Serialized Form (Maltcms Commands 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.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.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
```

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