJTable

javax.swing.JTable peffHeaderJTable

peptideAColorJPanel

javax.swing.JPanel peptideAColorJPanel

peptideACompositionJTextField

javax.swing.JTextField peptideACompositionJTextField

peptideAJScrollPane

javax.swing.JScrollPane peptideAJScrollPane

peptideAJXTable

org.jdesktop.swingx.JXTable peptideAJXTable

peptideAMzJTextField

javax.swing.JTextField peptideAMzJTextField

peptideBColorJPanel

javax.swing.JPanel peptideBColorJPanel

peptideBCompositionJTextField

javax.swing.JTextField peptideBCompositionJTextField

peptideBJScrollPane

javax.swing.JScrollPane peptideBJScrollPane

peptideBJXTable

org.jdesktop.swingx.JXTable peptideBJXTable

peptideBMzJTextField

javax.swing.JTextField peptideBMzJTextField

peptideSequenceAJTextField

javax.swing.JTextField peptideSequenceAJTextField

peptideSequenceBJTextField

javax.swing.JTextField peptideSequenceBJTextField

peptidesJPanel

javax.swing.JPanel peptidesJPanel

peptidesJTable

javax.swing.JTable peptidesJTable

peptidesScrollPane

javax.swing.JScrollPane peptidesScrollPane

positionJTextField

javax.swing.JTextField positionJTextField

profileSpectrumJCheckBox

javax.swing.JCheckBox profileSpectrumJCheckBox

proteinCoverageJScrollPane

javax.swing.JScrollPane proteinCoverageJScrollPane

proteinDigestionJLabel

javax.swing.JLabel proteinDigestionJLabel

proteinDigestionJPanel

javax.swing.JPanel proteinDigestionJPanel

proteinHeaderJTable

javax.swing.JTable proteinHeaderJTable

proteinSequenceCoverageJEditorPane

javax.swing.JEditorPane proteinSequenceCoverageJEditorPane

sequenceCoverageJPanel

javax.swing.JPanel sequenceCoverageJPanel

sequenceFileJTextField

javax.swing.JTextField sequenceFileJTextField

sequenceJTabbedPane

javax.swing.JTabbedPane sequenceJTabbedPane

silacLabelPeptideAJComboBox

javax.swing.JComboBox silacLabelPeptideAJComboBox

silacLabelPeptideBJComboBox

javax.swing.JComboBox silacLabelPeptideBJComboBox

siteJTextField

javax.swing.JTextField siteJTextField

spectraJPanel

javax.swing.JPanel spectraJPanel

spectrumAJPanel

javax.swing.JPanel spectrumAJPanel

spectrumBJPanel

javax.swing.JPanel spectrumBJPanel

spectrumJPanel

javax.swing.JPanel spectrumJPanel

spectrumPanelHelpJLabel

javax.swing.JLabel spectrumPanelHelpJLabel

spectrumPanelInfoJLabel

javax.swing.JLabel spectrumPanelInfoJLabel

upperMassJSpinner

javax.swing.JSpinner upperMassJSpinner

xIonsJCheckBox

javax.swing.JCheckBox xIonsJCheckBox

yIonsJCheckBox

javax.swing.JCheckBox yIonsJCheckBox

zIonsJCheckBox

javax.swing.JCheckBox zIonsJCheckBox

Package com.compomics.util.experiment

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

serialVersionUID: 4330394623824512352L

Serialized Fields

reference

java.lang.String reference
reference of the experiment


samples

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


analysis

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

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

serialVersionUID: -6738411343333889777L

Serialized Fields

index

int index
the analysis index


quantification

java.util.HashMap<K,V> quantification
Quantification results


identification

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

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

serialVersionUID: -5399187779025810060L

Serialized Fields

sample

Sample sample
The reference sample


analysis

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


Package com.compomics.util.experiment.biology

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

Serialized Fields

mass

double mass

name

java.lang.String name

letter

java.lang.String letter

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

serialVersionUID: -1852087173903613377L

Serialized Fields

id

int id

name

java.lang.String name

aminoAcidBefore

java.util.ArrayList<E> aminoAcidBefore

aminoAcidAfter

java.util.ArrayList<E> aminoAcidAfter

restrictionBefore

java.util.ArrayList<E> restrictionBefore

restrictionAfter

java.util.ArrayList<E> restrictionAfter

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

Serialized Fields

theoreticMass

double theoreticMass
Ion attribute - the theoretic mass


familyType

int familyType
Ion attribute - the ion family name

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

Serialized Fields

mass

double mass
The mass lost


name

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

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

serialVersionUID: 5632064601627536034L

Serialized Fields

sequence

java.lang.String sequence
The peptide sequence.


mass

java.lang.Double mass
The peptide mass.


parentProteins

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


modifications

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

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

serialVersionUID: 1987224639519365761L

Serialized Fields

accession

java.lang.String accession
The protein accession


decoy

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


sequence

java.lang.String sequence
The protein sequence


databaseType

Header.DatabaseType databaseType
The protein database type.

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

serialVersionUID: -545472596243822505L

Serialized Fields

type

int type
the modification type according to static field


residuesArray

java.util.ArrayList<E> residuesArray
the residues affected by this modification. '[' denotes N-term and ']' C-term


name

java.lang.String name
Name of the modification


shortName

java.lang.String shortName
Short name of the modification


mass

double mass
Mass difference produced by this modification


neutralLosses

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


reporterIons

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

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

serialVersionUID: 7935264190312934466L

Serialized Fields

ptmMap

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


defaultMods

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


userMods

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


omssaIndexes

java.util.HashMap<K,V> omssaIndexes
Map of omssa indexes

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

serialVersionUID: 303393644914835325L

Serialized Fields

reference

java.lang.String reference
sample reference


Package com.compomics.util.experiment.biology.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.Glycon extends Ion implements Serializable

Serialized Fields

theoreticMasses

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


name

java.lang.String name
Name of the glycon


shortName

java.lang.String shortName
Short name of the glycon

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

Serialized Fields

type

PeptideFragmentIon.PeptideFragmentIonType type
Type of ion


neutralLosses

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


number

int number
position of the ion in the peptide for peptide ions (for a, b, c, x, y and z ions)


residue

java.lang.String residue
Amino-acid generating the ion (for immonium ions)

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

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

Serialized Fields

name

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


Package com.compomics.util.experiment.identification

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

serialVersionUID: 4600458866001677754L

Serialized Fields

aaOccurences

java.util.HashMap<K,V> aaOccurences

totalAA

int totalAA

aaAfter

java.util.HashMap<K,V> aaAfter

totalAAAfter

java.util.HashMap<K,V> totalAAAfter

aaBefore

java.util.HashMap<K,V> aaBefore

totalAABefore

java.util.HashMap<K,V> totalAABefore

implementedAa

java.util.ArrayList<E> implementedAa

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

Serialized Fields

indexes

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


fileName

java.lang.String fileName
The FASTA file name


isDecoy

boolean isDecoy
Boolean indicating whether the database contains decoy sequences.


nTarget

int nTarget
Number of target sequences found in the database.

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

serialVersionUID: -2551700699384242554L

Serialized Fields

proteinIdentification

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


peptideIdentification

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


spectrumIdentification

java.util.ArrayList<E> spectrumIdentification
List of the keys of all imported psms.


proteinMap

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


methodUsed

int methodUsed
The method used.


cacheSize

int cacheSize
The cache size in number of matches. 20000 by default: should be enough to contain a velos file.


serializationDirectory

java.lang.String serializationDirectory
the directory where matches will be serialized


inMemory

boolean inMemory
boolean indicating whether the identification should be stored in memory or not. True by default, the serialization directory should be set. otherwise!


automatedMemoryManagement

boolean automatedMemoryManagement
boolean indicating whether the memory management should be done automatically. If true, the cache size will be extended to reach 90% of the available heap size when inMemory is wrong. True by default.


loadedMatchesMap

java.util.HashMap<K,V> loadedMatchesMap
Map of the loaded matches.


loadedMatches

java.util.ArrayList<E> loadedMatches
List of the loaded matches with the most used matches in the end.


modifiedMatches

java.util.HashMap<K,V> modifiedMatches
Map indicating whether a match is modified. Only modified matches will be serialized.


urParameters

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


longKeys

java.util.ArrayList<E> longKeys
Map of long keys which will be referenced by their index for file creation.

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

serialVersionUID: -9132138792119651421L

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

serialVersionUID: 4601179275244591663L

Serialized Fields

index

int index
index of the method

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

serialVersionUID: -4690159937753713106L

Serialized Fields

bBoundaries

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


yBoundaries

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

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

serialVersionUID: 3606509518581203063L

Serialized Fields

rank

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


peptide

Peptide peptide
The theoretic peptide


advocate

int advocate
The advocate


identificationCharge

Charge identificationCharge
The charge used for identification


eValue

double eValue
The e-value


file

java.lang.String file
the correspondig file


isDecoy

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


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

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

serialVersionUID: 1892975432623296983L

Serialized Fields

id

int id
index of the post-processor

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

serialVersionUID: 9162799394758139976L

Serialized Fields

id

int id
index of the search engine


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

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

serialVersionUID: -7242302146506873391L


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

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

serialVersionUID: 5753142782728884464L

Serialized Fields

peak

Peak peak
The matched peak


ion

Ion ion
The matching ion


charge

Charge charge
The supposed charge of the ion

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

serialVersionUID: 7129515983284796207L

Serialized Fields

theoreticPtm

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


variable

boolean variable
is the modification variable?


modifiedSite

int modifiedSite
the location in the peptide sequence

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

serialVersionUID: 7195830246336841081L

Serialized Fields

theoreticPeptide

Peptide theoreticPeptide
the theoretic peptide mathing


mainMatchKey

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


spectrumMatches

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


isDecoy

java.lang.Boolean isDecoy
is the peptide match a decoy hit

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

serialVersionUID: -6061842447053092696L

Serialized Fields

theoreticProtein

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


mainMatch

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


peptideMatches

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

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

serialVersionUID: 3227760855215444318L

Serialized Fields

spectrumKey

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


assumptions

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


bestAssumption

PeptideAssumption bestAssumption
The best assumption


firstHits

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


advocates

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


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

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

Serialized Fields

index

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


randomAccessFile

java.io.RandomAccessFile randomAccessFile
Andromeda result file in random access


fileName

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

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

Serialized Fields

inspectedFile

java.io.File inspectedFile
The inspected file.


iMascotDatfile

com.compomics.mascotdatfile.util.interfaces.MascotDatfileInf iMascotDatfile
Instance of the mascotdatfile parser.

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

Serialized Fields

identificationFile

java.io.File identificationFile
the inspected OMSSA omx file


modsFile

java.io.File modsFile
the modification file mods.xml


userModsFile

java.io.File userModsFile
the modification file usermods.xml


ptmFactory

PTMFactory ptmFactory
the PTM factory


omxFile

de.proteinms.omxparser.OmssaOmxFile omxFile
The instance of the inspected omx file

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

Serialized Fields

xTandemFile

de.proteinms.xtandemparser.xtandem.XTandemFile xTandemFile
the instance of the X!Tandem parser


modificationMap

de.proteinms.xtandemparser.xtandem.ModificationMap modificationMap
the modification map


proteinMap

de.proteinms.xtandemparser.xtandem.ProteinMap proteinMap
the protein map


peptideMap

de.proteinms.xtandemparser.xtandem.PeptideMap peptideMap
the peptide map


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

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

serialVersionUID: -5591103342266964263L

Serialized Fields

indexMap

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


spectrumTitles

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


fileName

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


maxRT

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


minRT

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


maxMz

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


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.


mz

double mz
The measured m/z of the precursor.


intensity

double intensity
The measured intensity of the precursor.


possibleCharges

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

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

serialVersionUID: 7152424141470431489L

Serialized Fields

spectrumTitle

java.lang.String spectrumTitle
Spectrum title.


fileName

java.lang.String fileName
Spectrum file name.


level

int level
The MS level.


peakList

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


scanNumber

java.lang.String scanNumber
Scan number or range.


scanStartTime

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


Package com.compomics.util.experiment.personalization

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

serialVersionUID: 1929697552061121072L

Serialized Fields

urParams

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


Package com.compomics.util.experiment.quantification

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

Serialized Fields

methodUsed

Quantification.QuantificationMethod methodUsed
The quantification method used


cacheSize

int cacheSize
The cache size in number of matches. 20000 by default: should be enough to contain a velos file.


serializationDirectory

java.lang.String serializationDirectory
the directory where matches will be serialized


inMemory

boolean inMemory
boolean indicating whether the identification should be stored in memory or not. True by default, the serialization directory should be set otherwise!


automatedMemoryManagement

boolean automatedMemoryManagement
boolean indicating whether the memory management should be done automatically. If true, the cache size will be extended to reach 90% of the available heap size when inMemory is wrong. True by default.


loadedMatchesMap

java.util.HashMap<K,V> loadedMatchesMap
Map of the loaded quantification matches


loadedMatches

java.util.ArrayList<E> loadedMatches
List of the loaded quantification matches with the most used matches in the end


modifiedMatches

java.util.HashMap<K,V> modifiedMatches
Map indicating whether a quantification match is modified. Only modified matches will be serialized.


urParameters

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


longKeys

java.util.ArrayList<E> longKeys
Map of long keys which will be referenced by their index for file creation


proteinQuantification

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


peptideQuantification

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


psmIDentificationToQuantification

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

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

Serialized Fields

referenceLabel

int referenceLabel
the reference label indexed by its corresponding reporter ion index


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.reporterion

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

Serialized Fields

ratios

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

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

Serialized Fields

sampleAssignement

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


referenceLabel

int referenceLabel
The reference label indexed by the reporter ion index


reporterMethod

ReporterIonQuantification.ReporterIonMethod reporterMethod
The reporter method

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

Serialized Fields

methods

java.util.ArrayList<E> methods

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

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

Serialized Fields

peptideKey

java.lang.String peptideKey
The identification peptide match


psmQuantification

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

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

Serialized Fields

proteinKey

java.lang.String proteinKey
The identification protein match key


peptideQuantification

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

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

Serialized Fields

spectrumKey

java.lang.String spectrumKey
The corresponding spectrum key


spectrumMatchKey

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


reporterMatches

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


deisotopedIntensities

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


Package com.compomics.util.experiment.refinementparameters

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

serialVersionUID: 1781298332459022056L

Serialized Fields

score

double score
The Mascot score


Package com.compomics.util.general

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

Serialized Fields

logger

org.apache.log4j.Logger logger

element

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


Package com.compomics.util.general.servlet

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

Serialized Fields

logger

org.apache.log4j.Logger logger

Package com.compomics.util.gui

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

Serialized Fields

logger

org.apache.log4j.Logger logger

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iMessages

java.lang.String[] iMessages

iThrowable

java.lang.Throwable iThrowable

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iData

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


txtData

javax.swing.JTextArea txtData

btnUnzip

javax.swing.JButton btnUnzip

btnSave

javax.swing.JButton btnSave

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

Serialized Fields

logger

org.apache.log4j.Logger logger

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iDateTimeFormat

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


iFrames

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


Package com.compomics.util.gui.dialogs

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iConnections

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


cmbConfigurations

javax.swing.JComboBox cmbConfigurations

txtDriver

javax.swing.JTextField txtDriver

txtUrl

javax.swing.JTextField txtUrl

txtUser

javax.swing.JTextField txtUser

txtPassword

javax.swing.JPasswordField txtPassword

btnOK

javax.swing.JButton btnOK

btnCancel

javax.swing.JButton btnCancel

iTarget

Connectable iTarget

iPropsFile

java.lang.String iPropsFile

iLastInitiatedConfiguration

java.lang.String iLastInitiatedConfiguration

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

Serialized Fields

iSelectedCalendar

java.util.Calendar iSelectedCalendar

iShownCalendar

java.util.Calendar iShownCalendar

iSelectedDayIndex

int iSelectedDayIndex

lblDayNames

javax.swing.JLabel[] lblDayNames

lblDays

javax.swing.JLabel[] lblDays

iDays

java.lang.Integer[] iDays

lblCurrentMonthYear

javax.swing.JLabel lblCurrentMonthYear

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iProgress

javax.swing.JProgressBar iProgress

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

Serialized Fields

progressDialogFrame

ProgressDialogParent progressDialogFrame
The progress dialog parent.


doNothingOnClose

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


progressBar

javax.swing.JProgressBar progressBar

Package com.compomics.util.gui.isotopic_calculator

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

Serialized Fields

logger

org.apache.log4j.Logger logger

txtSequence

javax.swing.JTextArea txtSequence

lblComp

javax.swing.JLabel lblComp

lblMass

javax.swing.JLabel lblMass

calculateButton

javax.swing.JButton calculateButton

table1

AlternateRowColoursJTable table1

jpanContent

javax.swing.JPanel jpanContent

headerTable

javax.swing.JPanel headerTable

spectrumPanel

javax.swing.JPanel spectrumPanel

spinCharge

javax.swing.JSpinner spinCharge

lblPeptide

javax.swing.JLabel lblPeptide

iSequence

AASequenceImpl iSequence
The amino acid sequence


iElements

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


iCharge

double iCharge
The charge


Package com.compomics.util.gui.protein

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

Serialized Fields

fragmentIonRectangles

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


iSequenceComponents

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


profiles

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


iBaseFont

java.awt.Font iBaseFont
The font to use.


iMaxBarHeight

double iMaxBarHeight
The maximum bar height.


iBarWidth

int iBarWidth
The width of the bars.


iHorizontalSpace

int iHorizontalSpace
The horizontal space.


iXStart

int iXStart
The x-axis start position.


iYStart

int iYStart
The y-axis start position.


isModifiedSequence

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


Package com.compomics.util.gui.renderers

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

Serialized Fields

align

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

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iData

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

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

Serialized Fields

minXAxisValue

double minXAxisValue
The minimum x-axis value.


maxXAxisValue

double maxXAxisValue
The maxium x-axis value.


delegate

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

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

Serialized Fields

logger

org.apache.log4j.Logger logger

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

Serialized Fields

tooltips

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


align

int align
The horizontal alignment of the text.


MAX_TOOLTIP_WIDTH

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


Package com.compomics.util.gui.spectrum

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

Serialized Fields

iChromatogramColor

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


iChromatogramPointColor

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

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

Serialized Fields

currentFragmentIonTypes

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


neutralLosses

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


singleCharge

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


twoCharges

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


tooltips

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


currentPeptide

Peptide currentPeptide
The current peptide.


peptideSequence

java.lang.String peptideSequence
The current peptide sequence.


allAnnotations

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


annotations

java.util.ArrayList<E> annotations
The spectrum annotations map when using more then one map.


allSpectra

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

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

Serialized Fields

subscriptAnnotationNumbers

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


peakWaterMarkColor

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


scientificXAxis

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


scientificYAxis

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


scientificPattern

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


referenceAreasXAxis

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


referenceAreasYAxis

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


miniature

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


yDataIsPositive

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


alphaLevel

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


deltaMassWindow

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


iXAxisLabel

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


iYAxisLabel

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


iFilenameColor

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


iDataPointAndLineColor

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


iAreaUnderCurveColor

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


iPointSize

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


iFilename

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


iSpecPanelListeners

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


iPointDetectionTolerance

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


iStartXLoc

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


iStartYLoc

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


iEndXLoc

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


xAxisZoomRangeLowerValue

double xAxisZoomRangeLowerValue
The lower range for the current zoom range.


xAxisZoomRangeUpperValue

double xAxisZoomRangeUpperValue
The upper range for the current zoom range.


iDragXLoc

int iDragXLoc
The current dragging location.


iXScaleUnit

double iXScaleUnit
Scale unit for the X axis


iYScaleUnit

double iYScaleUnit
Scale unit for the Y axis


iXUnit

int iXUnit
Graphical unit for the X axis


iYUnit

int iYUnit
Graphical unit for the Y axis


iXPadding

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


iTopPadding

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


iXAxisStartAtZero

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


iDragged

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


xTagCount

int xTagCount
The number of X-axis tags.


yTagCount

int yTagCount
The number of Y-axis tags.


padding

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


currentPadding

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


maxPadding

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


showFileName

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


showPrecursorDetails

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


showResolution

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


iXAxisData

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


iXAxisMin

double iXAxisMin
The minimum x-axis value to display.


iXAxisMax

double iXAxisMax
The maximum x-axis value to display.


iYAxisMin

double iYAxisMin
The minimum y-axis value to display.


iYAxisMax

double iYAxisMax
The maximum y-axis value to display.


iAnnotationYAxisThreshold

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


iYAxisData

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


iPrecursorMZ

double iPrecursorMZ
This variable holds the precursor M/Z.


iPrecursorCharge

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


iXAxisDataInPixels

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


iYAxisDataInPixels

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


iHighLight

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


iHighLightIndex

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


iHighLightDatasetIndex

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


iClicked

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


iClickedIndex

int iClickedIndex
Int that indicates which point was clicked.


iClickedDataSetIndex

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


iClickedList

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


iClickedListDatasetIndices

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


iStoredSequence

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


iStoredSequenceDatasetIndices

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


iAnnotations

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


iMinDrag

int iMinDrag
Minimal dragging distance in pixels.


iDrawStyle

int iDrawStyle
This variable holds the drawing style.


iDotRadius

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


iMSLevel

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


showAllPeaks

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


yAxisZoomExcludesBackgroundPeaks

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


currentGraphicsPanelType

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

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

Serialized Fields

chartPanel

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

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

Serialized Fields

logger

org.apache.log4j.Logger logger

aSpectrumPeakColor

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


aSpectrumProfileModeLineColor

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


peptideSequences

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


peptideCharges

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


iElements

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

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

Serialized Fields

useRelativeError

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


currentFragmentIons

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


includeSinglyCharge

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


includeDoublyCharge

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


includeMoreThanTwoCharges

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


currentlyUsedIonMatches

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


chartPanel

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

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

Serialized Fields

annotations

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


currentFragmentIons

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


includeSinglyCharge

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


includeDoublyCharge

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


includeMoreThanTwoCharges

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


currentlyUsedIonMatches

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


chartPanel

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


useRelativeError

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

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

Serialized Fields

tooltipRectangles

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


iSequenceComponents

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


iIonMatches

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


bIons

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


yIons

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


iBaseFont

java.awt.Font iBaseFont
The font to use.


iMaxBarHeight

double iMaxBarHeight
The maximum bar height.


iBarWidth

int iBarWidth
The width of the bars.


iHorizontalSpace

int iHorizontalSpace
The horizontal space.


iXStart

int iXStart
The x-axis start position.


isModifiedSequence

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


iHighlightModifications

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


iModificationColors

java.util.HashMap<K,V> iModificationColors
The modification colors. The keys as ,

, etc.


iModificationNames

java.util.HashMap<K,V> iModificationNames
The modification names map. E.g., key , element: oxidation of m.

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

Serialized Fields

aSpectrumPeakColor

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


aSpectrumProfileModeLineColor

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


Package com.compomics.util.io

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

Serialized Fields

logger

org.apache.log4j.Logger logger

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

Serialized Fields

logger

org.apache.log4j.Logger logger

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

Serialized Fields

logger

org.apache.log4j.Logger logger

Package com.compomics.util.pride

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

serialVersionUID: -2890434198335005181L

Serialized Fields

ontology

java.lang.String ontology
The ontology.


accession

java.lang.String accession
The accession number.


name

java.lang.String name
The name/term.


value

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

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

serialVersionUID: 7368502853292052566L

Serialized Fields

modToCvMap

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


Package com.compomics.util.pride.prideobjects

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

serialVersionUID: -9182316910747747823L

Serialized Fields

name

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


eMail

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


institution

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

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

serialVersionUID: -8802861658166703745L

Serialized Fields

name

java.lang.String name
The instrument name.


cvTerms

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


source

CvTerm source
The instrument source.


detector

CvTerm detector
The instrument detector.

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

serialVersionUID: -9045298216154032632L

Serialized Fields

name

java.lang.String name
The protcol name.


cvTerms

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

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

serialVersionUID: -5449836209751629549L

Serialized Fields

reference

java.lang.String reference
The reference text.


pmid

java.lang.String pmid
The PubMed ID.


doi

java.lang.String doi
The Digital Object Identifier.

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

serialVersionUID: -7142471175737857227L

Serialized Fields

name

java.lang.String name
The sample name.


cvTerms

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


Package com.compomics.util.protein

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

serialVersionUID: 7665784733371863163L

Serialized Fields

iID

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


iForeignID

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


iAccession

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


databaseType

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


iForeignAccession

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


iDescription

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


iForeignDescription

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


iRest

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


iAddenda

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


iStart

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


iEnd

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

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

Serialized Fields

logger

org.apache.log4j.Logger logger

iTemplate

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


iLocation

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


Package com.compomics.util.sun

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

Serialized Fields

logger

org.apache.log4j.Logger logger

model

javax.swing.table.TableModel model

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

Serialized Fields

logger

org.apache.log4j.Logger logger

indexes

int[] indexes

sortingColumns

java.util.Vector<E> sortingColumns

ascending

boolean ascending

compares

int compares

listMouseListener

java.awt.event.MouseAdapter listMouseListener



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