Serialized Form (Maltcms-Modules 1.3.0 API)

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
```
StatsMap statsMap
```
    - useAnchors
```
boolean useAnchors
```
    - anchorRadius
```
int anchorRadius
```
    - minScansBetweenAnchors
```
int minScansBetweenAnchors
```
    - 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.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
```
Package maltcms.commands.fragments.alignment
- Class maltcms.commands.fragments.alignment.CenterStarAlignment extends 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - ticPeaks
```
String ticPeaks
```
    - massValues
```
String massValues
```
    - scanIndex
```
String scanIndex
```
    - intensityValues
```
String intensityValues
```
    - anchorNames
```
String anchorNames
```
    - anchorTimes
```
String anchorTimes
```
    - anchorRetentionIndex
```
String anchorRetentionIndex
```
    - anchorScanIndex
```
String anchorScanIndex
```
    - binnedIntensities
```
String binnedIntensities
```
    - binnedScanIndex
```
String binnedScanIndex
```
    - scanAcquisitionTime
```
String scanAcquisitionTime
```
    - peakAreaVariable
```
String peakAreaVariable
```
    - useUserSuppliedAnchors
```
boolean useUserSuppliedAnchors
```
    - minCliqueSize
```
int minCliqueSize
```
    - savePeakSimilarities
```
boolean savePeakSimilarities
```
    - savePeakMatchRTTable
```
boolean savePeakMatchRTTable
```
    - savePeakMatchAreaTable
```
boolean savePeakMatchAreaTable
```
    - savePeakMatchAreaPercentTable
```
boolean savePeakMatchAreaPercentTable
```
    - saveXMLAlignment
```
boolean saveXMLAlignment
```
    - maxBBHErrors
```
int maxBBHErrors
```
      Deprecated.
    - minBbhFraction
```
double minBbhFraction
```
    - savePlots
```
boolean savePlots
```
    - saveUnmatchedPeaks
```
boolean saveUnmatchedPeaks
```
    - saveIncompatiblePeaks
```
boolean saveIncompatiblePeaks
```
    - saveUnassignedPeaks
```
boolean saveUnassignedPeaks
```
    - useSparseArrays
```
boolean useSparseArrays
```
    - use2DRetentionTimes
```
boolean use2DRetentionTimes
```
    - workerFactory
```
IWorkerFactory workerFactory
```
    - peakFactory
```
IPeakFactory peakFactory
```
    - rtNormalizationFactor
```
double rtNormalizationFactor
```
    - rtOutputFormat
```
String rtOutputFormat
```
    - postProcessCliques
```
boolean postProcessCliques
```
      Deprecated.
- Class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment extends AFragmentCommand implements Serializable
  - Serialized Fields
    - guideTreeClass
```
String guideTreeClass
```
Package maltcms.commands.fragments.alignment.peakCliqueAlignment
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.BBHPeakEdgeSet extends LinkedHashSet<Tuple2D<IBipacePeak,IBipacePeak>> implements Serializable
- 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
```
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker2D extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
    - lhsPeaks
```
List<E> lhsPeaks
```
    - rhsPeaks
```
List<E> rhsPeaks
```
    - similarityFunction
```
IScalarArraySimilarity similarityFunction
```
    - maxRTDifferenceRt1
```
double maxRTDifferenceRt1
```
    - maxRTDifferenceRt2
```
double maxRTDifferenceRt2
```
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.Peak2D extends PeakNG implements Serializable
  - Serialized Fields
    - firstColumnElutionTime
```
double firstColumnElutionTime
```
    - secondColumnElutionTime
```
double secondColumnElutionTime
```
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.UnmatchedPeaksSet extends LinkedHashSet<IBipacePeak> implements Serializable
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.Worker2DFactory extends Object implements Serializable
  - Serialized Fields
    - maxRTDifferenceRt1
```
double maxRTDifferenceRt1
```
    - maxRTDifferenceRt2
```
double maxRTDifferenceRt2
```
    - similarityFunction
```
IScalarArraySimilarity similarityFunction
```
    - assumeSymmetricSimilarity
```
boolean assumeSymmetricSimilarity
```
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.WorkerFactory extends Object implements Serializable
  - Serialized Fields
    - maxRTDifference
```
double maxRTDifference
```
    - similarityFunction
```
IScalarArraySimilarity similarityFunction
```
    - assumeSymmetricSimilarity
```
boolean assumeSymmetricSimilarity
```
Package maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.Peak1DFactory extends Object implements Serializable
  - Serialized Fields
    - peakAreaVar
```
String peakAreaVar
```
    - scanAcquisitionTimeVar
```
String scanAcquisitionTimeVar
```
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.Peak1DMSFactory extends Object implements Serializable
  - Serialized Fields
    - massesVar
```
String massesVar
```
    - scanIndexVar
```
String scanIndexVar
```
    - intensitiesVar
```
String intensitiesVar
```
    - binnedScanIndexVar
```
String binnedScanIndexVar
```
    - binnedMassesVar
```
String binnedMassesVar
```
    - binnedIntensitiesVar
```
String binnedIntensitiesVar
```
    - scanAcquisitionTimeVar
```
String scanAcquisitionTimeVar
```
- Class maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.Peak2DMSFactory extends Object implements Serializable
  - Serialized Fields
    - massesVar
```
String massesVar
```
    - scanIndexVar
```
String scanIndexVar
```
    - intensitiesVar
```
String intensitiesVar
```
    - binnedScanIndexVar
```
String binnedScanIndexVar
```
    - binnedMassesVar
```
String binnedMassesVar
```
    - binnedIntensitiesVar
```
String binnedIntensitiesVar
```
    - firstColumnElutionTimeVar
```
String firstColumnElutionTimeVar
```
    - secondColumnElutionTimeVar
```
String secondColumnElutionTimeVar
```
    - scanAcquisitionTimeVar
```
String scanAcquisitionTimeVar
```
Package maltcms.commands.fragments.assignment
- Class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment extends 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - normalize_scans
```
boolean normalize_scans
```
    - inputFiles
```
TupleND<T extends Serializable> inputFiles
```
    - consensus
```
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
```
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 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.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
```
Tuple2D<T,U> input
```
    - alignment
```
URI alignment
```
    - value
```
double value
```
    - statsMap
```
StatsMap statsMap
```
- Class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceWorker extends Object implements Serializable
  
  serialVersionUID:
  
  4556712389798130L
  - Serialized Fields
    - similarity
```
PairwiseFeatureSequenceSimilarity similarity
```
    - workflow
```
IWorkflow workflow
```
    - input
```
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 AFragmentCommand implements Serializable
  - Serialized Fields
    - ordinateValuesVariable
```
String ordinateValuesVariable
```
    - scanAcquisitionTimeVariable
```
String scanAcquisitionTimeVariable
```
    - actualSamplingIntervalVariable
```
String actualSamplingIntervalVariable
```
    - actualDelayTimeVariable
```
String actualDelayTimeVariable
```
- Class maltcms.commands.fragments.io.ANDIMSExporter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - skipAggregatedVariables
```
boolean skipAggregatedVariables
```
- Class maltcms.commands.fragments.io.CSVAnchorReader extends AFragmentCommand implements Serializable
  - Serialized Fields
    - omit
```
String omit
```
    - time
```
boolean time
```
    - index
```
boolean index
```
    - scan
```
boolean scan
```
    - location
```
List<E> location
```
    - fileDesignation
```
String fileDesignation
```
    - basedir
```
String basedir
```
    - max_names_length
```
int max_names_length
```
    - anchorNamesVariableName
```
String anchorNamesVariableName
```
    - anchorTimesVariableName
```
String anchorTimesVariableName
```
    - anchorRetentionIndexVariableName
```
String anchorRetentionIndexVariableName
```
    - anchorScanIndexVariableName
```
String anchorScanIndexVariableName
```
    - satVariableName
```
String satVariableName
```
- Class maltcms.commands.fragments.io.DataFileVariablePrinter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
- Class maltcms.commands.fragments.io.MSPExporter extends AFragmentCommand implements Serializable
- Class maltcms.commands.fragments.io.MZMLExporter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - psiMsVersion
```
String psiMsVersion
```
    - unitOntologyVersion
```
String unitOntologyVersion
```
    - compressSpectra
```
boolean compressSpectra
```
    - scanIndexVariable
```
String scanIndexVariable
```
    - massValuesVariable
```
String massValuesVariable
```
    - intensityValuesVariable
```
String intensityValuesVariable
```
    - totalIntensityVariable
```
String totalIntensityVariable
```
    - scanAcquisitionTimeVariable
```
String scanAcquisitionTimeVariable
```
- Class maltcms.commands.fragments.io.MZMLExporterWorker extends Object implements Serializable
  - Serialized Fields
    - inputFile
```
URI inputFile
```
    - inputFileId
```
String inputFileId
```
    - outputFile
```
URI outputFile
```
    - psiMsVersion
```
String psiMsVersion
```
    - unitOntologyVersion
```
String unitOntologyVersion
```
    - compressSpectra
```
boolean compressSpectra
```
    - scanIndexVariable
```
String scanIndexVariable
```
    - massValuesVariable
```
String massValuesVariable
```
    - intensityValuesVariable
```
String intensityValuesVariable
```
    - totalIntensityVariable
```
String totalIntensityVariable
```
    - scanAcquisitionTimeVariable
```
String scanAcquisitionTimeVariable
```
- Class maltcms.commands.fragments.io.ObiWarplmataExporter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - scanAcquisitionTimeVariableName
```
String scanAcquisitionTimeVariableName
```
    - binnedIntensitiesVariableName
```
String binnedIntensitiesVariableName
```
    - binnedScanIndexVariableName
```
String binnedScanIndexVariableName
```
    - binnedMassesVariableName
```
String binnedMassesVariableName
```
- Class maltcms.commands.fragments.io.PeakAreaTableExporter extends AFragmentCommand implements Serializable
- Class maltcms.commands.fragments.io.TICPeakListImporter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - filesToRead
```
List<E> filesToRead
```
    - scanIndexOffset
```
int scanIndexOffset
```
    - scanIndexColumnName
```
String scanIndexColumnName
```
    - ticPeakVarName
```
String ticPeakVarName
```
- Class maltcms.commands.fragments.io.VariableDataExporter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - varNames
```
ArrayList<E> varNames
```
Package maltcms.commands.fragments.io.mzml
- Class maltcms.commands.fragments.io.mzml.CachedSpectrumList extends uk.ac.ebi.jmzml.model.mzml.SpectrumList implements Serializable
  - Serialized Fields
    - idxToSpectrum
```
ICacheDelegate<K,V> idxToSpectrum
```
Package maltcms.commands.fragments.peakfinding
- Class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - binnedMassValues
```
String binnedMassValues
```
    - binnedIntensityValues
```
String binnedIntensityValues
```
    - binnedScanIndex
```
String binnedScanIndex
```
- Class maltcms.commands.fragments.peakfinding.CwtTicPeakFinder extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - peakThreshold
```
double peakThreshold
```
    - filterWindow
```
int filterWindow
```
- Class maltcms.commands.fragments.peakfinding.PeakAreaNormalizer extends AFragmentCommand implements Serializable
  - Serialized Fields
    - peakNormalizers
```
List<E> peakNormalizers
```
- Class maltcms.commands.fragments.peakfinding.TICPeakFinder extends 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
```
URI input
```
    - output
```
URI 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
```
URI input
```
    - output
```
URI 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - defaultVariables
```
List<E> defaultVariables
```
    - additionalVariables
```
List<E> additionalVariables
```
- Class maltcms.commands.fragments.preprocessing.DenseArrayProducer extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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
```
    - normalizeScans
```
boolean normalizeScans
```
    - 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - excludeMasses
```
List<E> excludeMasses
```
    - epsilon
```
double epsilon
```
    - massValuesVar
```
String massValuesVar
```
    - intensValuesVar
```
String intensValuesVar
```
    - scanIndexVar
```
String scanIndexVar
```
    - totalIntensVar
```
String totalIntensVar
```
    - invert
```
boolean invert
```
- Class maltcms.commands.fragments.preprocessing.ScanExtractor extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - totalIntensityVar
```
String totalIntensityVar
```
    - scanAcquisitionTimeVar
```
String scanAcquisitionTimeVar
```
    - scanIndexVar
```
String scanIndexVar
```
    - startScan
```
int startScan
```
    - endScan
```
int endScan
```
    - startTime
```
double startTime
```
    - endTime
```
double endTime
```
Package maltcms.commands.fragments.preprocessing.defaultVarLoader
- Class maltcms.commands.fragments.preprocessing.defaultVarLoader.DefaultVarLoaderWorker extends Object implements Serializable
  - Serialized Fields
    - fileToLoad
```
URI fileToLoad
```
    - fileToSave
```
URI fileToSave
```
    - defaultVariables
```
List<E> defaultVariables
```
    - additionalVariables
```
List<E> additionalVariables
```
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
```
URI fileToLoad
```
    - fileToSave
```
URI fileToSave
```
- Class maltcms.commands.fragments.preprocessing.denseArrayProducer.MinMaxMassFinderWorker extends Object implements Serializable
  - Serialized Fields
    - fileToLoad
```
URI fileToLoad
```
    - ignoreMinMaxMassArrays
```
boolean ignoreMinMaxMassArrays
```
    - minMassVariableName
```
String minMassVariableName
```
    - maxMassVariableName
```
String maxMassVariableName
```
    - fallbackVariableName
```
String fallbackVariableName
```
Package maltcms.commands.fragments.visualization
- Class maltcms.commands.fragments.visualization.Array1DVisualizer extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - drawEICs
```
List<E> drawEICs
```
    - eicBinSize
```
double eicBinSize
```
- Class maltcms.commands.fragments.visualization.MZIDistributionVisualizer extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - filea
```
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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - filename
```
String filename
```
    - reference_file_name
```
String reference_file_name
```
    - query_file_name
```
String query_file_name
```
    - format
```
String format
```
    - chromatogramHeight
```
int chromatogramHeight
```
    - left_chromatogram_var
```
String left_chromatogram_var
```
    - top_chromatogram_var
```
String top_chromatogram_var
```
    - path_i
```
String path_i
```
    - path_j
```
String path_j
```
    - full_spec
```
boolean full_spec
```
    - colorramp_location
```
String colorramp_location
```
    - sampleSize
```
int sampleSize
```
    - pairsWithFirstElement
```
boolean pairsWithFirstElement
```
    - drawPath
```
boolean drawPath
```
    - matrix_vars
```
List<E> matrix_vars
```
    - fontsize
```
int fontsize
```
- Class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - normalize
```
boolean normalize
```
    - normalize_global
```
boolean normalize_global
```
    - mapheight
```
int mapheight
```
    - total_intensity
```
String total_intensity
```
    - scan_acquisition_time
```
String scan_acquisition_time
```
    - substract_start_time
```
boolean substract_start_time
```
    - 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
```
    - ima
```
BufferedImage ima
```
    - imb
```
BufferedImage imb
```
    - map
```
BufferedImage map
```
- Class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - pairwiseDistanceVariable
```
String pairwiseDistanceVariable
```
- Class maltcms.commands.fragments.visualization.TICHeatmapCoplot extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - colorRampLocation
```
String colorRampLocation
```
    - totalIntensityVar
```
String totalIntensityVar
```
    - scanAcquisitionTimeVar
```
String scanAcquisitionTimeVar
```
Package maltcms.commands.fragments.warp
- Class maltcms.commands.fragments.warp.ChromatogramWarp extends AFragmentCommand implements Serializable
  - Serialized Fields
    - indexedVars
```
List<E> indexedVars
```
      Deprecated.
    - plainVars
```
List<E> plainVars
```
      Deprecated.
    - indexVar
```
String indexVar
```
      Deprecated.
    - anchorScanIndexVariableName
```
String anchorScanIndexVariableName
```
      Deprecated.
    - anchorNameVariableName
```
String anchorNameVariableName
```
      Deprecated.
    - average
```
boolean average
```
      Deprecated.
- Class maltcms.commands.fragments.warp.ChromatogramWarp2 extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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
```

Package maltcms.commands.fragments2d.peakfinding

Class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing extends 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.cwt
- Class maltcms.commands.fragments2d.peakfinding.cwt.CwtPeakFinder extends AFragmentCommand implements Serializable
  - Serialized Fields
    - minScale
```
int minScale
```
    - maxScale
```
int maxScale
```
    - maxRidgeCost
```
double maxRidgeCost
```
    - minRelativeIntensity
```
double minRelativeIntensity
```
    - modulationTime
```
double modulationTime
```
    - scanRate
```
double scanRate
```
- Class maltcms.commands.fragments2d.peakfinding.cwt.CwtRunnable extends Object implements Serializable
  
  serialVersionUID:
  
  -517839315109598824L
  - Serialized Fields
    - minScale
```
int minScale
```
    - maxScale
```
int maxScale
```
    - maxRidgeCost
```
double maxRidgeCost
```
    - minRelativeIntensity
```
double minRelativeIntensity
```
    - inputFile
```
URI inputFile
```
    - outputDir
```
String outputDir
```
    - modulationTime
```
double modulationTime
```
    - scanRate
```
double scanRate
```
    - ridgeTree
```
QuadTree<T> ridgeTree
```
Package maltcms.commands.fragments2d.peakfinding.output
- Class maltcms.commands.fragments2d.peakfinding.output.PeakExporter extends Object implements Serializable
  - Serialized Fields
    - 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
```
IFileFragment ff
```
Package maltcms.commands.fragments2d.preprocessing
- Class maltcms.commands.fragments2d.preprocessing.Data1Dto2DConverter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - outputFileName
```
String outputFileName
```
    - modulationTime
```
double modulationTime
```
- Class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer extends 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 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
```
    - intensityValuesVar
```
String intensityValuesVar
```
    - massValuesVar
```
String massValuesVar
```
    - scanIndexVar
```
String scanIndexVar
```
    - firstColumnElutionTimeVar
```
String firstColumnElutionTimeVar
```
    - secondColumnElutionTimeVar
```
String secondColumnElutionTimeVar
```
    - modulationTime
```
double modulationTime
```
    - scanDuration
```
double scanDuration
```
    - scanRate
```
double scanRate
```
    - scanAcquisitionTimeOffset
```
double scanAcquisitionTimeOffset
```
    - modulationIndex0Dimension
```
String modulationIndex0Dimension
```
    - modulationIndex1Dimension
```
String modulationIndex1Dimension
```
    - modulationTimeDimension
```
String modulationTimeDimension
```
    - scanRateDimension
```
String scanRateDimension
```
    - scanNumberDimension
```
String scanNumberDimension
```
    - estimateModulationTime
```
boolean estimateModulationTime
```
    - maxScanAcquisitionTimeDelta
```
double maxScanAcquisitionTimeDelta
```
- Class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter extends AFragmentCommand implements Serializable
  - Serialized Fields
    - snrthreshold
```
double snrthreshold
```
- Class maltcms.commands.fragments2d.preprocessing.MeanVarProducer extends 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 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 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 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
```
URI input
```
    - numberOfScans
```
int numberOfScans
```
    - offset
```
int offset
```
Package maltcms.commands.fragments2d.testing
- Class maltcms.commands.fragments2d.testing.Alignment2D extends 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - description
```
String description
```
    - workflowSlot
```
WorkflowSlot workflowSlot
```
    - 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 AFragmentCommand implements Serializable
  - Serialized Fields
    - colorrampLocation
```
String colorrampLocation
```
    - lowThreshold
```
double lowThreshold
```
- Class maltcms.commands.fragments2d.visualization.GradientVisualizer extends 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
```
    - similarity
```
IArraySimilarity similarity
```
    - absolut
```
boolean absolut
```
- Class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization extends 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 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 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
```
StatsMap gsm
```
    - ff
```
IFileFragment ff
```
    - vfs
```
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
```
    - 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
```
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
  - intensityValuesVar
```
String intensityValuesVar
```
  - scanIndexVar
```
String scanIndexVar
```
  - massValuesVar
```
String massValuesVar
```
  - useCache
```
boolean useCache
```
  - prefetch
```
boolean prefetch
```
  - cacheSize
```
int cacheSize
```
  - intensity
```
IVariableFragment intensity
```
  - mass
```
IVariableFragment mass
```
  - intensities
```
List<E> intensities
```
  - masses
```
List<E> masses
```

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

Serialized Fields

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
```
IVariableFragment scanIndex
```
massValues
```
IVariableFragment massValues
```
massIntensities
```
IVariableFragment massIntensities
```
iff
```
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

intensityValuesVar
```
String intensityValuesVar
```
scanIndexVar
```
String scanIndexVar
```
massValuesVar
```
String massValuesVar
```
maxRangeVar
```
String maxRangeVar
```
modulationVar
```
String modulationVar
```
scanRateVar
```
String scanRateVar
```
scanIndex
```
IVariableFragment scanIndex
```
massValues
```
IVariableFragment massValues
```
massIntensities
```
IVariableFragment massIntensities
```
iff
```
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

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
```
IVariableFragment scanIndex
```
massValues
```
IVariableFragment massValues
```
massIntensities
```
IVariableFragment massIntensities
```
iff
```
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.cluster
- Class maltcms.datastructures.cluster.ArrayStatsMap extends Object implements Serializable
  
  serialVersionUID:
  
  -8374451195942782968L
  - Serialized Fields
    - featureVector
```
DefaultFeatureVector featureVector
```
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
```
IFileFragment iff
```
    - uniqueId
```
UUID uniqueId
```
- Class maltcms.datastructures.feature.DefaultFeatureVector extends Object implements Serializable
  
  serialVersionUID:
  
  -2245293151270164895L
  - Serialized Fields
    - featureToIndex
```
Map<K,V> featureToIndex
```
    - datalist
```
List<E> datalist
```
    - uniqueId
```
UUID uniqueId
```
- 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
```
    - uniqueId
```
UUID uniqueId
```
- 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
```
IFileFragment iff
```
    - index
```
int index
```
    - uniqueId
```
UUID uniqueId
```
- Class maltcms.datastructures.feature.PairwiseValueMap extends Object implements Serializable
  - Serialized Fields
    - matrix
```
cern.colt.matrix.DoubleMatrix2D matrix
```
    - symmetric
```
boolean symmetric
```
    - id
```
UUID id
```
Package maltcms.datastructures.filters.array
- Class maltcms.datastructures.filters.array.ArrayMerge extends AArrayFilter implements Serializable

Package maltcms.datastructures.fragments

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

Serialized Fields

ff
```
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
```
IFileFragment ref
```
target
```
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
```
IWorkflow iw
```
predecessors
```
ArrayByte.D2 predecessors
```

normalizeAlignmentValueByMapWeights

boolean normalizeAlignmentValueByMapWeights

interppath
```
List<E> interppath
```

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

Serialized Fields

pwDistFileFragment
```
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

TupleND<T extends Serializable> alignments

iw
```
IWorkflow iw
```

Package maltcms.datastructures.ms

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

Serialized Fields

parent
```
IFileFragment parent
```
scanAcquisitionTimeUnit
```
String scanAcquisitionTimeUnit
```
scan_acquisition_time_var
```
String scan_acquisition_time_var
```

scanAcquisitionTimeVar

IVariableFragment scanAcquisitionTimeVar

massValues
```
List<E> massValues
```
intensityValues
```
List<E> intensityValues
```
massRange
```
Tuple2D<T,U> massRange
```
timeRange
```
Tuple2D<T,U> timeRange
```
numberOfScans
```
int numberOfScans
```
msLevel
```
Array msLevel
```
msScanMap
```
Map<K,V> msScanMap
```

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

Serialized Fields

parent
```
IFileFragment parent
```
isl
```
IScanLine isl
```
scanAcquisitionTimeUnit
```
String scanAcquisitionTimeUnit
```

secondColumnScanAcquisitionTimeUnit

String secondColumnScanAcquisitionTimeUnit

scan_acquisition_time_var
```
String scan_acquisition_time_var
```

scanAcquisitionTimeVar

IVariableFragment scanAcquisitionTimeVar

md
```
double md
```
spm
```
int spm
```
slc
```
int slc
```
satOffset
```
double satOffset
```
massRange
```
Tuple2D<T,U> massRange
```
timeRange
```
Tuple2D<T,U> timeRange
```
numberOfScans
```
int numberOfScans
```
msLevel
```
Array msLevel
```
msScanMap
```
Map<K,V> msScanMap
```

Class maltcms.datastructures.ms.ChromatogramFactory extends Object implements Serializable
- Serialized Fields
  - 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

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.Scan2D extends Scan1D implements Serializable

serialVersionUID:: -5785157824205744680L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Throws:: IOException; ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:: IOException

Package maltcms.datastructures.peak
- 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
```
    - uniqueId
```
UUID uniqueId
```
- 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
```
- Class maltcms.datastructures.peak.PeakEdge extends Object implements Serializable
  - Serialized Fields
    - sourcePeakId
```
UUID sourcePeakId
```
    - targetPeakId
```
UUID targetPeakId
```
    - similarity
```
double similarity
```
- Class maltcms.datastructures.peak.PeakNG extends DefaultFeatureVector implements Serializable
  
  serialVersionUID:
  
  -4337180586706400884L
  - Serialized Fields
    - scanIndex
```
int scanIndex
```
    - sat
```
double sat
```
    - name
```
String name
```
    - peakKey
```
String peakKey
```
    - peakIndex
```
int peakIndex
```
    - association
```
String association
```
    - storeOnlyBestSimilarities
```
boolean storeOnlyBestSimilarities
```
    - msIntensities
```
Array msIntensities
```
    - peakId
```
int peakId
```
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
```
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 PeakNG implements Serializable
  - Serialized Fields
    - retentionTime1
```
double retentionTime1
```
    - retentionTime2
```
double retentionTime2
```
Package maltcms.experimental.bipace.spi
- Class maltcms.experimental.bipace.spi.Peak1DSimilarityCalculator extends PeakSimilarityCalculator<IBipacePeak> 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
    - fileEnding
```
String[] fileEnding
```
    - updateAttributes
```
boolean updateAttributes
```
    - useNetcdfFileCache
```
boolean useNetcdfFileCache
```
    - saveNCML
```
boolean saveNCML
```
    - scanDimensionVars
```
List<E> scanDimensionVars
```
    - scanDimensionName
```
String scanDimensionName
```
    - pointDimensionVars
```
List<E> pointDimensionVars
```
    - pointDimensionName
```
String pointDimensionName
```
Package maltcms.io.csv.chromatof
- Class maltcms.io.csv.chromatof.TableRow extends LinkedHashMap<String,String> implements Serializable
Package maltcms.io.csv.fsa
- Class maltcms.io.csv.fsa.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.hdf5.mz5
- Class maltcms.io.hdf5.mz5.MZ5DataSource extends Object implements Serializable
  - Serialized Fields
    - fileEnding
```
String[] fileEnding
```
    - updateAttributes
```
boolean updateAttributes
```
    - scanDimensionVars
```
List<E> scanDimensionVars
```
    - scanDimensionName
```
String scanDimensionName
```
    - pointDimensionVars
```
List<E> pointDimensionVars
```
    - pointDimensionName
```
String pointDimensionName
```
Package maltcms.io.xlsx
- Class maltcms.io.xlsx.XLSXDataSource extends Object implements Serializable
Package maltcms.io.xlsx.impl
- Class maltcms.io.xlsx.impl.AgilentPeakReportDataSource extends Object implements Serializable
  - Serialized Fields
    - reportFileEnding
```
String[] reportFileEnding
```
    - fileEnding
```
String[] fileEnding
```
    - varnameToMapping
```
HashMap<K,V> varnameToMapping
```
    - variableToArrayCache
```
ICacheDelegate<K,V> variableToArrayCache
```
Package maltcms.io.xml.mzData
- Class maltcms.io.xml.mzData.MZDataDataSource extends Object implements Serializable
  - Serialized Fields
    - 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
```
    - variableToArrayCache
```
ICacheDelegate<K,V> variableToArrayCache
```

Package maltcms.io.xml.mzML

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

Serialized Fields

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
```
modulation_time
```
String modulation_time
```
modulationTimeAccession
```
String modulationTimeAccession
```
first_column_elution_time
```
String first_column_elution_time
```

first_column_elution_timeAccession

String first_column_elution_timeAccession

second_column_elution_time
```
String second_column_elution_time
```

second_column_elution_timeAccession

String second_column_elution_timeAccession

total_ion_current_chromatogram
```
String total_ion_current_chromatogram
```

total_ion_current_chromatogramAccession

String total_ion_current_chromatogramAccession

total_ion_current_chromatogram_scan_acquisition_time

String total_ion_current_chromatogram_scan_acquisition_time

total_ion_current_chromatogram_scan_acquisition_timeAccession

String total_ion_current_chromatogram_scan_acquisition_timeAccession

ms_level
```
String ms_level
```
msLevelAccession
```
String msLevelAccession
```

Package maltcms.io.xml.mzXML
- Class maltcms.io.xml.mzXML.MZXMLDataSource extends Object implements Serializable
  - Serialized Fields
    - ds
```
List<E> ds
```
    - fragmentToValidReaderMap
```
WeakHashMap<K,V> fragmentToValidReaderMap
```
- Class maltcms.io.xml.mzXML.MZXMLStaxDataSource extends Object implements Serializable
  - Serialized Fields
    - 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
```
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
```
- Class maltcms.math.functions.ProductSimilarity extends Object implements Serializable
  - Serialized Fields
    - scalarSimilarities
```
IScalarSimilarity[] scalarSimilarities
```
    - arraySimilarities
```
IArraySimilarity[] arraySimilarities
```
Package maltcms.math.functions.similarities
- Class maltcms.math.functions.similarities.ArrayBhattacharryya extends Object implements Serializable
- Class maltcms.math.functions.similarities.ArrayCorr extends Object implements Serializable
  - Serialized Fields
    - returnCoeffDetermination
```
boolean returnCoeffDetermination
```
    - pc
```
org.apache.commons.math.stat.correlation.PearsonsCorrelation pc
```
- Class maltcms.math.functions.similarities.ArrayCos extends Object implements Serializable
  - Serialized Fields
    - minimumSimilarity
```
double minimumSimilarity
```
- Class maltcms.math.functions.similarities.ArrayCosLp extends Object implements Serializable
  - Serialized Fields
    - cos
```
IArraySimilarity cos
```
    - lp
```
IArraySimilarity lp
```
- Class maltcms.math.functions.similarities.ArrayCov extends Object implements Serializable
  - Serialized Fields
    - returnCoeffDetermination
```
boolean returnCoeffDetermination
```
- Class maltcms.math.functions.similarities.ArrayDot extends Object implements Serializable
- Class maltcms.math.functions.similarities.ArrayDotLp extends Object implements Serializable
  - Serialized Fields
    - dot
```
IArraySimilarity dot
```
    - lp
```
IArraySimilarity lp
```
- Class maltcms.math.functions.similarities.ArrayDotMap extends Object implements Serializable
  - Serialized Fields
    - std
```
ArrayDouble.D1 std
```
    - score
```
IArraySimilarity score
```
- Class maltcms.math.functions.similarities.ArrayHamming extends Object implements Serializable
- Class maltcms.math.functions.similarities.ArrayLp extends Object implements Serializable
  - Serialized Fields
    - p
```
double p
```
    - normalizeByLength
```
boolean normalizeByLength
```
    - sqrtn
```
double sqrtn
```
- Class maltcms.math.functions.similarities.ArrayRankCorr extends Object implements Serializable
  - Serialized Fields
    - returnCoeffDetermination
```
boolean returnCoeffDetermination
```
    - sc
```
org.apache.commons.math.stat.correlation.SpearmansCorrelation sc
```
- Class maltcms.math.functions.similarities.ArrayTanimoto extends Object implements Serializable
- Class maltcms.math.functions.similarities.ArrayWeightedCosine extends Object implements Serializable
  - Serialized Fields
    - minimumSimilarity
```
double minimumSimilarity
```
- Class maltcms.math.functions.similarities.GaussianDifferenceSimilarity extends Object implements Serializable
  - Serialized Fields
    - tolerance
```
double tolerance
```
    - threshold
```
double threshold
```
- Class maltcms.math.functions.similarities.InverseGaussianDifferenceSimilarity extends Object implements Serializable
  - Serialized Fields
    - threshold
```
double threshold
```
    - lambda
```
double lambda
```
    - normalize
```
boolean normalize
```
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.mpaxs.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
```
    - 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
    - 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
```
    - 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<E> jComboBox1
```
    - jComboBox3
```
JComboBox<E> 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
```
    - 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
```
Package maltcms.ui.renderer
- Class maltcms.ui.renderer.LineVectorRenderer extends org.jfree.chart.renderer.xy.VectorRenderer implements Serializable
  
  serialVersionUID:
  
  7297064254819024794L
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.db.search.api.similarities
- Class net.sf.maltcms.db.search.api.similarities.AMetabolitePredicate extends com.db4o.query.Predicate<IMetabolite> implements Serializable
  - Serialized Fields
    - scoreThreshold
```
double scoreThreshold
```
    - maxHits
```
int maxHits
```
    - scan
```
IScan scan
```
    - maskedMasses
```
List<E> maskedMasses
```
    - spectrum
```
TreeMap<K,V> spectrum
```
    - scoreMap
```
TreeSet<E> scoreMap
```
    - cache
```
ICacheDelegate<K,V> cache
```
Package net.sf.maltcms.db.search.spi.similarities
- Class net.sf.maltcms.db.search.spi.similarities.Cosine extends AMetabolitePredicate implements Serializable
  - Serialized Fields
    - toggle
```
boolean toggle
```
    - iadc
```
IArraySimilarity iadc
```
    - resolution
```
double resolution
```
    - lastMin
```
double lastMin
```
    - lastMax
```
double lastMax
```
    - normalize
```
boolean normalize
```
    - forward
```
boolean forward
```
    - comparator
```
Comparator<T> comparator
```
- Class net.sf.maltcms.db.search.spi.similarities.CosineWithMassBonus extends AMetabolitePredicate implements Serializable
  - Serialized Fields
    - toggle
```
boolean toggle
```
    - iadc
```
IArraySimilarity iadc
```
    - resolution
```
double resolution
```
    - lastMin
```
double lastMin
```
    - lastMax
```
double lastMax
```
    - normalize
```
boolean normalize
```
    - comparator
```
Comparator<T> comparator
```
    - threshold
```
double threshold
```
- Class net.sf.maltcms.db.search.spi.similarities.RetentionIndexMatcher extends AMetabolitePredicate implements Serializable
  - Serialized Fields
    - delegate
```
AMetabolitePredicate delegate
```
    - retentionIndex
```
double retentionIndex
```
    - metabolites
```
List<E> metabolites
```
    - window
```
double window
```
- Class net.sf.maltcms.db.search.spi.similarities.SteinAndScott extends AMetabolitePredicate implements Serializable
  - Serialized Fields
    - toggle
```
boolean toggle
```
    - iadc
```
AMDISMSSimilarity iadc
```
    - resolution
```
double resolution
```
    - lastMin
```
double lastMin
```
    - lastMax
```
double lastMax
```
    - normalize
```
boolean normalize
```
    - comparator
```
Comparator<T> comparator
```
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
```
    - uniqueId
```
UUID uniqueId
```
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
```
    - uniqueId
```
UUID uniqueId
```
Package net.sf.maltcms.evaluation.api.classification
- Class net.sf.maltcms.evaluation.api.classification.Category extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
- Class net.sf.maltcms.evaluation.api.classification.Entity extends Object implements Serializable
  - Serialized Fields
    - classLabel
```
String classLabel
```
    - c
```
Category c
```
    - featureVector
```
IFeatureVector featureVector
```
- Class net.sf.maltcms.evaluation.api.classification.EntityGroup extends Object implements Serializable
  - Serialized Fields
    - categoryToEntityMap
```
HashMap<K,V> categoryToEntityMap
```
Package net.sf.maltcms.evaluation.api.tasks
Package net.sf.maltcms.evaluation.spi.classification
- Class net.sf.maltcms.evaluation.spi.classification.Peak1DFeatureVector extends Object implements Serializable
  
  serialVersionUID:
  
  -5936343655074144856L
  - Serialized Fields
    - rt
```
double rt
```
    - area
```
double area
```
    - rowIndex
```
int rowIndex
```
    - name
```
String name
```
    - uniqueId
```
UUID uniqueId
```
- Class net.sf.maltcms.evaluation.spi.classification.Peak2DFeatureVector extends Object implements Serializable
  
  serialVersionUID:
  
  -5936343655074144856L
  - Serialized Fields
    - rt1
```
double rt1
```
    - rt2
```
double rt2
```
    - area
```
double area
```
    - rowIndex
```
int rowIndex
```
    - name
```
String name
```
    - uniqueId
```
UUID uniqueId
```
- Class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector extends Object implements Serializable
  
  serialVersionUID:
  
  -5936343655074144856L
  - Serialized Fields
    - rt
```
ArrayDouble.D0 rt
```
    - area
```
ArrayDouble.D0 area
```
    - name
```
String name
```
    - uniqueId
```
UUID uniqueId
```
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.mpaxs.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
```
    - uniqueId
```
UUID uniqueId
```
Package net.sf.maltcms.tutorials
- Class net.sf.maltcms.tutorials.MyFragmentCommand extends AFragmentCommand implements Serializable
  - Serialized Fields
    - filter
```
List<E> filter
```
Package smueller
- Class smueller.SymbolicRepresentationAlignment extends AFragmentCommand implements Serializable
  - Serialized Fields
    - pairsWithFirst
```
boolean pairsWithFirst
```
    - minArrayComp
```
String minArrayComp
```

Serialized Form

Package maltcms.commands.distances

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

Serialized Fields

comp_weight

exp_weight

diag_weight

globalGapPenalty

minimize

directions

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

Serialized Fields

similarityFunction

nthreads

pad

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

Serialized Fields

shape

pa

costFunction

satRef

satQuery

ref

query

Package maltcms.commands.distances.dtw

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

Serialized Fields

recurrence

scan_acquisition_time

pairwiseFeatureSimilarity

statsMap

useAnchors

anchorRadius

minScansBetweenAnchors

workflow

precalculatePairwiseDistances

pa

globalBand

bandWidthPercentage

extension

saveLayoutImage

sample

saveDtwMatrix

savePairwiseSimilarityMatrix

normalizeAlignmentValue

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

Serialized Fields

numberOfEICsToSelect

useSparseArrays

mass_values

intensity_values

mass_range_min

mass_range_max

scan_index

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

Serialized Fields

arrayVariable

Package maltcms.commands.distances.dtwng

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

Serialized Fields

leftHandSideId

rightHandSideId

similarity

alignmentMap

area

defaultValue

optimizationFunction

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

Serialized Fields

scoreFunction

arrayFeatureName

timeFeatureName

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

Serialized Fields

minimize

weights

ins

del

NW

N