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Serialized Form

Package maltcms.commands

Class maltcms.commands.ArrayStatsMap extends Object implements Serializable

serialVersionUID: -8374451195942782968L

Serialized Fields

featureVector

DefaultFeatureVector featureVector

Package maltcms.commands.distances

Class maltcms.commands.distances.DtwRecurrence extends Object implements Serializable

Serialized Fields

comp_weight

double comp_weight

exp_weight

double exp_weight

diag_weight

double diag_weight

globalGapPenalty

double globalGapPenalty

minimize

boolean minimize

directions

String[] directions

Class maltcms.commands.distances.PairwiseFeatureSimilarity extends Object implements Serializable

serialVersionUID: -2087449317783907180L

Serialized Fields

similarityFunction

IDtwSimilarityFunction similarityFunction

nthreads

int nthreads

pad

IArrayD2Double pad

Class maltcms.commands.distances.PartitionCalculator extends Object implements Serializable

serialVersionUID: -7473548606374882072L

Serialized Fields

shape

Rectangle shape

pa

IArrayD2Double pa

costFunction

IDtwSimilarityFunction costFunction

satRef

ArrayDouble.D1 satRef

satQuery

ArrayDouble.D1 satQuery

ref

List<E> ref

query

List<E> query

Package maltcms.commands.distances.dtw

Class maltcms.commands.distances.dtw.ADynamicTimeWarp extends Object implements Serializable

Serialized Fields

recurrence

DtwRecurrence recurrence

scan_acquisition_time

String scan_acquisition_time

pairwiseFeatureSimilarity

PairwiseFeatureSimilarity pairwiseFeatureSimilarity

statsMap

cross.datastructures.StatsMap statsMap

useAnchors

boolean useAnchors

anchorRadius

int anchorRadius

minScansBetweenAnchors

int minScansBetweenAnchors

workflow

cross.datastructures.workflow.IWorkflow workflow

precalculatePairwiseDistances

boolean precalculatePairwiseDistances

pa

PairwiseAlignment pa

globalBand

boolean globalBand

bandWidthPercentage

double bandWidthPercentage

extension

String extension

saveLayoutImage

boolean saveLayoutImage

sample

boolean sample

saveDtwMatrix

boolean saveDtwMatrix

savePairwiseSimilarityMatrix

boolean savePairwiseSimilarityMatrix

normalizeAlignmentValue

boolean normalizeAlignmentValue

Class maltcms.commands.distances.dtw.MZIDynamicTimeWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

numberOfEICsToSelect

int numberOfEICsToSelect

useSparseArrays

boolean useSparseArrays

mass_values

String mass_values

intensity_values

String intensity_values

mass_range_min

String mass_range_min

mass_range_max

String mass_range_max

scan_index

String scan_index

Class maltcms.commands.distances.dtw.TICDynamicTimeWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

arrayVariable

String arrayVariable

Package maltcms.commands.distances.dtwng

Class maltcms.commands.distances.dtwng.DTW extends Object implements Serializable

serialVersionUID: -4958589994859792653L

Serialized Fields

leftHandSideId

String leftHandSideId

rightHandSideId

String rightHandSideId

similarity

TwoFeatureVectorOperation similarity

alignmentMap

List<E> alignmentMap

area

Area area

defaultValue

double defaultValue

optimizationFunction

IOptimizationFunction optimizationFunction

Class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity extends TwoFeatureVectorOperation implements Serializable

Serialized Fields

scoreFunction

IDtwSimilarityFunction scoreFunction

arrayFeatureName

String arrayFeatureName

timeFeatureName

String timeFeatureName

Class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization extends Object implements Serializable

Serialized Fields

minimize

boolean minimize

weights

double[] weights

ins

double ins

del

double del

NW

ThreePredecessorsOptimization.State NW

N

ThreePredecessorsOptimization.State N

W

ThreePredecessorsOptimization.State W

tfvo

TwoFeatureVectorOperation tfvo

l

List<E> l

r

List<E> r

trace

List<E> trace

stateSequence

List<E> stateSequence

stateSequenceString

String stateSequenceString

cumulatedScores

IArrayD2Double cumulatedScores

pwScores

IArrayD2Double pwScores

traceMatrix

ThreePredecessorsOptimization.State[][] traceMatrix

opcounter

int[] opcounter

saveCDM

boolean saveCDM

savePWDM

boolean savePWDM

cumulativeDistanceVariableName

String cumulativeDistanceVariableName

pairwiseDistanceVariableName

String pairwiseDistanceVariableName

normalizeAlignmentValueByMapWeights

boolean normalizeAlignmentValueByMapWeights

Class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation extends Object implements Serializable

Package maltcms.commands.filters

Class maltcms.commands.filters.AElementFilter extends Object implements Serializable

Package maltcms.commands.filters.array

Class maltcms.commands.filters.array.AArrayFilter extends Object implements Serializable

Serialized Fields

copyArray

boolean copyArray

Class maltcms.commands.filters.array.AdditionFilter extends AArrayFilter implements Serializable

Serialized Fields

aef

AElementFilter aef

add

double add

Class maltcms.commands.filters.array.AddRandomNoise extends AArrayFilter implements Serializable

Serialized Fields

rg

Random rg

mean

double mean

stddev

double stddev

Class maltcms.commands.filters.array.ArrayMerge extends AArrayFilter implements Serializable

Class maltcms.commands.filters.array.BottomHatFilter extends AArrayFilter implements Serializable

Serialized Fields

window

int window

Class maltcms.commands.filters.array.ExpFilter extends AArrayFilter implements Serializable

Serialized Fields

aef

AElementFilter aef

naturalLog

boolean naturalLog

Class maltcms.commands.filters.array.FirstDerivativeFilter extends AArrayFilter implements Serializable

Class maltcms.commands.filters.array.LogFilter extends AArrayFilter implements Serializable

Serialized Fields

aef

AElementFilter aef

naturalLog

boolean naturalLog

Class maltcms.commands.filters.array.MeanStdDevNormalizationFilter extends AArrayFilter implements Serializable

Serialized Fields

mean

double mean

stddev

double stddev

Class maltcms.commands.filters.array.MedianBaselineFilter extends AArrayFilter implements Serializable

Serialized Fields

scans

int scans

channels

int channels

medianWindow

int medianWindow

snrMinimum

double snrMinimum

Class maltcms.commands.filters.array.MinimumFilter extends AArrayFilter implements Serializable

Serialized Fields

aef

AElementFilter aef

Class maltcms.commands.filters.array.MinMaxNormalizationFilter extends AArrayFilter implements Serializable

Serialized Fields

min

double min

max

double max

Class maltcms.commands.filters.array.MovingAverageFilter extends AArrayFilter implements Serializable

Serialized Fields

window

int window

Class maltcms.commands.filters.array.MovingMedianFilter extends AArrayFilter implements Serializable

Serialized Fields

window

int window

Class maltcms.commands.filters.array.MultiplicationFilter extends AArrayFilter implements Serializable

Serialized Fields

factor

double factor

Class maltcms.commands.filters.array.NormalizationFilter extends AArrayFilter implements Serializable

Serialized Fields

normalization

String normalization

normalizeGlobal

boolean normalizeGlobal

log

boolean log

Class maltcms.commands.filters.array.SavitzkyGolayFilter extends AArrayFilter implements Serializable

Serialized Fields

window

int window

Class maltcms.commands.filters.array.SqrtFilter extends AArrayFilter implements Serializable

Serialized Fields

aef

AElementFilter aef

Class maltcms.commands.filters.array.TopHatFilter extends AArrayFilter implements Serializable

Serialized Fields

window

int window

Package maltcms.commands.filters.array.wavelet

Class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter extends AArrayFilter implements Serializable

Serialized Fields

scale

double scale

variance

double variance

w

IWavelet w

cwt

ContinuousWaveletTransform cwt

log

org.slf4j.Logger log

Package maltcms.commands.fragments.alignment

Class maltcms.commands.fragments.alignment.CenterStarAlignment extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

pairwiseDistanceMatrixVariableName

String pairwiseDistanceMatrixVariableName

pairwiseDistanceNamesVariableName

String pairwiseDistanceNamesVariableName

minimizingArrayCompVariableName

String minimizingArrayCompVariableName

multipleAlignmentVariableName

String multipleAlignmentVariableName

multipleAlignmentNamesVariableName

String multipleAlignmentNamesVariableName

multipleAlignmentTypeVariableName

String multipleAlignmentTypeVariableName

multipleAlignmentCreatorVariableName

String multipleAlignmentCreatorVariableName

minimizeDist

boolean minimizeDist

alignToFirst

boolean alignToFirst

centerSequence

String centerSequence

Class maltcms.commands.fragments.alignment.PeakCliqueAlignment extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

ticPeaks

String ticPeaks

massValues

String massValues

scanIndex

String scanIndex

intensityValues

String intensityValues

useUserSuppliedAnchors

boolean useUserSuppliedAnchors

minCliqueSize

int minCliqueSize

anchorNames

String anchorNames

anchorTimes

String anchorTimes

anchorRetentionIndex

String anchorRetentionIndex

anchorScanIndex

String anchorScanIndex

binnedIntensities

String binnedIntensities

binnedScanIndex

String binnedScanIndex

scanAcquisitionTime

String scanAcquisitionTime

savePeakSimilarities

boolean savePeakSimilarities

saveXMLAlignment

boolean saveXMLAlignment

maxBBHErrors

int maxBBHErrors

savePlots

boolean savePlots

useSparseArrays

boolean useSparseArrays

peakToClique

HashMap<K,V> peakToClique

workerFactory

WorkerFactory workerFactory

saveUnmatchedPeaks

boolean saveUnmatchedPeaks

saveIncompatiblePeaks

boolean saveIncompatiblePeaks

saveUnassignedPeaks

boolean saveUnassignedPeaks

peakAreaVariable

String peakAreaVariable

Class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

guideTreeClass

String guideTreeClass

Package maltcms.commands.fragments.alignment.peakCliqueAlignment

Class maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker extends Object implements Serializable

Serialized Fields

name

String name

lhsPeaks

List<E> lhsPeaks

rhsPeaks

List<E> rhsPeaks

similarityFunction

IScalarArraySimilarity similarityFunction

maxRTDifference

double maxRTDifference

Package maltcms.commands.fragments.assignment

Class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

dblocation

List<E> dblocation

threshold

double threshold

maxk

int maxk

Package maltcms.commands.fragments.cluster

Class maltcms.commands.fragments.cluster.ClusteringAlgorithm extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

normalize_scans

boolean normalize_scans

inputFiles

cross.datastructures.tuple.TupleND<T extends Serializable> inputFiles

consensus

cross.datastructures.fragments.IFileFragment consensus

dist

double[][] dist

names

String[] names

L

int L

usedIndices

HashSet<E> usedIndices

cluster

HashMap<K,V> cluster

fragments

HashMap<K,V> fragments

nameToNameLookup

HashMap<K,V> nameToNameLookup

chromatogramDistanceFunctionClass

PairwiseFeatureSequenceSimilarity chromatogramDistanceFunctionClass

clusterNames

String[] clusterNames

pairwiseDistanceMatrixVariableName

String pairwiseDistanceMatrixVariableName

pairwiseDistanceNamesVariableName

String pairwiseDistanceNamesVariableName

minimizingArrayCompVariableName

String minimizingArrayCompVariableName

chromatogramWarpCommandClass

cross.commands.fragments.AFragmentCommand chromatogramWarpCommandClass

minimizeDist

boolean minimizeDist

drawTICs

boolean drawTICs

drawEICs

boolean drawEICs

alignments

List<E> alignments

pwds

ArrayDouble.D2 pwds

minArrayComp

String minArrayComp

Class maltcms.commands.fragments.cluster.CompleteLinkageAlgorithm extends ClusteringAlgorithm implements Serializable

Class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm extends ClusteringAlgorithm implements Serializable

Serialized Fields

R

double[] R

Class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

minimizingLocalDistance

boolean minimizingLocalDistance

pairsWithFirstElement

boolean pairsWithFirstElement

minArrayComp

String minArrayComp

pwdExtension

String pwdExtension

workerFactory

AWorkerFactory workerFactory

Class maltcms.commands.fragments.cluster.SingleLinkageAlgorithm extends ClusteringAlgorithm implements Serializable

Class maltcms.commands.fragments.cluster.UPGMAAlgorithm extends ClusteringAlgorithm implements Serializable

Package maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.ApplicationContextWorkerFactory extends AWorkerFactory implements Serializable

serialVersionUID: 8253151151321756579L

Serialized Fields

context

org.springframework.context.ApplicationContext context

beanId

String beanId

Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.AWorkerFactory extends Object implements Serializable

Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.MziDtwWorkerFactory extends AWorkerFactory implements Serializable

serialVersionUID: 626200987946759092L

Serialized Fields

bandWidthPercentage

double bandWidthPercentage

globalGapPenalty

double globalGapPenalty

extension

String extension

globalBand

boolean globalBand

minScansBetweenAnchors

int minScansBetweenAnchors

precalculatePairwiseDistances

boolean precalculatePairwiseDistances

saveLayoutImage

boolean saveLayoutImage

useAnchors

boolean useAnchors

numberOfEICsToSelect

int numberOfEICsToSelect

useSparseArrays

boolean useSparseArrays

anchorRadius

int anchorRadius

similarity

IDtwSimilarityFunction similarity

saveDtwMatrix

boolean saveDtwMatrix

savePairwiseSimilarityMatrix

boolean savePairwiseSimilarityMatrix

normalizeAlignmentValue

boolean normalizeAlignmentValue

Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceResult extends Object implements Serializable

serialVersionUID: 60123098123486L

Serialized Fields

input

cross.datastructures.tuple.Tuple2D<T,U> input

alignment

File alignment

value

double value

statsMap

cross.datastructures.StatsMap statsMap

Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceWorker extends Object implements Serializable

serialVersionUID: 4556712389798130L

Serialized Fields

similarity

PairwiseFeatureSequenceSimilarity similarity

workflow

cross.datastructures.workflow.IWorkflow workflow

input

cross.datastructures.tuple.Tuple2D<T,U> input

outputDirectory

File outputDirectory

jobNumber

int jobNumber

nJobs

int nJobs

Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.TicDtwWorkerFactory extends AWorkerFactory implements Serializable

serialVersionUID: -8359038356253166675L

Serialized Fields

bandWidthPercentage

double bandWidthPercentage

globalGapPenalty

double globalGapPenalty

extension

String extension

globalBand

boolean globalBand

minScansBetweenAnchors

int minScansBetweenAnchors

precalculatePairwiseDistances

boolean precalculatePairwiseDistances

saveLayoutImage

boolean saveLayoutImage

useAnchors

boolean useAnchors

anchorRadius

int anchorRadius

similarity

IDtwSimilarityFunction similarity

saveDtwMatrix

boolean saveDtwMatrix

savePairwiseSimilarityMatrix

boolean savePairwiseSimilarityMatrix

normalizeAlignmentValue

boolean normalizeAlignmentValue

Package maltcms.commands.fragments.io

Class maltcms.commands.fragments.io.ANDIChromImporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

ordinateValuesVariable

String ordinateValuesVariable

scanAcquisitionTimeVariable

String scanAcquisitionTimeVariable

actualSamplingIntervalVariable

String actualSamplingIntervalVariable

actualDelayTimeVariable

String actualDelayTimeVariable

Class maltcms.commands.fragments.io.ANDIMSExporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Class maltcms.commands.fragments.io.CSVAnchorReader extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

omit

String omit

time

boolean time

index

boolean index

location

List<E> location

fileDesignation

String fileDesignation

basedir

String basedir

scan

boolean scan

max_names_length

int max_names_length

anchorNamesVariableName

String anchorNamesVariableName

anchorTimesVariableName

String anchorTimesVariableName

anchorRetentionIndexVariableName

String anchorRetentionIndexVariableName

anchorScanIndexVariableName

String anchorScanIndexVariableName

useAnchors

boolean useAnchors

satVariableName

String satVariableName

Class maltcms.commands.fragments.io.MSPExporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Class maltcms.commands.fragments.io.ObiWarplmataExporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

scanAcquisitionTimeVariableName

String scanAcquisitionTimeVariableName

binnedIntensitiesVariableName

String binnedIntensitiesVariableName

binnedScanIndexVariableName

String binnedScanIndexVariableName

binnedMassesVariableName

String binnedMassesVariableName

Class maltcms.commands.fragments.io.PeakAreaTableExporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Class maltcms.commands.fragments.io.TICPeakListImporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

filesToRead

List<E> filesToRead

scanIndexOffset

int scanIndexOffset

scanIndexColumnName

String scanIndexColumnName

ticPeakVarName

String ticPeakVarName

Class maltcms.commands.fragments.io.VariableDataExporter extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

varNames

ArrayList<E> varNames

Package maltcms.commands.fragments.peakfinding

Class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder extends cross.commands.fragments.AFragmentCommand implements Serializable

Class maltcms.commands.fragments.peakfinding.CwtTicPeakFinder extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

minScale

int minScale

maxScale

int maxScale

minPercentile

double minPercentile

integratePeaks

boolean integratePeaks

integrateRawTic

boolean integrateRawTic

saveGraphics

boolean saveGraphics

Class maltcms.commands.fragments.peakfinding.EICPeakFinder extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

peakThreshold

double peakThreshold

filterWindow

int filterWindow

Class maltcms.commands.fragments.peakfinding.TICPeakFinder extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

peakThreshold

double peakThreshold

saveGraphics

boolean saveGraphics

integratePeaks

boolean integratePeaks

integrateTICPeaks

boolean integrateTICPeaks

snrWindow

int snrWindow

ticVarName

String ticVarName

satVarName

String satVarName

ticPeakVarName

String ticPeakVarName

ticFilteredVarName

String ticFilteredVarName

integrateRawTic

boolean integrateRawTic

peakSeparationWindow

int peakSeparationWindow

removeOverlappingPeaks

boolean removeOverlappingPeaks

baselineEstimator

IBaselineEstimator baselineEstimator

filter

List<E> filter

peakNormalizers

List<E> peakNormalizers

Package maltcms.commands.fragments.peakfinding.cwtEicPeakFinder

Class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtEicPeakFinderCallable extends Object implements Serializable

Serialized Fields

minScale

int minScale

maxScale

int maxScale

input

File input

output

File output

mz

double mz

eic

double[] eic

minPercentile

double minPercentile

Class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtTicPeakFinderCallable extends Object implements Serializable

Serialized Fields

minScale

int minScale

maxScale

int maxScale

input

File input

output

File output

minPercentile

double minPercentile

integratePeaks

boolean integratePeaks

integrateRawTic

boolean integrateRawTic

storeScaleogram

boolean storeScaleogram

peakNormalizers

List<E> peakNormalizers

Package maltcms.commands.fragments.preprocessing

Class maltcms.commands.fragments.preprocessing.DefaultVarLoader extends cross.commands.fragments.AFragmentCommand implements Serializable

Class maltcms.commands.fragments.preprocessing.DenseArrayProducer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

normalizeScans

boolean normalizeScans

massValues

String massValues

intensityValues

String intensityValues

scanIndex

String scanIndex

totalIntensity

String totalIntensity

binnedIntensityValues

String binnedIntensityValues

binnedMassValues

String binnedMassValues

binnedScanIndex

String binnedScanIndex

massRangeMin

String massRangeMin

massRangeMax

String massRangeMax

maskedMasses

List<E> maskedMasses

invertMaskedMasses

boolean invertMaskedMasses

ignoreMinMaxMassArrays

boolean ignoreMinMaxMassArrays

normalizeMeanVariance

boolean normalizeMeanVariance

normalizeEicsToUnity

boolean normalizeEicsToUnity

massBinResolution

double massBinResolution

Class maltcms.commands.fragments.preprocessing.MassFilter extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

excludeMasses

List<E> excludeMasses

epsilon

double epsilon

massValuesVar

String massValuesVar

intensValuesVar

String intensValuesVar

scanIndexVar

String scanIndexVar

totalIntensVar

String totalIntensVar

invert

boolean invert

Package maltcms.commands.fragments.preprocessing.defaultVarLoader

Class maltcms.commands.fragments.preprocessing.defaultVarLoader.DefaultVarLoaderWorker extends Object implements Serializable

Serialized Fields

fileToLoad

File fileToLoad

fileToSave

File fileToSave

Package maltcms.commands.fragments.preprocessing.denseArrayProducer

Class maltcms.commands.fragments.preprocessing.denseArrayProducer.DenseArrayProducerWorker extends Object implements Serializable

Serialized Fields

massValues

String massValues

intensityValues

String intensityValues

scanIndex

String scanIndex

totalIntensity

String totalIntensity

binnedIntensityValues

String binnedIntensityValues

binnedMassValues

String binnedMassValues

binnedScanIndex

String binnedScanIndex

normalizeScans

boolean normalizeScans

maskedMasses

List<E> maskedMasses

invertMaskedMasses

boolean invertMaskedMasses

normalizeEicsToZeroMeanUnitVariance

boolean normalizeEicsToZeroMeanUnitVariance

normalizeEicsToUnity

boolean normalizeEicsToUnity

massBinResolution

double massBinResolution

minMass

double minMass

maxMass

double maxMass

minMaxIntensities

List<E> minMaxIntensities

fileToLoad

File fileToLoad

fileToSave

File fileToSave

Class maltcms.commands.fragments.preprocessing.denseArrayProducer.MinMaxMassFinderWorker extends Object implements Serializable

Serialized Fields

fileToLoad

File fileToLoad

ignoreMinMaxMassArrays

boolean ignoreMinMaxMassArrays

minMassVariableName

String minMassVariableName

maxMassVariableName

String maxMassVariableName

fallbackVariableName

String fallbackVariableName

Package maltcms.commands.fragments.spectratyping

Class maltcms.commands.fragments.spectratyping.VBetaFamilyComparison extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

controlFile

String controlFile

intervals

List<E> intervals

minPercentage

double minPercentage

Package maltcms.commands.fragments.visualization

Class maltcms.commands.fragments.visualization.Array1DVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

variableName

String variableName

scanAcquisitionTimeVariableName

String scanAcquisitionTimeVariableName

xAxisLabel

String xAxisLabel

yAxisLabel

String yAxisLabel

pairwise

boolean pairwise

pairwiseWithFirst

boolean pairwiseWithFirst

substractStartTime

boolean substractStartTime

allInOneChart

boolean allInOneChart

timeUnit

String timeUnit

Class maltcms.commands.fragments.visualization.ChromatogramVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

mzVariableName

String mzVariableName

scanAcquisitionTimeVariableName

String scanAcquisitionTimeVariableName

format

String format

colorrampLocation

String colorrampLocation

sampleSize

int sampleSize

lowThreshold

double lowThreshold

substractStartTime

boolean substractStartTime

timeUnit

String timeUnit

Class maltcms.commands.fragments.visualization.EICHeatmapCoplot extends TICHeatmapCoplot implements Serializable

Serialized Fields

drawEICs

List<E> drawEICs

Class maltcms.commands.fragments.visualization.MZIDistributionVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

filea

cross.datastructures.fragments.IFileFragment filea

x_var

String x_var

y_var

String y_var

one_for_each

boolean one_for_each

Class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

t

Thread t

filename

String filename

format

String format

chromatogramHeight

int chromatogramHeight

left_chromatogram_var

String left_chromatogram_var

top_chromatogram_var

String top_chromatogram_var

reference_file_name

String reference_file_name

query_file_name

String query_file_name

path_i

String path_i

path_j

String path_j

mz_var

String mz_var

inten_var

String inten_var

scan_index_var

String scan_index_var

mass_range_min_var

String mass_range_min_var

mass_range_max_var

String mass_range_max_var

full_spec

boolean full_spec

colorramp_location

String colorramp_location

sampleSize

int sampleSize

pairsWithFirstElement

boolean pairsWithFirstElement

drawPath

boolean drawPath

matrix_vars

ArrayList<E> matrix_vars

showMZs

boolean showMZs

normalize

boolean normalize

normalize_global

boolean normalize_global

mapheight

int mapheight

total_intensity

String total_intensity

scan_acquisition_time

String scan_acquisition_time

ima

BufferedImage ima

imb

BufferedImage imb

map

BufferedImage map

substract_start_time

boolean substract_start_time

jp

JPanel jp

pairsWithFirstElement

boolean pairsWithFirstElement

showChromatogramHeatmap

boolean showChromatogramHeatmap

chromheight

int chromheight

timeUnit

String timeUnit

createMapTICChart

boolean createMapTICChart

createComparativeTICChart

boolean createComparativeTICChart

createDifferentialTICChart

boolean createDifferentialTICChart

createRatioTICChart

boolean createRatioTICChart

createSuperimposedTICChart

boolean createSuperimposedTICChart

y_axis_label

String y_axis_label

Class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Class maltcms.commands.fragments.visualization.TICHeatmapCoplot extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

colorRampLocation

String colorRampLocation

totalIntensityVar

String totalIntensityVar

scanAcquisitionTimeVar

String scanAcquisitionTimeVar

Package maltcms.commands.fragments.warp

Class maltcms.commands.fragments.warp.ChromatogramWarp extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

indexedVars

List<E> indexedVars

Deprecated.

plainVars

List<E> plainVars

Deprecated.

indexVar

String indexVar

Deprecated.

log

org.slf4j.Logger log

Deprecated.

anchorScanIndexVariableName

String anchorScanIndexVariableName

Deprecated.

anchorNameVariableName

String anchorNameVariableName

Deprecated.

average

boolean average

Deprecated.

Class maltcms.commands.fragments.warp.ChromatogramWarp2 extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

indexedVars

List<E> indexedVars

plainVars

List<E> plainVars

indexVar

String indexVar

anchorScanIndexVariableName

String anchorScanIndexVariableName

anchorNameVariableName

String anchorNameVariableName

multipleAlignmentVariableName

String multipleAlignmentVariableName

multipleAlignmentNamesVariableName

String multipleAlignmentNamesVariableName

multipleAlignmentTypeVariableName

String multipleAlignmentTypeVariableName

multipleAlignmentCreatorVariableName

String multipleAlignmentCreatorVariableName

averageCompressions

boolean averageCompressions

alignmentLocation

String alignmentLocation

satvar

String satvar

Class maltcms.commands.fragments.warp.PathWarp extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

total_intensity

String total_intensity

riname

String riname

rinamename

String rinamename

indexVar

String indexVar

massValuesVar

String massValuesVar

intensValuesVar

String intensValuesVar

average

boolean average

minScansBetweenAnchors

int minScansBetweenAnchors

Class maltcms.commands.fragments.warp.RTGroupCorrectionWarp extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

indexedVars

List<E> indexedVars

plainVars

List<E> plainVars

indexVar

String indexVar

anchorScanIndexVariableName

String anchorScanIndexVariableName

anchorNameVariableName

String anchorNameVariableName

average

boolean average

Package maltcms.commands.fragments2d.peakfinding

Class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

minScale

int minScale

maxScale

int maxScale

maxRidgeCost

double maxRidgeCost

minRelativeIntensity

double minRelativeIntensity

rmiServerConfigFile

String rmiServerConfigFile

Class maltcms.commands.fragments2d.peakfinding.CwtRunnable extends Object implements Serializable

serialVersionUID: -517839315109598824L

Serialized Fields

minScale

int minScale

maxScale

int maxScale

maxRidgeCost

double maxRidgeCost

minRelativeIntensity

double minRelativeIntensity

inputFile

File inputFile

outputDir

String outputDir

modulationTime

double modulationTime

scanRate

double scanRate

ridgeTree

QuadTree<T> ridgeTree

Class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

scanRateVar

String scanRateVar

modulationTimeVar

String modulationTimeVar

secondScanIndexVar

String secondScanIndexVar

peakListVar

String peakListVar

scanAcquTime1DVar

String scanAcquTime1DVar

secondColumnTimeVar

String secondColumnTimeVar

regionIndexListVar

String regionIndexListVar

regionPeakIndexVar

String regionPeakIndexVar

boundaryIndexListVar

String boundaryIndexListVar

boundaryPeakIndexVar

String boundaryPeakIndexVar

format

String format

colorrampLocation

String colorrampLocation

doubleFillValue

double doubleFillValue

threshold

double threshold

doBBH

boolean doBBH

pickingClass

String pickingClass

srgClass

String srgClass

bbhClass

String bbhClass

identificationClass

String identificationClass

integrationClass

String integrationClass

exportClass

String exportClass

separate

boolean separate

secondRun

boolean secondRun

doNormalization

boolean doNormalization

doIntegration

boolean doIntegration

secondSeedMinDistance

double secondSeedMinDistance

seedNotInRegion

boolean seedNotInRegion

scansPerModulation

int scansPerModulation

similaritySecondRun

IScalarArraySimilarity similaritySecondRun

peakPicking

IPeakPicking peakPicking

regionGrowing

IRegionGrowing regionGrowing

bbh

IBidirectionalBestHit bbh

identification

IPeakIdentification identification

integration

IPeakIntegration integration

peakExporter

IPeakExporter peakExporter

peakSeparator

PeakSeparator peakSeparator

peakLists

List<E> peakLists

Package maltcms.commands.fragments2d.peakfinding.bbh

Class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit extends Object implements Serializable

Serialized Fields

useMeanMS

boolean useMeanMS

threshold

Double threshold

peaklists

List<E> peaklists

similarity

IScalarArraySimilarity similarity

doneList

List<E> doneList

Class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit extends Object implements Serializable

Serialized Fields

similarity

IScalarArraySimilarity similarity

useMeanMS

boolean useMeanMS

Class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit extends Object implements Serializable

Serialized Fields

useMeanMS

boolean useMeanMS

threshold

Double threshold

maxRetDiff

double maxRetDiff

similarity

IScalarArraySimilarity similarity

doneList

List<E> doneList

counter

int counter

fcounter

int fcounter

Package maltcms.commands.fragments2d.peakfinding.output

Class maltcms.commands.fragments2d.peakfinding.output.PeakExporter extends Object implements Serializable

Serialized Fields

workflow

cross.datastructures.workflow.IWorkflow workflow

compareAllAgainstAll

boolean compareAllAgainstAll

formatString

String formatString

formatter

NumberFormat formatter

Class maltcms.commands.fragments2d.peakfinding.output.PeakIdentification extends Object implements Serializable

Serialized Fields

mqdb

MetaboliteQueryDB mqdb

doSearch

boolean doSearch

dbFile

String dbFile

dbFiles

List<E> dbFiles

threshold

double threshold

k

int k

dbAvailable

boolean dbAvailable

similarity

IArraySimilarity similarity

masqMasses

List<E> masqMasses

dbMetabolitesList

List<E> dbMetabolitesList

Class maltcms.commands.fragments2d.peakfinding.output.PeakIntegration extends Object implements Serializable

Serialized Fields

k

int k

plotIntegration

boolean plotIntegration

Package maltcms.commands.fragments2d.peakfinding.picking

Class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking extends Object implements Serializable

Serialized Fields

totalIntensityRedoVar

String totalIntensityRedoVar

totalIntensityVar

String totalIntensityVar

secondScanIndexVar

String secondScanIndexVar

maxDx

int maxDx

maxDy

int maxDy

minVerticalScanIndex

int minVerticalScanIndex

k

int k

Class maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking extends Object implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

secondScanIndexVar

String secondScanIndexVar

maxDx

int maxDx

maxDy

int maxDy

minVerticalScanIndex

int minVerticalScanIndex

stdPerc

double stdPerc

Package maltcms.commands.fragments2d.peakfinding.srg

Class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing extends Object implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

usedMassValuesVar

String usedMassValuesVar

secondScanIndexVar

String secondScanIndexVar

minDistance

double minDistance

similarity

IArraySimilarity similarity

minPeakSize

int minPeakSize

maxPeakSize

int maxPeakSize

filterMS

boolean filterMS

useAlternativFiltering

boolean useAlternativFiltering

useMeanMS

boolean useMeanMS

discardPeaksWithMaxArea

boolean discardPeaksWithMaxArea

discardPeaksWithMinArea

boolean discardPeaksWithMinArea

timesum

long timesum

count

int count

scansPerModulation

int scansPerModulation

hold

List<E> hold

intensities

ArrayDouble.D1 intensities

slc

IScanLine slc

ff

cross.datastructures.fragments.IFileFragment ff

Package maltcms.commands.fragments2d.preprocessing

Class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

totalIntensityFilteredVar

String totalIntensityFilteredVar

scanRateVar

String scanRateVar

modulationTimeVar

String modulationTimeVar

secondScanIndexVar

String secondScanIndexVar

applyMovingAverage

boolean applyMovingAverage

movingAverageWindow

int movingAverageWindow

applyMovingMedian

boolean applyMovingMedian

movingMedianWindow

int movingMedianWindow

applyTopHatFilter

boolean applyTopHatFilter

topHatFilterWindow

int topHatFilterWindow

Class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

modulationTimeVar

String modulationTimeVar

scanRateVar

String scanRateVar

scanDurationVar

String scanDurationVar

secondColumnTimeVar

String secondColumnTimeVar

secondColumnScanIndexVar

String secondColumnScanIndexVar

totalIntensity1dVar

String totalIntensity1dVar

scanAcquisitionTimeVar

String scanAcquisitionTimeVar

scanAcquisitionTime1dVar

String scanAcquisitionTime1dVar

totalIntensity2dVar

String totalIntensity2dVar

modulationTime

double modulationTime

scanDuration

double scanDuration

scanRate

double scanRate

modulationIndex0Dimension

String modulationIndex0Dimension

modulationIndex1Dimension

String modulationIndex1Dimension

modulationTimeDimension

String modulationTimeDimension

scanRateDimension

String scanRateDimension

scanNumberDimension

String scanNumberDimension

estimateModulationTime

boolean estimateModulationTime

Class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

snrthreshold

double snrthreshold

Class maltcms.commands.fragments2d.preprocessing.MeanVarProducer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

meanMSIntensityVar

String meanMSIntensityVar

varMSIntensityVar

String varMSIntensityVar

sdMSIntensityVar

String sdMSIntensityVar

vIntensityVar

String vIntensityVar

vIntensity1DVar

String vIntensity1DVar

meanMSHorizontalVar

String meanMSHorizontalVar

meanMSHorizontalIndexVar

String meanMSHorizontalIndexVar

meanMSVerticalVar

String meanMSVerticalVar

meanMSVerticalIndexVar

String meanMSVerticalIndexVar

maxMSHorizontalVar

String maxMSHorizontalVar

maxMSHorizontalIndexVar

String maxMSHorizontalIndexVar

maxMSVerticalVar

String maxMSVerticalVar

maxMSVerticalIndexVar

String maxMSVerticalIndexVar

usedMassValuesVar

String usedMassValuesVar

minStandardDeviationQuantil

double minStandardDeviationQuantil

minStandardDeviation

double minStandardDeviation

Class maltcms.commands.fragments2d.preprocessing.MeanVarVis extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

varMSIntensityVar

String varMSIntensityVar

sdMSIntensityVar

String sdMSIntensityVar

meanMSIntensityVar

String meanMSIntensityVar

totalIntensity1dVar

String totalIntensity1dVar

vtotalIntensity1DVar

String vtotalIntensity1DVar

scanAcquisitionTime1dVar

String scanAcquisitionTime1dVar

meanMSHorizontalVar

String meanMSHorizontalVar

meanMSHorizontalIndexVar

String meanMSHorizontalIndexVar

meanMSVerticalVar

String meanMSVerticalVar

meanMSVerticalIndexVar

String meanMSVerticalIndexVar

maxMSHorizontalVar

String maxMSHorizontalVar

maxMSHorizontalIndexVar

String maxMSHorizontalIndexVar

maxMSVerticalVar

String maxMSVerticalVar

maxMSVerticalIndexVar

String maxMSVerticalIndexVar

usedMassValuesVar

String usedMassValuesVar

format

String format

colorrampLocation

String colorrampLocation

lowThreshold

double lowThreshold

differentVisualizations

boolean differentVisualizations

useLogScale

boolean useLogScale

Class maltcms.commands.fragments2d.preprocessing.ModulationExtractor extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

modulationTimeVar

String modulationTimeVar

scanRateVar

String scanRateVar

scanAcquisitionTimeVar

String scanAcquisitionTimeVar

scanIndexVar

String scanIndexVar

startModulation

int startModulation

endModulation

int endModulation

Class maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

tic_var

String tic_var

Deprecated.

mass_var

String mass_var

Deprecated.

inten_var

String inten_var

Deprecated.

secondColumnTime

double secondColumnTime

Deprecated.

scanRate

double scanRate

Deprecated.

es

ExecutorService es

Deprecated.

doubleFillValue

double doubleFillValue

Deprecated.

threshold

double threshold

Deprecated.

Package maltcms.commands.fragments2d.preprocessing.default2dVarLoader

Class maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask extends Object implements Serializable

Serialized Fields

input

File input

numberOfScans

int numberOfScans

offset

int offset

Package maltcms.commands.fragments2d.testing

Class maltcms.commands.fragments2d.testing.Alignment2D extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

horizontalVar

String horizontalVar

horizontalIndexVar

String horizontalIndexVar

verticalVar

String verticalVar

verticalIndexVar

String verticalIndexVar

totalIntensity

String totalIntensity

secondColumnScanIndexVar

String secondColumnScanIndexVar

dtwSimilarity

TwoFeatureVectorOperation dtwSimilarity

filter

boolean filter

scale

boolean scale

Package maltcms.commands.fragments2d.visualization

Class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

secondScanIndexVar

String secondScanIndexVar

scanRateVar

String scanRateVar

modulationTimeVar

String modulationTimeVar

scanAcquTime

String scanAcquTime

secondColumnScanIndexVar

String secondColumnScanIndexVar

secondColumnTimeVar

String secondColumnTimeVar

colorrampLocation

String colorrampLocation

format

String format

doubleFillValue

double doubleFillValue

threshold

double threshold

substractMean

boolean substractMean

Class maltcms.commands.fragments2d.visualization.DeltaMasses extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

colorrampLocation

String colorrampLocation

lowThreshold

double lowThreshold

Class maltcms.commands.fragments2d.visualization.GradientVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

totalIntensityVar

String totalIntensityVar

secondScanIndexVar

String secondScanIndexVar

scanRateVar

String scanRateVar

modulationTimeVar

String modulationTimeVar

colorrampLocation

String colorrampLocation

format

String format

doubleFillValue

double doubleFillValue

threshold

double threshold

distClass

String distClass

similarity

IArraySimilarity similarity

absolut

boolean absolut

Class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

modulationVar

String modulationVar

scanRateVar

String scanRateVar

indices

int[] indices

Package maltcms.commands.fragments2d.warp

Class maltcms.commands.fragments2d.warp.CreateHorizontalTicVector extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

warpPathi

String warpPathi

warpPathj

String warpPathj

totalIntensity

String totalIntensity

modulationVar

String modulationVar

scanRateVar

String scanRateVar

secondColumnScanIndexVar

String secondColumnScanIndexVar

Class maltcms.commands.fragments2d.warp.DTW2DPeakAreaVisualizer extends DTW2DTicVisualizer implements Serializable

Serialized Fields

boundaryPeakListVar

String boundaryPeakListVar

regionIndexListVar

String regionIndexListVar

fillPeakArea

boolean fillPeakArea

Class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

warpPathi

String warpPathi

warpPathj

String warpPathj

totalIntensity

String totalIntensity

scanAcquTime

String scanAcquTime

modulationVar

String modulationVar

scanRateVar

String scanRateVar

secondColumnScanIndexVar

String secondColumnScanIndexVar

secondColumnTimeVar

String secondColumnTimeVar

scanspermodulation

int scanspermodulation

createSerialized

boolean createSerialized

format

String format

visualizerClass

String visualizerClass

visualizer

IVisualization visualizer

Class maltcms.commands.fragments2d.warp.ScanlineFilterTicWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

totalIntensity

String totalIntensity

secondColumnScanIndexVar

String secondColumnScanIndexVar

transpose

boolean transpose

Class maltcms.commands.fragments2d.warp.ScanlineHorizontalTicWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

scale

boolean scale

k

int k

Class maltcms.commands.fragments2d.warp.ScanlineMaxMSWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

maxMSHorizontalVar

String maxMSHorizontalVar

maxMSHorizontalIndexVar

String maxMSHorizontalIndexVar

maxMSVerticalVar

String maxMSVerticalVar

maxMSVerticalIndexVar

String maxMSVerticalIndexVar

usedMassValuesVar

String usedMassValuesVar

meanMSVar

String meanMSVar

meanMSIndexVar

String meanMSIndexVar

horizontal

boolean horizontal

scale

boolean scale

filter

boolean filter

Class maltcms.commands.fragments2d.warp.ScanlineMeanMSWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

meanMSHorizontalVar

String meanMSHorizontalVar

meanMSHorizontalIndexVar

String meanMSHorizontalIndexVar

meanMSVerticalVar

String meanMSVerticalVar

meanMSVerticalIndexVar

String meanMSVerticalIndexVar

maxMSHorizontalVar

String maxMSHorizontalVar

maxMSHorizontalIndexVar

String maxMSHorizontalIndexVar

maxMSVerticalVar

String maxMSVerticalVar

maxMSVerticalIndexVar

String maxMSVerticalIndexVar

usedMassValuesVar

String usedMassValuesVar

meanMSVar

String meanMSVar

meanMSIndexVar

String meanMSIndexVar

horizontal

boolean horizontal

useMean

boolean useMean

scale

boolean scale

filter

boolean filter

Class maltcms.commands.fragments2d.warp.ScanlineTicWarp extends ADynamicTimeWarp implements Serializable

Serialized Fields

totalIntensity

String totalIntensity

secondColumnScanIndexVar

String secondColumnScanIndexVar

Package maltcms.commands.fragments2d.warp.visualization

Class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer extends Object implements Serializable

Serialized Fields

peakListVar

String peakListVar

holdi

boolean holdi

holdj

boolean holdj

globalmax

boolean globalmax

black

boolean black

filter

boolean filter

normalize

boolean normalize

threshold

double threshold

horizontal

boolean horizontal

currentrasterline

int currentrasterline

binSize

int binSize

Class maltcms.commands.fragments2d.warp.visualization.Ident2DTWVisualizer extends Default2DTWVisualizer implements Serializable

Serialized Fields

currentrasterline

int currentrasterline

Package maltcms.commands.scanners

Class maltcms.commands.scanners.ArrayStatsScanner extends Object implements Serializable

Serialized Fields

gsm

cross.datastructures.StatsMap gsm

ff

cross.datastructures.fragments.IFileFragment ff

vfs

cross.datastructures.fragments.IVariableFragment[] vfs

ignorePositiveInfinity

boolean ignorePositiveInfinity

ignoreNegativeInfinity

boolean ignoreNegativeInfinity

Package maltcms.datastructures

Package maltcms.datastructures.array

Class maltcms.datastructures.array.DenseArray extends Object implements Serializable

Serialized Fields

data

ArrayDouble.D2 data

defaultValue

double defaultValue

Class maltcms.datastructures.array.PartitionedArray extends Object implements Serializable

Serialized Fields

shape

Area shape

colStart

ArrayInt.D1 colStart

dataArray

ArrayDouble.D1 dataArray

defaultValue

double defaultValue

elemsToCalculate

float elemsToCalculate

log

org.slf4j.Logger log

neighborhoods

List<E> neighborhoods

nPartitions

int nPartitions

partitions

List<E> partitions

row

int row

rowLength

ArrayInt.D1 rowLength

rowOffset

ArrayInt.D1 rowOffset

totalNumElements

float totalNumElements

virtualCols

int virtualCols

virtualRows

int virtualRows

Class maltcms.datastructures.array.SparseArray extends Object implements Serializable

Serialized Fields

sdm

cern.colt.matrix.impl.SparseDoubleMatrix2D sdm

Class maltcms.datastructures.array.TiledArray extends Object implements Serializable

serialVersionUID: -3193556606479661979L

Serialized Fields

arrays

IArrayD2Double[] arrays

tilesPerRow

int tilesPerRow

tileSizeRows

int tileSizeRows

tileSizeCols

int tileSizeCols

cols

int cols

rows

int rows

defaultValue

double defaultValue

filenames

File[] filenames

pq

PriorityQueue<E> pq

arrayATime

long[] arrayATime

Package maltcms.datastructures.caches

Class maltcms.datastructures.caches.AScanLineCache extends Object implements Serializable

Serialized Fields

scanIndexVar

String scanIndexVar

maxRangeVar

String maxRangeVar

modulationVar

String modulationVar

scanRateVar

String scanRateVar

iff

cross.datastructures.fragments.IFileFragment iff

lastIndex

int lastIndex

scansPerModulation

int scansPerModulation

binSize

int binSize

cacheModulations

boolean cacheModulations

Class maltcms.datastructures.caches.CachedScanLineList extends AScanLineCache implements Serializable

Serialized Fields

log

org.slf4j.Logger log

intensityValuesVar

String intensityValuesVar

scanIndexVar

String scanIndexVar

massValuesVar

String massValuesVar

useCache

boolean useCache

prefetch

boolean prefetch

cacheSize

int cacheSize

intensity

cross.datastructures.fragments.IVariableFragment intensity

mass

cross.datastructures.fragments.IVariableFragment mass

intensities

List<E> intensities

masses

List<E> masses

Class maltcms.datastructures.caches.ScanLineCache extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

intensityValuesVar

String intensityValuesVar

scanIndexVar

String scanIndexVar

massValuesVar

String massValuesVar

maxRangeVar

String maxRangeVar

modulationVar

String modulationVar

scanRateVar

String scanRateVar

secondColumnIndexVar

String secondColumnIndexVar

xyToScanIndexMap

List<E> xyToScanIndexMap

scanIndex

cross.datastructures.fragments.IVariableFragment scanIndex

massValues

cross.datastructures.fragments.IVariableFragment massValues

massIntensities

cross.datastructures.fragments.IVariableFragment massIntensities

iff

cross.datastructures.fragments.IFileFragment iff

lastIndex

int lastIndex

scansPerModulation

int scansPerModulation

binSize

int binSize

cache

HashMap<K,V> cache

cachemiss

int cachemiss

cachehit

int cachehit

loads

int loads

loadnew

int loadnew

cacheModulations

boolean cacheModulations

Class maltcms.datastructures.caches.ScanLineCacheOld extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

intensityValuesVar

String intensityValuesVar

scanIndexVar

String scanIndexVar

massValuesVar

String massValuesVar

maxRangeVar

String maxRangeVar

modulationVar

String modulationVar

scanRateVar

String scanRateVar

scanIndex

cross.datastructures.fragments.IVariableFragment scanIndex

massValues

cross.datastructures.fragments.IVariableFragment massValues

massIntensities

cross.datastructures.fragments.IVariableFragment massIntensities

iff

cross.datastructures.fragments.IFileFragment iff

lastIndex

int lastIndex

scansPerModulation

int scansPerModulation

binSize

int binSize

cache

HashMap<K,V> cache

cachemiss

int cachemiss

cachehit

int cachehit

loads

int loads

loadnew

int loadnew

cacheModulations

boolean cacheModulations

Class maltcms.datastructures.caches.SparseScanLineCache extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

intensityValuesVar

String intensityValuesVar

scanIndexVar

String scanIndexVar

massValuesVar

String massValuesVar

maxRangeVar

String maxRangeVar

modulationVar

String modulationVar

scanRateVar

String scanRateVar

secondColumnIndexVar

String secondColumnIndexVar

xyToScanIndexMap

List<E> xyToScanIndexMap

scanIndex

cross.datastructures.fragments.IVariableFragment scanIndex

massValues

cross.datastructures.fragments.IVariableFragment massValues

massIntensities

cross.datastructures.fragments.IVariableFragment massIntensities

iff

cross.datastructures.fragments.IFileFragment iff

lastIndex

int lastIndex

scansPerModulation

int scansPerModulation

binSize

int binSize

cache

HashMap<K,V> cache

cachemiss

int cachemiss

cachehit

int cachehit

loads

int loads

loadnew

int loadnew

cacheModulations

boolean cacheModulations

Package maltcms.datastructures.feature

Class maltcms.datastructures.feature.DefaultBinnedMSFeatureVector extends Object implements Serializable

serialVersionUID: 4737942765869140810L

Serialized Fields

binned_mass_values

List<E> binned_mass_values

binned_intensity_values

List<E> binned_intensity_values

sat

ArrayDouble.D0 sat

tic

ArrayDouble.D0 tic

i

int i

iff

cross.datastructures.fragments.IFileFragment iff

Class maltcms.datastructures.feature.DefaultFeatureVector extends Object implements Serializable

serialVersionUID: -2245293151270164895L

Serialized Fields

featureToIndex

Map<K,V> featureToIndex

datalist

List<E> datalist

Class maltcms.datastructures.feature.FastBinnedMSFeatureVector extends Object implements Serializable

serialVersionUID: 2026476569387259118L

Serialized Fields

binnedMasses

Array binnedMasses

binnedIntens

Array binnedIntens

sat

ArrayDouble.D0 sat

tic

ArrayDouble.D0 tic

Class maltcms.datastructures.feature.FeatureVectorList extends Object implements Serializable

Serialized Fields

l

List<E> l

featureNames

List<E> featureNames

Class maltcms.datastructures.feature.MaltcmsFeatureVector extends Object implements Serializable

serialVersionUID: 1423070246312970401L

Serialized Fields

iff

cross.datastructures.fragments.IFileFragment iff

index

int index

Package maltcms.datastructures.fragments

Class maltcms.datastructures.fragments.PairwiseAlignment extends Object implements Serializable

Serialized Fields

ff

cross.datastructures.fragments.IFileFragment ff

savePWDM

boolean savePWDM

saveCDM

boolean saveCDM

alignment

IArrayD2Double alignment

distance

IArrayD2Double distance

isMinimize

boolean isMinimize

refsize

int refsize

querysize

int querysize

cd

IRecurrence cd

result

ArrayDouble.D0 result

resultVector

ArrayDouble.D1 resultVector

pwd

PairwiseFeatureSimilarity pwd

ref

cross.datastructures.fragments.IFileFragment ref

target

cross.datastructures.fragments.IFileFragment target

path

List<E> path

creator

Class<T> creator

localPathOptima

List<E> localPathOptima

anchors

DefaultPairSet<T extends IAnchor> anchors

cumulativeDistanceVariableName

String cumulativeDistanceVariableName

pairwiseDistanceVariableName

String pairwiseDistanceVariableName

arrayComparatorVariableName

String arrayComparatorVariableName

arrayDistanceClassName

String arrayDistanceClassName

iw

cross.datastructures.workflow.IWorkflow iw

predecessors

byte[][] predecessors

normalizeAlignmentValueByMapWeights

boolean normalizeAlignmentValueByMapWeights

interppath

List<E> interppath

Class maltcms.datastructures.fragments.PairwiseDistances extends Object implements Serializable

Serialized Fields

pwDistFileFragment

cross.datastructures.fragments.IFileFragment pwDistFileFragment

pairwiseDistances

ArrayDouble.D2 pairwiseDistances

pwDistMatrixVariableName

String pwDistMatrixVariableName

pwDistVariableName

String pwDistVariableName

pwDistAlignmentsVarName

String pwDistAlignmentsVarName

name

String name

minimize

boolean minimize

minArrayComp

String minArrayComp

names

ArrayChar.D2 names

alignments

cross.datastructures.tuple.TupleND<T extends Serializable> alignments

iw

cross.datastructures.workflow.IWorkflow iw

Package maltcms.datastructures.ms

Class maltcms.datastructures.ms.Chromatogram1D extends Object implements Serializable

Serialized Fields

parent

cross.datastructures.fragments.IFileFragment parent

scanAcquisitionTimeUnit

String scanAcquisitionTimeUnit

scan_acquisition_time_var

String scan_acquisition_time_var

massValues

List<E> massValues

intensityValues

List<E> intensityValues

Class maltcms.datastructures.ms.Chromatogram2D extends Object implements Serializable

Serialized Fields

parent

cross.datastructures.fragments.IFileFragment parent

isl

IScanLine isl

scanAcquisitionTimeUnit

String scanAcquisitionTimeUnit

secondColumnScanAcquisitionTimeUnit

String secondColumnScanAcquisitionTimeUnit

md

double md

spm

int spm

slc

int slc

satOffset

double satOffset

Class maltcms.datastructures.ms.ChromatogramFactory extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

cfg

org.apache.commons.configuration.Configuration cfg

Class maltcms.datastructures.ms.Experiment1D extends Object implements Serializable

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:: IOException; ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:: IOException

Class maltcms.datastructures.ms.Experiment2D extends Experiment1D implements Serializable

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:: IOException; ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:: IOException

Class maltcms.datastructures.ms.ProfileChromatogram1D extends Chromatogram1D implements Serializable

Class maltcms.datastructures.ms.Scan1D extends Object implements Serializable

serialVersionUID: 2937381605461829269L

Serialized Fields

scanNumber

ArrayInt.D0 scanNumber

scanAcquisitionTime

ArrayDouble.D0 scanAcquisitionTime

total_intensity

ArrayDouble.D0 total_intensity

masses

Array masses

intensities

Array intensities

Class maltcms.datastructures.ms.Scan2D extends Scan1D implements Serializable

serialVersionUID: -5785157824205744680L

Serialized Fields

fctime

double fctime

sctime

double sctime

fcind

int fcind

scind

int scind

Package maltcms.datastructures.peak

Class maltcms.datastructures.peak.Peak extends Object implements Serializable

serialVersionUID: -4337180586706400884L

Serialized Fields

scanIndex

int scanIndex

msIntensities

Array msIntensities

sat

double sat

sims

HashMap<K,V> sims

sortedPeaks

HashMap<K,V> sortedPeaks

name

String name

peakIndex

int peakIndex

association

String association

storeOnlyBestSimilarities

boolean storeOnlyBestSimilarities

Class maltcms.datastructures.peak.Peak1D extends Object implements Serializable

serialVersionUID: -8878754902179218064L

Serialized Fields

startIndex

int startIndex

apexIndex

int apexIndex

stopIndex

int stopIndex

apexIntensity

double apexIntensity

startTime

double startTime

stopTime

double stopTime

apexTime

double apexTime

area

double area

normalizedArea

double normalizedArea

mw

double mw

extractedIonCurrent

double[] extractedIonCurrent

snr

double snr

file

String file

peakType

PeakType peakType

normalizationMethods

String[] normalizationMethods

name

String name

peakAnnotations

List<E> peakAnnotations

baselineStartTime

double baselineStartTime

baselineStopTime

double baselineStopTime

baselineStartValue

double baselineStartValue

baselineStopValue

double baselineStopValue

Class maltcms.datastructures.peak.Peak2D extends Peak1D implements Serializable

serialVersionUID: 6343209775465424292L

Serialized Fields

peakArea

PeakArea2D peakArea

scanIndex

int scanIndex

index

int index

firstRetTime

double firstRetTime

secondRetTime

double secondRetTime

identification

List<E> identification

reference

Peak2D reference

Package maltcms.datastructures.quadTree

Class maltcms.datastructures.quadTree.ElementNotFoundException extends RuntimeException implements Serializable

serialVersionUID: 7864374322427340984L

Package maltcms.db.predicates.metabolite

Class maltcms.db.predicates.metabolite.MAggregatePredicate extends MetabolitePredicate implements Serializable

serialVersionUID: -2688853916226964219L

Serialized Fields

mpl

Collection<E> mpl

Class maltcms.db.predicates.metabolite.MetabolitePredicate extends com.db4o.query.Predicate<IMetabolite> implements Serializable

serialVersionUID: 4401086253537298137L

Serialized Fields

im

IMatchPredicate<T> im

Class maltcms.db.predicates.metabolite.MetaboliteSimilarity extends com.db4o.query.Predicate<IMetabolite> implements Serializable

Serialized Fields

similarityFunction

IArraySimilarity similarityFunction

resolution

double resolution

scoreThreshold

double scoreThreshold

massThreshold

double massThreshold

numberOfHitsToReturn

int numberOfHitsToReturn

normalize

boolean normalize

scan

IScan scan

lastMin

double lastMin

lastMax

double lastMax

matches

List<E> matches

comparator

Comparator<T> comparator

Class maltcms.db.predicates.metabolite.MNumRangePredicate extends MetabolitePredicate implements Serializable

serialVersionUID: 4384503672151011994L

Serialized Fields

lB

Number lB

uB

Number uB

Class maltcms.db.predicates.metabolite.MSimilarityPredicate extends MetabolitePredicate implements Serializable

serialVersionUID: -3684834963267981958L

Serialized Fields

s

MetaboliteSimilarity s

Class maltcms.db.predicates.metabolite.MStringContainsPredicate extends MStringMatchPredicate implements Serializable

serialVersionUID: -8108747283945214056L

Class maltcms.db.predicates.metabolite.MStringMatchPredicate extends MetabolitePredicate implements Serializable

serialVersionUID: 7126522681487993030L

Serialized Fields

match

String match

matchCaseInsensitive

boolean matchCaseInsensitive

Package maltcms.db.ui

Class maltcms.db.ui.MetaboliteListCellRenderer extends JLabel implements Serializable

serialVersionUID: -2284912996792720438L

Class maltcms.db.ui.MetaboliteQueryAction extends AbstractAction implements Serializable

serialVersionUID: 8174435563633316055L

Serialized Fields

mvm

MetaboliteViewModel mvm

ap

com.db4o.query.Predicate<ExtentType> ap

jtf

JTextField jtf

filter

String filter

af

IAggregatePredicateFactory<T> af

Class maltcms.db.ui.MetaboliteQueryPanel extends JPanel implements Serializable

serialVersionUID: -3658654429470080006L

Serialized Fields

jtf

JTextField jtf

sb

JButton sb

spb

JButton spb

mvm

MetaboliteViewModel mvm

Class maltcms.db.ui.MetaboliteSearchPreferences extends JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

mvm

MetaboliteViewModel mvm

textFields

HashMap<K,V> textFields

panels

HashMap<K,V> panels

submitFilterButton

JButton submitFilterButton

buttonPanel

JPanel buttonPanel

error

boolean error

Class maltcms.db.ui.MetaboliteViewModel extends AbstractTableModel implements Serializable

serialVersionUID: -38817321732051832L

Serialized Fields

COMMENTS

String COMMENTS

DATE

String DATE

FORMULA

String FORMULA

ID

String ID

MASSWEIGHT

String MASSWEIGHT

MASSSPECTRUM

String MASSSPECTRUM

MAXINTENSITY

String MAXINTENSITY

MAXINTNORM

String MAXINTNORM

MAXMASS

String MAXMASS

MININTENSITY

String MININTENSITY

MININTNORM

String MININTNORM

MINMASS

String MINMASS

NAME

String NAME

RETINDEX

String RETINDEX

RETTIME

String RETTIME

RETTIMEUNIT

String RETTIMEUNIT

SP

String SP

SCANINDEX

String SCANINDEX

SHORTNAME

String SHORTNAME

pmg

PublicMemberGetters<T> pmg

tableHeader

String[] tableHeader

elements

Vector<E> elements

map

TreeMap<K,V> map

oc

com.db4o.ObjectContainer oc

s

ExecutorService s

mv

MetaboliteView mv

headerVisible

boolean[] headerVisible

Class maltcms.db.ui.QueryResultListCellRenderer extends JLabel implements Serializable

serialVersionUID: 5980514459833450228L

Package maltcms.experimental.bipace

Class maltcms.experimental.bipace.PeakList extends Object implements Serializable

Serialized Fields

fragment

cross.datastructures.fragments.IFileFragment fragment

peaks

List<E> peaks

index

int index

Package maltcms.experimental.bipace.api

Class maltcms.experimental.bipace.api.PeakSimilarityCalculator extends Object implements Serializable

Serialized Fields

uniqueId

UUID uniqueId

peakListA

List<E> peakListA

peakListB

List<E> peakListB

similarityFunction

IScalarArraySimilarity similarityFunction

storeOnlyBestSimilarities

boolean storeOnlyBestSimilarities

Package maltcms.experimental.bipace.datastructures.api

Class maltcms.experimental.bipace.datastructures.api.Result extends Object implements Serializable

Serialized Fields

result

Serializable result

producerId

UUID producerId

Package maltcms.experimental.bipace.datastructures.spi

Class maltcms.experimental.bipace.datastructures.spi.PairwisePeakListSimilarities extends Result<cern.colt.matrix.DoubleMatrix2D> implements Serializable

Class maltcms.experimental.bipace.datastructures.spi.Peak2D extends Peak implements Serializable

Serialized Fields

retentionTime1

double retentionTime1

retentionTime2

double retentionTime2

Package maltcms.experimental.bipace.spi

Class maltcms.experimental.bipace.spi.Peak1DSimilarityCalculator extends PeakSimilarityCalculator<Peak> implements Serializable

Serialized Fields

maxRtDifference

double maxRtDifference

Class maltcms.experimental.bipace.spi.Peak2DSimilarityCalculator extends PeakSimilarityCalculator<Peak2D> implements Serializable

Serialized Fields

maxRt1Difference

double maxRt1Difference

maxRt2Difference

double maxRt2Difference

Package maltcms.experimental.operations

Class maltcms.experimental.operations.MSPeaklistAlignment extends TwoFeatureVectorOperation implements Serializable

Serialized Fields

mass_values

String mass_values

intensity_values

String intensity_values

Package maltcms.experimental.ui

Class maltcms.experimental.ui.ImagePanel extends JPanel implements Serializable

serialVersionUID: 4300139196647706338L

Serialized Fields

bi

BufferedImage bi

Package maltcms.io.andims

Class maltcms.io.andims.NetcdfDataSource extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

fileEnding

String[] fileEnding

updateAttributes

boolean updateAttributes

useNetcdfFileCache

boolean useNetcdfFileCache

Deprecated.

saveNCML

boolean saveNCML

scanDimensionVars

List<E> scanDimensionVars

scanDimensionName

String scanDimensionName

pointDimensionVars

List<E> pointDimensionVars

pointDimensionName

String pointDimensionName

Package maltcms.io.csv

Class maltcms.io.csv.FsaTxtDataSource extends Object implements Serializable

Serialized Fields

fileEnding

String[] fileEnding

scanDimensionVars

List<E> scanDimensionVars

scanDimensionName

String scanDimensionName

pointDimensionVars

List<E> pointDimensionVars

pointDimensionName

String pointDimensionName

ndf

NetcdfDataSource ndf

dataFieldToRead

int dataFieldToRead

Package maltcms.io.xml.mzData

Class maltcms.io.xml.mzData.MZDataDataSource extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

fileEnding

String[] fileEnding

mass_values

String mass_values

intensity_values

String intensity_values

total_intensity

String total_intensity

scan_acquisition_time

String scan_acquisition_time

scan_index

String scan_index

mass_range_min

String mass_range_min

mass_range_max

String mass_range_max

ndf

NetcdfDataSource ndf

source_files

String source_files

Package maltcms.io.xml.mzML

Class maltcms.io.xml.mzML.MZMLDataSource extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

fileEnding

String[] fileEnding

mass_values

String mass_values

intensity_values

String intensity_values

total_intensity

String total_intensity

scan_acquisition_time

String scan_acquisition_time

scan_index

String scan_index

mass_range_min

String mass_range_min

mass_range_max

String mass_range_max

ndf

NetcdfDataSource ndf

source_files

String source_files

Package maltcms.io.xml.mzXML

Class maltcms.io.xml.mzXML.MZXMLDataSource extends Object implements Serializable

Serialized Fields

ds

List<E> ds

log

org.slf4j.Logger log

fragmentToValidReaderMap

WeakHashMap<K,V> fragmentToValidReaderMap

Class maltcms.io.xml.mzXML.MZXMLSaxDataSource extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

fileEnding

String[] fileEnding

mass_values

String mass_values

intensity_values

String intensity_values

total_intensity

String total_intensity

scan_acquisition_time

String scan_acquisition_time

scan_index

String scan_index

mass_range_min

String mass_range_min

mass_range_max

String mass_range_max

ndf

NetcdfDataSource ndf

source_files

String source_files

mslevel

int mslevel

parser

org.systemsbiology.jrap.MSXMLParser parser

variableToArrayCache

cross.datastructures.ehcache.ICacheDelegate<K,V> variableToArrayCache

Class maltcms.io.xml.mzXML.MZXMLStaxDataSource extends Object implements Serializable

Serialized Fields

log

org.slf4j.Logger log

fileEnding

String[] fileEnding

mass_values

String mass_values

intensity_values

String intensity_values

total_intensity

String total_intensity

scan_acquisition_time

String scan_acquisition_time

scan_index

String scan_index

mass_range_min

String mass_range_min

mass_range_max

String mass_range_max

ndf

NetcdfDataSource ndf

source_files

String source_files

mslevel

int mslevel

parser

org.systemsbiology.jrap.stax.MSXMLParser parser

variableToArrayCache

cross.datastructures.ehcache.ICacheDelegate<K,V> variableToArrayCache

Package maltcms.math.functions

Class maltcms.math.functions.DtwPairwiseSimilarity extends Object implements Serializable

Serialized Fields

expansionWeight

double expansionWeight

matchWeight

double matchWeight

compressionWeight

double compressionWeight

denseMassSpectraSimilarity

IArraySimilarity denseMassSpectraSimilarity

Class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity extends Object implements Serializable

Serialized Fields

expansionWeight

double expansionWeight

matchWeight

double matchWeight

compressionWeight

double compressionWeight

retentionTimeSimilarity

IScalarSimilarity retentionTimeSimilarity

denseMassSpectraSimilarity

IArraySimilarity denseMassSpectraSimilarity

Package maltcms.mpaxs

Class maltcms.mpaxs.MaltcmsConfigurableRunnable extends Object implements Serializable

Class maltcms.mpaxs.TestCallable extends Object implements Serializable

Class maltcms.mpaxs.TestConfigurableCallable extends Object implements Serializable

Serialized Fields

progress

net.sf.maltcms.execution.api.job.Progress progress

finished

long finished

Class maltcms.mpaxs.TestRunnable extends Object implements Serializable

Package maltcms.tools

Class maltcms.tools.PathTools extends Object implements Serializable

Serialized Fields

threshold

double threshold

nbranches

int nbranches

symbolicPath

String symbolicPath

map

List<E> map

nexp

int nexp

ncomp

int ncomp

ndiag

int ndiag

window

int window

Package maltcms.ui

Class maltcms.ui.TabbedPanel extends JPanel implements Serializable

serialVersionUID: 7611857256393422827L

Serialized Fields

pa

PartitionedArray pa

paSize

Dimension paSize

paIm

BufferedImage paIm

rr

maltcms.ui.TabbedPanel.RepaintRunnable rr

aps

AnchorPairSet aps

Package maltcms.ui.charts

Class maltcms.ui.charts.AChart extends Object implements Serializable

Serialized Fields

yaxis_min

double yaxis_min

yaxis_max

double yaxis_max

Class maltcms.ui.charts.AlignmentMapChart extends AChart<org.jfree.chart.plot.XYPlot> implements Serializable

Serialized Fields

map

List<E> map

height

int height

title

String title

domain1

Array domain1

domain2

Array domain2

x_label

String x_label

log

org.slf4j.Logger log

stride

int stride

Class maltcms.ui.charts.BHeatMapChart extends AChart<XYBPlot> implements Serializable

Serialized Fields

xlabel

String xlabel

ylabel

String ylabel

label

String label

title

String title

filename

String filename

xaxis

ArrayDouble.D1 xaxis

yaxis

ArrayDouble.D1 yaxis

Class maltcms.ui.charts.CombinedDomainXYChart extends AChart<org.jfree.chart.plot.XYPlot> implements Serializable

Serialized Fields

title

String title

x_axis

String x_axis

subplots

List<E> subplots

cdxyp

org.jfree.chart.plot.CombinedDomainXYPlot cdxyp

gap

int gap

Class maltcms.ui.charts.EPlotRunner extends PlotRunner implements Serializable

Serialized Fields

log

org.slf4j.Logger log

chart

org.jfree.chart.JFreeChart chart

Class maltcms.ui.charts.GradientPaintScale extends Object implements Serializable

serialVersionUID: 1121734275349109897L

Serialized Fields

ramp

int[][] ramp

sampleTable

double[] sampleTable

breakPoints

double[] breakPoints

st

double[] st

min

double min

max

double max

alpha

double alpha

beta

double beta

lookupImage

BufferedImage lookupImage

colors

Color[] colors

lookupColors

Color[] lookupColors

Class maltcms.ui.charts.HeatMapChart extends AChart<org.jfree.chart.plot.XYPlot> implements Serializable

Serialized Fields

hm

BufferedImage hm

xlabel

String xlabel

ylabel

String ylabel

label

String label

title

String title

xaxis

ArrayDouble.D1 xaxis

yaxis

ArrayDouble.D1 yaxis

Class maltcms.ui.charts.JFreeChartViewer extends JFrame implements Serializable

serialVersionUID: -830245788879399345L

Serialized Fields

jtp

JTabbedPane jtp

lastOpenDir

File lastOpenDir

jmb

JMenuBar jmb

fileMenu

JMenu fileMenu

status

JLabel status

Class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction extends AbstractAction implements Serializable

serialVersionUID: 425194552644224115L

Serialized Fields

jfc

org.jfree.chart.JFreeChart jfc

Class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction extends AbstractAction implements Serializable

serialVersionUID: 5547094237664337509L

Class maltcms.ui.charts.JFreeChartViewer.FileOpenAction extends AbstractAction implements Serializable

serialVersionUID: -8133108907581040380L

Serialized Fields

parent

Component parent

Class maltcms.ui.charts.MassSpectrumPlot extends AChart<org.jfree.chart.plot.XYPlot> implements Serializable

Serialized Fields

title

String title

legendName

List<E> legendName

values

List<E> values

useLogScale

boolean useLogScale

showLegend

boolean showLegend

seriesColor

List<E> seriesColor

barWidth

double barWidth

barDistance

double barDistance

maxAnnotations

int maxAnnotations

Class maltcms.ui.charts.PlotRunner extends Object implements Serializable

Serialized Fields

plot

org.jfree.chart.plot.Plot plot

title

String title

filetype

String filetype

filename

String filename

outputDir

File outputDir

fontFamily

String fontFamily

imgwidth

int imgwidth

imgheight

int imgheight

sizeOverride

boolean sizeOverride

headless

boolean headless

stop

boolean stop

file

File file

targetContainer

JFrame targetContainer

log

org.slf4j.Logger log

serializeJFreeChart

boolean serializeJFreeChart

saveGraphics

boolean saveGraphics

Class maltcms.ui.charts.SpiderWebChart extends AChart<org.jfree.chart.plot.SpiderWebPlot> implements Serializable

Serialized Fields

title

String title

cd

org.jfree.data.category.CategoryDataset cd

Class maltcms.ui.charts.VariableSelectionPanel extends JPanel implements Serializable

serialVersionUID: -1731263966310777412L

Serialized Fields

jCheckBox1

JCheckBox jCheckBox1

jComboBox1

JComboBox jComboBox1

jComboBox3

JComboBox jComboBox3

jLabel1

JLabel jLabel1

jLabel4

JLabel jLabel4

jSeparator1

JSeparator jSeparator1

Class maltcms.ui.charts.XYBPlot extends org.jfree.chart.plot.XYPlot implements Serializable

serialVersionUID: 1311452000544833279L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Responsible for the reading of serialized objects.

Throws:: IOException - Includes any I/O exceptions that may occur; ClassNotFoundException - Includes any class not found exception that may occur

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Is responsible for the serialization and to store all needed object in a way, that readObject can find it again.

Throws:: IOException - Includes any I/O exceptions that may occur

Serialized Fields

maxUpperXAxisBound

Double maxUpperXAxisBound

maxUpperYAxisBound

Double maxUpperYAxisBound

minLowerXAxisBound

Double minLowerXAxisBound

minLowerYAxisBound

Double minLowerYAxisBound

backgroundImageFilename

String backgroundImageFilename

Class maltcms.ui.charts.XYChart extends AChart<org.jfree.chart.plot.XYPlot> implements Serializable

Serialized Fields

xaxis

String xaxis

yaxis

String yaxis

labels

List<E> labels

annotations

List<E> annotations

arrays

List<E> arrays

domains

Array[] domains

title

String title

annotation_positions_x

Array annotation_positions_x

annotation_positions_y

Array annotation_positions_y

renderArea

boolean renderArea

fgAlpha

float fgAlpha

diffRender

boolean diffRender

log

org.slf4j.Logger log

logScale

boolean logScale

Class maltcms.ui.charts.XYZChart extends AChart<org.jfree.chart.plot.XYPlot> implements Serializable

Serialized Fields

x

Array x

y

ArrayList<E> y

z

ArrayList<E> z

name

String name

xaxis

String xaxis

yaxis

String yaxis

title

String title

log

org.slf4j.Logger log

Package maltcms.ui.renderer

Class maltcms.ui.renderer.LineVectorRenderer extends org.jfree.chart.renderer.xy.VectorRenderer implements Serializable

serialVersionUID: 7297064254819024794L

Package maltcms.ui.wizard

Class maltcms.ui.wizard.AlignmentPane extends org.netbeans.spi.wizard.WizardPage implements Serializable

serialVersionUID: -5324638127680705898L

Serialized Fields

dcbm

DefaultComboBoxModel dcbm

jComboBox1

JComboBox jComboBox1

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

jLabel3

JLabel jLabel3

jLabel4

JLabel jLabel4

jTextField1

JTextField jTextField1

jTextField2

JTextField jTextField2

jTextField3

JTextField jTextField3

Class maltcms.ui.wizard.AnchorDefinitionPane extends org.netbeans.spi.wizard.WizardPage implements Serializable

serialVersionUID: 4887167150661489442L

Serialized Fields

dtm

DefaultTableModel dtm

longestString

String longestString

files

HashSet<E> files

dlm

DefaultComboBoxModel dlm

activeFile

String activeFile

anchorID

int anchorID

cwd

File cwd

hasSaved

boolean hasSaved

hasLoaded

boolean hasLoaded

fileToAnchorsMap

HashMap<K,V> fileToAnchorsMap

jButton1

JButton jButton1

jButton2

JButton jButton2

jButton3

JButton jButton3

jButton4

JButton jButton4

jButton5

JButton jButton5

jComboBox1

JComboBox jComboBox1

jLabel6

JLabel jLabel6

jScrollPane2

JScrollPane jScrollPane2

jTable1

JTable jTable1

Class maltcms.ui.wizard.FileInputOutputPane extends org.netbeans.spi.wizard.WizardPage implements Serializable

serialVersionUID: 8468582599008051433L

Serialized Fields

cwd

File cwd

cod

File cod

dlm

DefaultListModel dlm

jButton1

JButton jButton1

jButton3

JButton jButton3

jButton4

JButton jButton4

jCheckBox1

JCheckBox jCheckBox1

jLabel1

JLabel jLabel1

jLabel6

JLabel jLabel6

jLabel7

JLabel jLabel7

jList1

JList jList1

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jScrollPane1

JScrollPane jScrollPane1

jTextField5

JTextField jTextField5

jTextField6

JTextField jTextField6

Class maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction extends AbstractAction implements Serializable

serialVersionUID: -6216223747360194482L

Serialized Fields

pw

PipelineWizard pw

Class maltcms.ui.wizard.PipelineWizard.EditConfigurationAction extends AbstractAction implements Serializable

serialVersionUID: -4941454703967935783L

Serialized Fields

pw

PipelineWizard pw

Class maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction extends AbstractAction implements Serializable

serialVersionUID: -3371831501616427849L

Serialized Fields

jf

Container jf

Class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction extends AbstractAction implements Serializable

serialVersionUID: 7614497705493470346L

Serialized Fields

c

Container c

cfg

org.apache.commons.configuration.PropertiesConfiguration cfg

Class maltcms.ui.wizard.PreprocessingPane extends org.netbeans.spi.wizard.WizardPage implements Serializable

serialVersionUID: 4992924104511397101L

Serialized Fields

dlm1

DefaultListModel dlm1

jButton2

JButton jButton2

jButton5

JButton jButton5

jCheckBox1

JCheckBox jCheckBox1

jLabel1

JLabel jLabel1

jLabel8

JLabel jLabel8

jList2

JList jList2

jScrollPane2

JScrollPane jScrollPane2

jTextField7

JTextField jTextField7

Class maltcms.ui.wizard.VisualizationPane extends org.netbeans.spi.wizard.WizardPage implements Serializable

serialVersionUID: 1009564289591217777L

Serialized Fields

jCheckBox1

JCheckBox jCheckBox1

jCheckBox2

JCheckBox jCheckBox2

jCheckBox3

JCheckBox jCheckBox3

jCheckBox4

JCheckBox jCheckBox4

jCheckBox5

JCheckBox jCheckBox5

jCheckBox6

JCheckBox jCheckBox6

jComboBox1

JComboBox jComboBox1

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

jLabel3

JLabel jLabel3

jLabel4

JLabel jLabel4

jLabel5

JLabel jLabel5

jTextField1

JTextField jTextField1

jTextField2

JTextField jTextField2

jTextField3

JTextField jTextField3

jTextField4

JTextField jTextField4

Package net.sf.maltcms.apps

Class net.sf.maltcms.apps.MetaboliteBrowser extends JFrame implements Serializable

serialVersionUID: 6217168349675106268L

Serialized Fields

selectTableHeaders

HashMap<K,V> selectTableHeaders

mvm

MetaboliteViewModel mvm

qpanel

JPanel qpanel

Package net.sf.maltcms.evaluation.api

Class net.sf.maltcms.evaluation.api.PeakRTFeatureVector extends Object implements Serializable

serialVersionUID: -5936343655074144856L

Serialized Fields

rt

ArrayDouble.D0 rt

Package net.sf.maltcms.evaluation.api.alignment

Class net.sf.maltcms.evaluation.api.alignment.AlignmentColumn extends Object implements Serializable

serialVersionUID: -5936343655074144856L

Serialized Fields

values

ArrayDouble.D1 values

Package net.sf.maltcms.evaluation.api.tasks

Package net.sf.maltcms.evaluation.spi.classification

Class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformancePostProcessor extends Object implements Serializable

Serialized Fields

groundTruthFile

File groundTruthFile

delta

double delta

oc

com.db4o.ObjectContainer oc

toolFileName

String toolFileName

Class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector extends Object implements Serializable

serialVersionUID: -5936343655074144856L

Serialized Fields

rt

ArrayDouble.D0 rt

Package net.sf.maltcms.evaluation.spi.hohenheim

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.AggregatePeakPredicate extends Eval.PeakPredicate implements Serializable

serialVersionUID: -6754630453106703429L

Serialized Fields

p

com.db4o.query.Predicate<ExtentType>[] p

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNameFilenameRTPeakPredicate extends Eval.PeakPredicate implements Serializable

serialVersionUID: -3389850465308219316L

Serialized Fields

rt

double rt

maxrtdev

double maxrtdev

name

String name

chromname

String chromname

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakNamePredicate extends Eval.PeakPredicate implements Serializable

serialVersionUID: 6463510990923985730L

Serialized Fields

name

String name

peakName

String peakName

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakPredicate extends Eval.PeakPredicate implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakNamePeakPredicate extends com.db4o.query.Predicate<Peak> implements Serializable

serialVersionUID: 4469891680424542881L

Serialized Fields

file

String file

creator

String creator

peakname

String peakname

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakPredicate extends com.db4o.query.Predicate<Peak> implements Serializable

serialVersionUID: 5009287857661674974L

Serialized Fields

file

String file

creator

String creator

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramNamePredicate extends com.db4o.query.Predicate<Chromatogram> implements Serializable

serialVersionUID: -2493853621255366827L

Serialized Fields

name

String name

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPeakPredicate extends Eval.PeakPredicate implements Serializable

serialVersionUID: 5009287857661674974L

Serialized Fields

file

String file

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPredicate extends com.db4o.query.Predicate<Chromatogram> implements Serializable

serialVersionUID: -55691937902127499L

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPeakPredicate extends Eval.PeakPredicate implements Serializable

serialVersionUID: -3734257468780932748L

Serialized Fields

creator

String creator

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPredicate extends com.db4o.query.Predicate<Creator> implements Serializable

serialVersionUID: -3543269480153995134L

Serialized Fields

name

String name

Class net.sf.maltcms.evaluation.spi.hohenheim.Eval.PeakPredicate extends com.db4o.query.Predicate<Peak> implements Serializable

serialVersionUID: -1948551337371019623L

Package net.sf.maltcms.evaluation.spi.tasks

Class net.sf.maltcms.evaluation.spi.tasks.Task extends Object implements Serializable

serialVersionUID: 986719239076016L

Serialized Fields

commandLine

List<E> commandLine

additionalEnvironment

HashMap<K,V> additionalEnvironment

workingDirectory

File workingDirectory

postProcessors

List<E> postProcessors

outputDirectory

File outputDirectory

taskId

UUID taskId

Package net.sf.maltcms.evaluation.spi.tasks.execution

Class net.sf.maltcms.evaluation.spi.tasks.execution.APipeline extends Object implements Serializable

Serialized Fields

pipelines

List<E> pipelines

name

String name

ics

net.sf.maltcms.execution.api.ICompletionService<T> ics

Class net.sf.maltcms.evaluation.spi.tasks.execution.FilePipeline extends APipeline<File> implements Serializable

Package net.sf.maltcms.evaluation.spi.tasks.maltcms

Class net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult extends Object implements Serializable

Serialized Fields

taskInputs

List<E> taskInputs

taskOutputs

List<E> taskOutputs

Class net.sf.maltcms.evaluation.spi.tasks.maltcms.MaltcmsTaskResult extends DefaultTaskResult implements Serializable

serialVersionUID: -4395347427746465402L

Serialized Fields

workflow

File workflow

Package net.sf.maltcms.evaluation.spi.xcalibur

Class net.sf.maltcms.evaluation.spi.xcalibur.Peak extends Object implements Serializable

Serialized Fields

parent

Chromatogram parent

name

String name

creatorname

String creatorname

rt

double rt

rtstart

double rtstart

rtstop

double rtstop

mw

double[] mw

area

double area

height

double height

Package smueller

Class smueller.SymbolicRepresentationAlignment extends cross.commands.fragments.AFragmentCommand implements Serializable

Serialized Fields

pairsWithFirst

boolean pairsWithFirst

log

org.slf4j.Logger log

minArrayComp

String minArrayComp

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