Index (Maltcms Commands 1.3.0 API)

A C D E F G I M N P S T V

A

ADynamicTimeWarp - Class in maltcms.commands.distances.dtw: Base class for dynamic time warping implementations.
ADynamicTimeWarp() - Constructor for class maltcms.commands.distances.dtw.ADynamicTimeWarp
align(Tuple2D<List<Array>, List<Array>>, AnchorPairSet, double, ArrayDouble.D1, ArrayDouble.D1) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
align(Tuple2D<List<Array>, List<Array>>, AnchorPairSet, double, ArrayDouble.D1, ArrayDouble.D1) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
AlignmentFactory - Class in maltcms.commands.distances.dtwng
AlignmentFactory() - Constructor for class maltcms.commands.distances.dtwng.AlignmentFactory
appendXML(Element) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
appendXML(Element) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
appendXML(Element) - Method in class maltcms.datastructures.fragments.PairwiseDistances
apply(IFileFragment, IFileFragment) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
apply(Tuple2D<Array[], Array[]>) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
apply(List<IFeatureVector>, List<IFeatureVector>) - Method in class maltcms.commands.distances.dtwng.DTW
apply(IFeatureVector, IFeatureVector) - Method in class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity
apply(int...) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
apply(List<IFeatureVector>, List<IFeatureVector>) - Method in interface maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation
apply(int...) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
apply(IFeatureVector, IFeatureVector) - Method in class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation
apply(int, int, double, double, Array, Array) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction: if i1 && i2 > 0 => apply distance to indices only else apply to all elements of array
apply(IFileFragment, IFileFragment) - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity
apply(int, int, double, double, Array, Array) - Method in class maltcms.math.functions.DtwPairwiseSimilarity
apply(int, int, double, double, Array, Array) - Method in class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity
apply(Array, Array) - Method in interface maltcms.math.functions.IArraySimilarity
apply(double[], double[], Array, Array) - Method in interface maltcms.math.functions.IScalarArraySimilarity
apply(double, double) - Method in interface maltcms.math.functions.IScalarSimilarity
apply(double[], double[], Array, Array) - Method in class maltcms.math.functions.ProductSimilarity
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayBhattacharryya
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCorr
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCos
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCosLp
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCov
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayDot
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayDotLp
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayDotMap
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayHamming
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayLp
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayRankCorr
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayTanimoto
apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayWeightedCosine
apply(double, double) - Method in class maltcms.math.functions.similarities.GaussianDifferenceSimilarity: Calculates the scalar
apply(double, double) - Method in class maltcms.math.functions.similarities.InverseGaussianDifferenceSimilarity: Calculates the scalar
ArrayBhattacharryya - Class in maltcms.math.functions.similarities
ArrayBhattacharryya() - Constructor for class maltcms.math.functions.similarities.ArrayBhattacharryya
ArrayCorr - Class in maltcms.math.functions.similarities: Calculates Pearson's product moment correlation as similarity between arrays.
ArrayCorr() - Constructor for class maltcms.math.functions.similarities.ArrayCorr
ArrayCos - Class in maltcms.math.functions.similarities: Cosine similarity between arrays.
ArrayCos() - Constructor for class maltcms.math.functions.similarities.ArrayCos
ArrayCosLp - Class in maltcms.math.functions.similarities: Combinded distance of ArrayCos and ArrayLp.
ArrayCosLp() - Constructor for class maltcms.math.functions.similarities.ArrayCosLp
ArrayCov - Class in maltcms.math.functions.similarities: Calculates Pearson's product moment correlation as similarity between arrays.
ArrayCov() - Constructor for class maltcms.math.functions.similarities.ArrayCov
ArrayDot - Class in maltcms.math.functions.similarities: Dot product as similarity measure between arrays.
ArrayDot() - Constructor for class maltcms.math.functions.similarities.ArrayDot
ArrayDotLp - Class in maltcms.math.functions.similarities
ArrayDotLp() - Constructor for class maltcms.math.functions.similarities.ArrayDotLp
ArrayDotMap - Class in maltcms.math.functions.similarities: Calculates the dotmap, but instead of the weighting by mz bin this class uses the standard deviation.
ArrayDotMap() - Constructor for class maltcms.math.functions.similarities.ArrayDotMap
ArrayHamming - Class in maltcms.math.functions.similarities: Hamming distance between binary vectors.
ArrayHamming() - Constructor for class maltcms.math.functions.similarities.ArrayHamming
ArrayLp - Class in maltcms.math.functions.similarities: Lp-norm based distance between arrays.
ArrayLp() - Constructor for class maltcms.math.functions.similarities.ArrayLp
ArrayRankCorr - Class in maltcms.math.functions.similarities: Calculates Spearman's rank correlation as similarity between arrays.
ArrayRankCorr() - Constructor for class maltcms.math.functions.similarities.ArrayRankCorr
ArrayTanimoto - Class in maltcms.math.functions.similarities: Implementation of Tanimoto score.
ArrayTanimoto() - Constructor for class maltcms.math.functions.similarities.ArrayTanimoto
ArrayWeightedCosine - Class in maltcms.math.functions.similarities
ArrayWeightedCosine() - Constructor for class maltcms.math.functions.similarities.ArrayWeightedCosine

C

calculatePairwiseDistances(IArrayD2Double, ArrayDouble.D1, ArrayDouble.D1, List<Array>, List<Array>) - Method in class maltcms.commands.distances.PairwiseFeatureSimilarity: This method can be called for precalculation of all distances/similarites.
call() - Method in class maltcms.commands.distances.PartitionCalculator
configure(Configuration) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
configure(Configuration) - Method in class maltcms.commands.distances.dtw.MZIDynamicTimeWarp
configure(Configuration) - Method in class maltcms.commands.distances.dtw.TICDynamicTimeWarp
configure(Configuration) - Method in class maltcms.commands.distances.dtwng.DTW
configure(Configuration) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
configure(Configuration) - Method in class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation
configure(Configuration) - Method in class maltcms.commands.distances.DtwRecurrence
configure(Configuration) - Method in class maltcms.commands.distances.PairwiseFeatureSimilarity
configure(Configuration) - Method in class maltcms.commands.distances.PartitionCalculator
configure(Configuration) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
configure(Configuration) - Method in class maltcms.datastructures.fragments.PairwiseDistances
configure(Configuration) - Method in class maltcms.math.functions.DtwPairwiseSimilarity
configure(Configuration) - Method in class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity
ContinuityArgmaxNodeBuilder - Class in maltcms.commands.distances.dtwng
ContinuityArgmaxNodeBuilder(int) - Constructor for class maltcms.commands.distances.dtwng.ContinuityArgmaxNodeBuilder
createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.distances.dtw.MZIDynamicTimeWarp
createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.distances.dtw.TICDynamicTimeWarp

D

DTW - Class in maltcms.commands.distances.dtwng
DTW() - Constructor for class maltcms.commands.distances.dtwng.DTW
DtwPairwiseSimilarity - Class in maltcms.math.functions
DtwPairwiseSimilarity() - Constructor for class maltcms.math.functions.DtwPairwiseSimilarity
DtwRecurrence - Class in maltcms.commands.distances: Objects of this type are used to calculate the cumulative distance within the ADynamicTimeWarp Implementations.
DtwRecurrence() - Constructor for class maltcms.commands.distances.DtwRecurrence
DtwTimePenalizedPairwiseSimilarity - Class in maltcms.math.functions
DtwTimePenalizedPairwiseSimilarity() - Constructor for class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity

E

eval(List<double[]>, int) - Method in class maltcms.commands.distances.dtwng.ContinuityArgmaxNodeBuilder
eval(List<double[]>, int) - Method in class maltcms.commands.distances.dtwng.IdentityNodeBuilder
eval(List<double[]>, int) - Method in class maltcms.commands.distances.dtwng.NodeBuilder
eval(int, int, IArrayD2Double, double, ArrayByte.D2) - Method in class maltcms.commands.distances.DtwRecurrence
eval(int, int, IArrayD2Double, IArrayD2Double, double) - Method in class maltcms.commands.distances.DtwRecurrence
eval(int, int, IArrayD2Double, double, ArrayByte.D2) - Method in interface maltcms.commands.distances.IRecurrence
eval(int, int, IArrayD2Double, IArrayD2Double, double) - Method in interface maltcms.commands.distances.IRecurrence

F

FeatureVectorDtwSimilarity - Class in maltcms.commands.distances.dtwng
FeatureVectorDtwSimilarity() - Constructor for class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity
fromFileFragment(IFileFragment) - Static method in class maltcms.datastructures.fragments.PairwiseDistances: Static factory method which reconstructs a PairwiseDistances object from the given FileFragment.

G

GaussianDifferenceSimilarity - Class in maltcms.math.functions.similarities
GaussianDifferenceSimilarity() - Constructor for class maltcms.math.functions.similarities.GaussianDifferenceSimilarity
getAlignment() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getAlignments() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getAnchors() - Method in class maltcms.datastructures.fragments.PairwiseAlignment: Retrieve paired anchors
getArrayDistanceClassName() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getArraySimilarities() - Method in interface maltcms.math.functions.IScalarArraySimilarity
getCd() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getCompressionWeight() - Method in class maltcms.commands.distances.DtwRecurrence
getCompressionWeight() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
getConstraints() - Method in class maltcms.commands.distances.dtwng.DTW
getConstraints() - Method in interface maltcms.commands.distances.dtwng.IAlignment
getCreator() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getCumulativeDistance() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
getDefaultValue() - Method in class maltcms.commands.distances.dtwng.DTW
getDefaultValue() - Method in interface maltcms.commands.distances.dtwng.IAlignment
getDiagonalWeight() - Method in class maltcms.commands.distances.DtwRecurrence
getDistance(int, int, double, double, Array, Array) - Method in class maltcms.commands.distances.PairwiseFeatureSimilarity: Returns the IDtwSimilarityFunction Object used to calculate pairwise distances/similarities.
getDistance() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getDTWInstance() - Method in class maltcms.commands.distances.dtwng.AlignmentFactory: Returns a new DTW instance, configured by ObjectFactory.
getDTWInstance(IOptimizationFunction, TwoFeatureVectorOperation, Area) - Method in class maltcms.commands.distances.dtwng.AlignmentFactory
getExpansionWeight() - Method in class maltcms.commands.distances.DtwRecurrence
getExpansionWeight() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
getExtension() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
getFf() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getGlobalGapPenalty() - Method in class maltcms.commands.distances.DtwRecurrence
getGlobalGapPenalty() - Method in interface maltcms.commands.distances.IRecurrence
getInterppath() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getLeftHandSideId() - Method in class maltcms.commands.distances.dtwng.DTW
getLeftHandSideId() - Method in interface maltcms.commands.distances.dtwng.IAlignment
getMap() - Method in class maltcms.commands.distances.dtwng.DTW
getMap() - Method in interface maltcms.commands.distances.dtwng.IAlignment
getMatchWeight() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
getMinArrayComp() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getNodes() - Method in class maltcms.commands.distances.dtwng.NodeBuilder
getNodesByDimension(int, double[]) - Method in class maltcms.commands.distances.dtwng.NodeBuilder
getOptimalOperationSequenceString() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
getOptimalOperationSequenceString() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
getOptimalValue() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
getOptimalValue() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
getOptimizationFunction() - Method in class maltcms.commands.distances.dtwng.DTW
getOptimizationFunction() - Method in interface maltcms.commands.distances.dtwng.IAlignment
getPairwiseDistances() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getPairwiseFeatureSimilarity() - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
getPairwiseFeatureVectorOperation() - Method in class maltcms.commands.distances.dtwng.DTW
getPairwiseFeatureVectorOperation() - Method in interface maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation
getPath() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getPointList(List<double[]>) - Method in class maltcms.commands.distances.dtwng.NodeBuilder
getPredecessors() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getPwd() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getPwDistAlignmentsVarName() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getPwDistMatrixVariableName() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getPwDistVariableName() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getQuerysize() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getRecurrence() - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
getRef() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getRefsize() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getResult() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity
getResult() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getResultFileFragment() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
getResultFileFragment() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity
getResultVector() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity
getResultVector() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getRightHandSideId() - Method in class maltcms.commands.distances.dtwng.DTW
getRightHandSideId() - Method in interface maltcms.commands.distances.dtwng.IAlignment
getScalarSimilarities() - Method in interface maltcms.math.functions.IScalarArraySimilarity
getStates() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
getStates() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
getStatsMap() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity
getTarget() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getTrace() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
getTrace() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
getWeight(String) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
getWeight(String) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
getWorkflow() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
getWorkflow() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getWorkflow() - Method in class maltcms.datastructures.fragments.PairwiseDistances
getWorkflowSlot() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
getWorkflowSlot() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
getWorkflowSlot() - Method in class maltcms.datastructures.fragments.PairwiseDistances

I

IAlignment - Interface in maltcms.commands.distances.dtwng
IArraySimilarity - Interface in maltcms.math.functions: Interface to define classes, comparing arrays, especially mass spectra by some function and returning a generic type as result.
IdentityNodeBuilder - Class in maltcms.commands.distances.dtwng
IdentityNodeBuilder() - Constructor for class maltcms.commands.distances.dtwng.IdentityNodeBuilder
IDtwSimilarityFunction - Interface in maltcms.commands.distances: Interface to define classes, comparing arrays, especially mass spectra by some function and returning a double value as result.
IDynamicTimeWarp - Interface in maltcms.commands.distances.dtw: Refinement of PairwiseFeatureSequenceSimilarity, adding necessary methods for alignment with DTW.
init(List<IFeatureVector>, List<IFeatureVector>, IArrayD2Double, IArrayD2Double, TwoFeatureVectorOperation) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
init(List<IFeatureVector>, List<IFeatureVector>, IArrayD2Double, IArrayD2Double, TwoFeatureVectorOperation) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
InverseGaussianDifferenceSimilarity - Class in maltcms.math.functions.similarities
InverseGaussianDifferenceSimilarity() - Constructor for class maltcms.math.functions.similarities.InverseGaussianDifferenceSimilarity
IOptimizationFunction - Interface in maltcms.commands.distances.dtwng
IPairwiseFeatureVectorSequenceOperation<RESULT> - Interface in maltcms.commands.distances.dtwng
IRecurrence - Interface in maltcms.commands.distances: Interface for classes performing a recurring operation, e.g. dynamic programming.
IScalarArraySimilarity - Interface in maltcms.math.functions
IScalarSimilarity - Interface in maltcms.math.functions: The implemented similarity function should have the following properties: The maximal function value must be greater than the minimal function value, assuming that a similarity between two scalars is maximal iff both entities are identical/equal and minimal iff they are completely unrelated and that increasing similarity is reflected by a greater value of the function.
isMinimize() - Method in class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity
isMinimize() - Method in class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation
isMinimize() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
isMinimize() - Method in class maltcms.datastructures.fragments.PairwiseDistances
isNormalizeByMapWeights() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
isSaveCDM() - Method in class maltcms.datastructures.fragments.PairwiseAlignment
isSavePWDM() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

M

maltcms.commands.distances - package maltcms.commands.distances
maltcms.commands.distances.dtw - package maltcms.commands.distances.dtw
maltcms.commands.distances.dtwng - package maltcms.commands.distances.dtwng
maltcms.datastructures.fragments - package maltcms.datastructures.fragments
maltcms.math.functions - package maltcms.math.functions
maltcms.math.functions.similarities - package maltcms.math.functions.similarities
minimize() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
minimize() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
minimize() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity: Returns true, if this LDF is a distance between Arrays, false if LDF is a similarity.
minimize() - Method in class maltcms.math.functions.DtwPairwiseSimilarity
minimize() - Method in class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity
modify(IFileFragment) - Method in class maltcms.commands.distances.dtwng.DTW
modify(IFileFragment) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
modify(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseDistances
MZIDynamicTimeWarp - Class in maltcms.commands.distances.dtw: Implementation of Pairwise Dynamic-Time-Warping for time-series data with an evenly gridded array of mass over charge (mz) vs intensity for each time-point (scan).
MZIDynamicTimeWarp() - Constructor for class maltcms.commands.distances.dtw.MZIDynamicTimeWarp

N

NodeBuilder - Class in maltcms.commands.distances.dtwng
NodeBuilder() - Constructor for class maltcms.commands.distances.dtwng.NodeBuilder

P

PairwiseAlignment - Class in maltcms.datastructures.fragments: Implementation of IFileFragmentProvider for PairwiseAlignment.
PairwiseAlignment() - Constructor for class maltcms.datastructures.fragments.PairwiseAlignment
PairwiseDistances - Class in maltcms.datastructures.fragments
PairwiseDistances() - Constructor for class maltcms.datastructures.fragments.PairwiseDistances
PairwiseFeatureSequenceSimilarity - Interface in maltcms.commands.distances: Interface to allow the values of comparison of multiple arrays to also be used as a cost/score measure.
PairwiseFeatureSimilarity - Class in maltcms.commands.distances: Class used to calculate a pairwise score or cost between mass-spectra.
PairwiseFeatureSimilarity() - Constructor for class maltcms.commands.distances.PairwiseFeatureSimilarity
PartitionCalculator - Class in maltcms.commands.distances
PartitionCalculator(Rectangle, IArrayD2Double, ArrayDouble.D1, ArrayDouble.D1, List<Array>, List<Array>) - Constructor for class maltcms.commands.distances.PartitionCalculator
ProductSimilarity - Class in maltcms.math.functions
ProductSimilarity() - Constructor for class maltcms.math.functions.ProductSimilarity
provideFileFragment() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

S

set(double, double, double) - Method in class maltcms.commands.distances.DtwRecurrence
set(double, double, double) - Method in interface maltcms.commands.distances.IRecurrence
setAlignment(IArrayD2Double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setAlignments(TupleND<IFileFragment>) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setAnchors(DefaultPairSet<IAnchor>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment: Set paired anchors
setArrayDistanceClassName(String) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setArraySimilarities(IArraySimilarity...) - Method in interface maltcms.math.functions.IScalarArraySimilarity
setCd(IRecurrence) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setCompressionWeight(double) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
setConstraints(Area) - Method in class maltcms.commands.distances.dtwng.DTW
setConstraints(Area) - Method in interface maltcms.commands.distances.dtwng.IAlignment
setCreator(Class<?>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setCumulativeDistance(DtwRecurrence) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setDefaultValue(double) - Method in class maltcms.commands.distances.dtwng.DTW
setDefaultValue(double) - Method in interface maltcms.commands.distances.dtwng.IAlignment
setDistance(IArrayD2Double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setExpansionWeight(double) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
setExtension(String) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
setFf(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setFileFragments(IFileFragment, IFileFragment) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp
setFileFragments(IFileFragment, IFileFragment) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
setFileFragments(IFileFragment, IFileFragment, Class<?>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setInterppath(List<Tuple2DI>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setIsMinimizing(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setLeftHandSideId(String) - Method in class maltcms.commands.distances.dtwng.DTW
setLeftHandSideId(String) - Method in interface maltcms.commands.distances.dtwng.IAlignment
setMatchWeight(double) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction
setMinArrayComp(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setMinimize(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setMinimize(boolean) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setMinimizing(boolean) - Method in class maltcms.commands.distances.DtwRecurrence
setMinimizing(boolean) - Method in interface maltcms.commands.distances.IRecurrence
setName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setNames(ArrayChar.D2) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setNodes(List<double[]>) - Method in class maltcms.commands.distances.dtwng.NodeBuilder
setNormalizeByMapLength(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setNumberOfScansQuery(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setNumberOfScansReference(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setOptimizationFunction(IOptimizationFunction) - Method in class maltcms.commands.distances.dtwng.DTW
setOptimizationFunction(IOptimizationFunction) - Method in interface maltcms.commands.distances.dtwng.IAlignment
setPairwiseDistance(PairwiseFeatureSimilarity) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setPairwiseDistances(IArrayD2Double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setPairwiseDistances(ArrayDouble.D2) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setPairwiseFeatureSimilarity(PairwiseFeatureSimilarity) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
setPairwiseFeatureVectorOperation(TwoFeatureVectorOperation) - Method in class maltcms.commands.distances.dtwng.DTW
setPairwiseFeatureVectorOperation(TwoFeatureVectorOperation) - Method in interface maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation
setPath(List<Tuple2DI>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setPredecessors(ArrayByte.D2) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setPwd(PairwiseFeatureSimilarity) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setPwDistAlignmentsVarName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setPwDistMatrixVariableName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setPwDistVariableName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances
setQuerysize(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setRecurrence(DtwRecurrence) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp
setRef(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setRefsize(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setResult(double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setRightHandSideId(String) - Method in class maltcms.commands.distances.dtwng.DTW
setRightHandSideId(String) - Method in interface maltcms.commands.distances.dtwng.IAlignment
setSaveCDM(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setSavePWDM(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setScalarSimilarities(IScalarSimilarity...) - Method in interface maltcms.math.functions.IScalarArraySimilarity
setStatsMap(StatsMap) - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity
setStdArray(ArrayDouble.D1) - Method in class maltcms.math.functions.similarities.ArrayDotMap: Setter.
setTarget(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setTraceMatrix(ArrayByte.D2) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setWeight(String, double) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction
setWeight(String, double) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
setWorkflow(IWorkflow) - Method in class maltcms.datastructures.fragments.PairwiseAlignment
setWorkflow(IWorkflow) - Method in class maltcms.datastructures.fragments.PairwiseDistances
showCumScoreMatrix() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
showPwScoreMatrix() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
SimilarityTools - Class in maltcms.math.functions.similarities
SimilarityTools() - Constructor for class maltcms.math.functions.similarities.SimilarityTools

T

ThreePredecessorsOptimization - Class in maltcms.commands.distances.dtwng
ThreePredecessorsOptimization() - Constructor for class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization
ThreePredecessorsOptimization.State - Enum in maltcms.commands.distances.dtwng
TICDynamicTimeWarp - Class in maltcms.commands.distances.dtw: Dynamic Time Warp on univariate Time Series, e.g. the total ion current (TIC).
TICDynamicTimeWarp() - Constructor for class maltcms.commands.distances.dtw.TICDynamicTimeWarp
toDistance(IArraySimilarity, Array, Array) - Static method in class maltcms.math.functions.similarities.SimilarityTools
toSimilarity(double) - Static method in class maltcms.math.functions.similarities.SimilarityTools
toString(ThreePredecessorsOptimization.State) - Static method in enum maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State
TwoFeatureVectorOperation - Class in maltcms.commands.distances.dtwng
TwoFeatureVectorOperation() - Constructor for class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation

V

valueOf(String) - Static method in enum maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State: Returns the enum constant of this type with the specified name.
values() - Static method in enum maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State: Returns an array containing the constants of this enum type, in the order they are declared.

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