PairwiseDistanceCalculator

Variables

var.minimizing_array_comp
var.pairwise_distance_matrix
var.pairwise_distance_names

Configurable Properties

Name: minArrayComp
Default Value: minimizing_array_comp
Description:
Sets the variable name used to store whether the similarity or distance function used required minimization (1) or maximization (0)

Name: minimizingLocalDistance
Default Value: false
Description:
If true, assumes that the comparison function between mass spectra behaves like a cost function (smaller is better). If false, assumes that the function behaves like a similarity or score function (larger is better).

Name: pairsWithFirstElement
Default Value: false
Description:
If true, calculates similarities / distances only with the first chromatogram. If false, calculates all (n-1)*n/2 alignments.

Name: pwdExtension
Default Value: ``
Description:
Suffix for the pairwise_distances.cdf files. E.g. for “_CUST”, the result file will be named “pairwise_distances_CUST.cdf” .

Name: workerFactory
Default Value: MziDtwWorkerFactory(bandWidthPercentage=0.25, globalGapPenalty=1.0, extension=, globalBand=false, minScansBetweenAnchors=10, precalculatePairwiseDistances=false, saveLayoutImage=false, useAnchors=false, numberOfEICsToSelect=0, useSparseArrays=false, anchorRadius=0, similarity=DtwTimePenalizedPairwiseSimilarity(expansionWeight=1.0, matchWeight=1.0, compressionWeight=1.0, retentionTimeSimilarity=GaussianDifferenceSimilarity(tolerance=5.0, threshold=0.0), denseMassSpectraSimilarity=ArrayCos{}), saveDtwMatrix=false, savePairwiseSimilarityMatrix=false, normalizeAlignmentValue=false)
Description:
The worker factory to use for chromatogram / MS comparison. Use either TicDtwWorkerFactory or MziDtwWorkerFactory.