Serialized Form
serialVersionUID: -8374451195942782968L
featureVector
DefaultFeatureVector featureVector
Package maltcms.commands.distances |
comp_weight
double comp_weight
exp_weight
double exp_weight
diag_weight
double diag_weight
globalGapPenalty
double globalGapPenalty
minimize
boolean minimize
directions
String[] directions
serialVersionUID: -2087449317783907180L
similarityFunction
IDtwSimilarityFunction similarityFunction
nthreads
int nthreads
pad
IArrayD2Double pad
serialVersionUID: -7473548606374882072L
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 |
recurrence
DtwRecurrence recurrence
scan_acquisition_time
String scan_acquisition_time
pairwiseFeatureSimilarity
PairwiseFeatureSimilarity pairwiseFeatureSimilarity
statsMap
cross.datastructures.StatsMap statsMap
useAnchors
boolean useAnchors
anchorRadius
int anchorRadius
minScansBetweenAnchors
int minScansBetweenAnchors
workflow
cross.datastructures.workflow.IWorkflow workflow
precalculatePairwiseDistances
boolean precalculatePairwiseDistances
pa
PairwiseAlignment pa
globalBand
boolean globalBand
bandWidthPercentage
double bandWidthPercentage
extension
String extension
saveLayoutImage
boolean saveLayoutImage
sample
boolean sample
saveDtwMatrix
boolean saveDtwMatrix
savePairwiseSimilarityMatrix
boolean savePairwiseSimilarityMatrix
normalizeAlignmentValue
boolean normalizeAlignmentValue
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
arrayVariable
String arrayVariable
Package maltcms.commands.distances.dtwng |
serialVersionUID: -4958589994859792653L
leftHandSideId
String leftHandSideId
rightHandSideId
String rightHandSideId
similarity
TwoFeatureVectorOperation similarity
alignmentMap
List<E> alignmentMap
area
Area area
defaultValue
double defaultValue
optimizationFunction
IOptimizationFunction optimizationFunction
scoreFunction
IDtwSimilarityFunction scoreFunction
arrayFeatureName
String arrayFeatureName
timeFeatureName
String timeFeatureName
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
Package maltcms.commands.filters |
Package maltcms.commands.filters.array |
copyArray
boolean copyArray
aef
AElementFilter aef
add
double add
rg
Random rg
mean
double mean
stddev
double stddev
window
int window
aef
AElementFilter aef
naturalLog
boolean naturalLog
aef
AElementFilter aef
naturalLog
boolean naturalLog
mean
double mean
stddev
double stddev
scans
int scans
channels
int channels
medianWindow
int medianWindow
snrMinimum
double snrMinimum
aef
AElementFilter aef
min
double min
max
double max
window
int window
window
int window
factor
double factor
normalization
String normalization
normalizeGlobal
boolean normalizeGlobal
log
boolean log
window
int window
aef
AElementFilter aef
window
int window
Package maltcms.commands.filters.array.wavelet |
scale
double scale
variance
double variance
w
IWavelet w
cwt
ContinuousWaveletTransform cwt
log
org.slf4j.Logger log
Package maltcms.commands.fragments.alignment |
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
ticPeaks
String ticPeaks
massValues
String massValues
scanIndex
String scanIndex
intensityValues
String intensityValues
useUserSuppliedAnchors
boolean useUserSuppliedAnchors
minCliqueSize
int minCliqueSize
anchorNames
String anchorNames
anchorTimes
String anchorTimes
anchorRetentionIndex
String anchorRetentionIndex
anchorScanIndex
String anchorScanIndex
binnedIntensities
String binnedIntensities
binnedScanIndex
String binnedScanIndex
scanAcquisitionTime
String scanAcquisitionTime
savePeakSimilarities
boolean savePeakSimilarities
saveXMLAlignment
boolean saveXMLAlignment
maxBBHErrors
int maxBBHErrors
savePlots
boolean savePlots
useSparseArrays
boolean useSparseArrays
peakToClique
HashMap<K,V> peakToClique
workerFactory
WorkerFactory workerFactory
saveUnmatchedPeaks
boolean saveUnmatchedPeaks
saveIncompatiblePeaks
boolean saveIncompatiblePeaks
saveUnassignedPeaks
boolean saveUnassignedPeaks
peakAreaVariable
String peakAreaVariable
guideTreeClass
String guideTreeClass
Package maltcms.commands.fragments.alignment.peakCliqueAlignment |
name
String name
lhsPeaks
List<E> lhsPeaks
rhsPeaks
List<E> rhsPeaks
similarityFunction
IScalarArraySimilarity similarityFunction
maxRTDifference
double maxRTDifference
Package maltcms.commands.fragments.assignment |
dblocation
List<E> dblocation
threshold
double threshold
maxk
int maxk
Package maltcms.commands.fragments.cluster |
normalize_scans
boolean normalize_scans
inputFiles
cross.datastructures.tuple.TupleND<T extends Serializable> inputFiles
consensus
cross.datastructures.fragments.IFileFragment consensus
dist
double[][] dist
names
String[] names
L
int L
usedIndices
HashSet<E> usedIndices
cluster
HashMap<K,V> cluster
fragments
HashMap<K,V> fragments
nameToNameLookup
HashMap<K,V> nameToNameLookup
chromatogramDistanceFunctionClass
PairwiseFeatureSequenceSimilarity chromatogramDistanceFunctionClass
clusterNames
String[] clusterNames
pairwiseDistanceMatrixVariableName
String pairwiseDistanceMatrixVariableName
pairwiseDistanceNamesVariableName
String pairwiseDistanceNamesVariableName
minimizingArrayCompVariableName
String minimizingArrayCompVariableName
chromatogramWarpCommandClass
cross.commands.fragments.AFragmentCommand chromatogramWarpCommandClass
minimizeDist
boolean minimizeDist
drawTICs
boolean drawTICs
drawEICs
boolean drawEICs
alignments
List<E> alignments
pwds
ArrayDouble.D2 pwds
minArrayComp
String minArrayComp
R
double[] R
minimizingLocalDistance
boolean minimizingLocalDistance
pairsWithFirstElement
boolean pairsWithFirstElement
minArrayComp
String minArrayComp
pwdExtension
String pwdExtension
workerFactory
AWorkerFactory workerFactory
Package maltcms.commands.fragments.cluster.pairwiseDistanceCalculator |
serialVersionUID: 8253151151321756579L
context
org.springframework.context.ApplicationContext context
beanId
String beanId
serialVersionUID: 626200987946759092L
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
serialVersionUID: 60123098123486L
input
cross.datastructures.tuple.Tuple2D<T,U> input
alignment
File alignment
value
double value
statsMap
cross.datastructures.StatsMap statsMap
serialVersionUID: 4556712389798130L
similarity
PairwiseFeatureSequenceSimilarity similarity
workflow
cross.datastructures.workflow.IWorkflow workflow
input
cross.datastructures.tuple.Tuple2D<T,U> input
outputDirectory
File outputDirectory
jobNumber
int jobNumber
nJobs
int nJobs
serialVersionUID: -8359038356253166675L
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 |
ordinateValuesVariable
String ordinateValuesVariable
scanAcquisitionTimeVariable
String scanAcquisitionTimeVariable
actualSamplingIntervalVariable
String actualSamplingIntervalVariable
actualDelayTimeVariable
String actualDelayTimeVariable
omit
String omit
time
boolean time
index
boolean index
location
List<E> location
fileDesignation
String fileDesignation
basedir
String basedir
scan
boolean scan
max_names_length
int max_names_length
anchorNamesVariableName
String anchorNamesVariableName
anchorTimesVariableName
String anchorTimesVariableName
anchorRetentionIndexVariableName
String anchorRetentionIndexVariableName
anchorScanIndexVariableName
String anchorScanIndexVariableName
useAnchors
boolean useAnchors
satVariableName
String satVariableName
scanAcquisitionTimeVariableName
String scanAcquisitionTimeVariableName
binnedIntensitiesVariableName
String binnedIntensitiesVariableName
binnedScanIndexVariableName
String binnedScanIndexVariableName
binnedMassesVariableName
String binnedMassesVariableName
filesToRead
List<E> filesToRead
scanIndexOffset
int scanIndexOffset
scanIndexColumnName
String scanIndexColumnName
ticPeakVarName
String ticPeakVarName
varNames
ArrayList<E> varNames
Package maltcms.commands.fragments.peakfinding |
minScale
int minScale
maxScale
int maxScale
minPercentile
double minPercentile
integratePeaks
boolean integratePeaks
integrateRawTic
boolean integrateRawTic
saveGraphics
boolean saveGraphics
peakThreshold
double peakThreshold
filterWindow
int filterWindow
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 |
minScale
int minScale
maxScale
int maxScale
input
File input
output
File output
mz
double mz
eic
double[] eic
minPercentile
double minPercentile
minScale
int minScale
maxScale
int maxScale
input
File input
output
File output
minPercentile
double minPercentile
integratePeaks
boolean integratePeaks
integrateRawTic
boolean integrateRawTic
storeScaleogram
boolean storeScaleogram
peakNormalizers
List<E> peakNormalizers
Package maltcms.commands.fragments.preprocessing |
normalizeScans
boolean normalizeScans
massValues
String massValues
intensityValues
String intensityValues
scanIndex
String scanIndex
totalIntensity
String totalIntensity
binnedIntensityValues
String binnedIntensityValues
binnedMassValues
String binnedMassValues
binnedScanIndex
String binnedScanIndex
massRangeMin
String massRangeMin
massRangeMax
String massRangeMax
maskedMasses
List<E> maskedMasses
invertMaskedMasses
boolean invertMaskedMasses
ignoreMinMaxMassArrays
boolean ignoreMinMaxMassArrays
normalizeMeanVariance
boolean normalizeMeanVariance
normalizeEicsToUnity
boolean normalizeEicsToUnity
massBinResolution
double massBinResolution
excludeMasses
List<E> excludeMasses
epsilon
double epsilon
massValuesVar
String massValuesVar
intensValuesVar
String intensValuesVar
scanIndexVar
String scanIndexVar
totalIntensVar
String totalIntensVar
invert
boolean invert
Package maltcms.commands.fragments.preprocessing.defaultVarLoader |
fileToLoad
File fileToLoad
fileToSave
File fileToSave
Package maltcms.commands.fragments.preprocessing.denseArrayProducer |
massValues
String massValues
intensityValues
String intensityValues
scanIndex
String scanIndex
totalIntensity
String totalIntensity
binnedIntensityValues
String binnedIntensityValues
binnedMassValues
String binnedMassValues
binnedScanIndex
String binnedScanIndex
normalizeScans
boolean normalizeScans
maskedMasses
List<E> maskedMasses
invertMaskedMasses
boolean invertMaskedMasses
normalizeEicsToZeroMeanUnitVariance
boolean normalizeEicsToZeroMeanUnitVariance
normalizeEicsToUnity
boolean normalizeEicsToUnity
massBinResolution
double massBinResolution
minMass
double minMass
maxMass
double maxMass
minMaxIntensities
List<E> minMaxIntensities
fileToLoad
File fileToLoad
fileToSave
File fileToSave
fileToLoad
File fileToLoad
ignoreMinMaxMassArrays
boolean ignoreMinMaxMassArrays
minMassVariableName
String minMassVariableName
maxMassVariableName
String maxMassVariableName
fallbackVariableName
String fallbackVariableName
Package maltcms.commands.fragments.spectratyping |
controlFile
String controlFile
intervals
List<E> intervals
minPercentage
double minPercentage
Package maltcms.commands.fragments.visualization |
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
mzVariableName
String mzVariableName
scanAcquisitionTimeVariableName
String scanAcquisitionTimeVariableName
format
String format
colorrampLocation
String colorrampLocation
sampleSize
int sampleSize
lowThreshold
double lowThreshold
substractStartTime
boolean substractStartTime
timeUnit
String timeUnit
drawEICs
List<E> drawEICs
filea
cross.datastructures.fragments.IFileFragment filea
x_var
String x_var
y_var
String y_var
one_for_each
boolean one_for_each
t
Thread t
filename
String filename
format
String format
chromatogramHeight
int chromatogramHeight
left_chromatogram_var
String left_chromatogram_var
top_chromatogram_var
String top_chromatogram_var
reference_file_name
String reference_file_name
query_file_name
String query_file_name
path_i
String path_i
path_j
String path_j
mz_var
String mz_var
inten_var
String inten_var
scan_index_var
String scan_index_var
mass_range_min_var
String mass_range_min_var
mass_range_max_var
String mass_range_max_var
full_spec
boolean full_spec
colorramp_location
String colorramp_location
sampleSize
int sampleSize
pairsWithFirstElement
boolean pairsWithFirstElement
drawPath
boolean drawPath
matrix_vars
ArrayList<E> matrix_vars
fontsize
int fontsize
showMZs
boolean showMZs
normalize
boolean normalize
normalize_global
boolean normalize_global
mapheight
int mapheight
total_intensity
String total_intensity
scan_acquisition_time
String scan_acquisition_time
ima
BufferedImage ima
imb
BufferedImage imb
map
BufferedImage map
substract_start_time
boolean substract_start_time
jp
JPanel jp
pairsWithFirstElement
boolean pairsWithFirstElement
showChromatogramHeatmap
boolean showChromatogramHeatmap
chromheight
int chromheight
timeUnit
String timeUnit
createMapTICChart
boolean createMapTICChart
createComparativeTICChart
boolean createComparativeTICChart
createDifferentialTICChart
boolean createDifferentialTICChart
createRatioTICChart
boolean createRatioTICChart
createSuperimposedTICChart
boolean createSuperimposedTICChart
y_axis_label
String y_axis_label
colorRampLocation
String colorRampLocation
totalIntensityVar
String totalIntensityVar
scanAcquisitionTimeVar
String scanAcquisitionTimeVar
Package maltcms.commands.fragments.warp |
indexedVars
List<E> indexedVars
- Deprecated.
plainVars
List<E> plainVars
- Deprecated.
indexVar
String indexVar
- Deprecated.
log
org.slf4j.Logger log
- Deprecated.
anchorScanIndexVariableName
String anchorScanIndexVariableName
- Deprecated.
anchorNameVariableName
String anchorNameVariableName
- Deprecated.
average
boolean average
- Deprecated.
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
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
indexedVars
List<E> indexedVars
plainVars
List<E> plainVars
indexVar
String indexVar
anchorScanIndexVariableName
String anchorScanIndexVariableName
anchorNameVariableName
String anchorNameVariableName
average
boolean average
Package maltcms.commands.fragments2d.peakfinding |
minScale
int minScale
maxScale
int maxScale
maxRidgeCost
double maxRidgeCost
minRelativeIntensity
double minRelativeIntensity
rmiServerConfigFile
String rmiServerConfigFile
serialVersionUID: -517839315109598824L
minScale
int minScale
maxScale
int maxScale
maxRidgeCost
double maxRidgeCost
minRelativeIntensity
double minRelativeIntensity
inputFile
File inputFile
outputDir
String outputDir
modulationTime
double modulationTime
scanRate
double scanRate
ridgeTree
QuadTree<T> ridgeTree
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 |
useMeanMS
boolean useMeanMS
threshold
Double threshold
peaklists
List<E> peaklists
similarity
IScalarArraySimilarity similarity
doneList
List<E> doneList
similarity
IScalarArraySimilarity similarity
useMeanMS
boolean useMeanMS
useMeanMS
boolean useMeanMS
threshold
Double threshold
maxRetDiff
double maxRetDiff
similarity
IScalarArraySimilarity similarity
doneList
List<E> doneList
counter
int counter
fcounter
int fcounter
Package maltcms.commands.fragments2d.peakfinding.output |
workflow
cross.datastructures.workflow.IWorkflow workflow
compareAllAgainstAll
boolean compareAllAgainstAll
formatString
String formatString
formatter
NumberFormat formatter
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
k
int k
plotIntegration
boolean plotIntegration
Package maltcms.commands.fragments2d.peakfinding.picking |
totalIntensityRedoVar
String totalIntensityRedoVar
totalIntensityVar
String totalIntensityVar
secondScanIndexVar
String secondScanIndexVar
maxDx
int maxDx
maxDy
int maxDy
minVerticalScanIndex
int minVerticalScanIndex
k
int k
totalIntensityVar
String totalIntensityVar
secondScanIndexVar
String secondScanIndexVar
maxDx
int maxDx
maxDy
int maxDy
minVerticalScanIndex
int minVerticalScanIndex
stdPerc
double stdPerc
Package maltcms.commands.fragments2d.peakfinding.srg |
totalIntensityVar
String totalIntensityVar
usedMassValuesVar
String usedMassValuesVar
secondScanIndexVar
String secondScanIndexVar
minDistance
double minDistance
similarity
IArraySimilarity similarity
minPeakSize
int minPeakSize
maxPeakSize
int maxPeakSize
filterMS
boolean filterMS
useAlternativFiltering
boolean useAlternativFiltering
useMeanMS
boolean useMeanMS
discardPeaksWithMaxArea
boolean discardPeaksWithMaxArea
discardPeaksWithMinArea
boolean discardPeaksWithMinArea
timesum
long timesum
count
int count
scansPerModulation
int scansPerModulation
hold
List<E> hold
intensities
ArrayDouble.D1 intensities
slc
IScanLine slc
ff
cross.datastructures.fragments.IFileFragment ff
Package maltcms.commands.fragments2d.preprocessing |
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
totalIntensityVar
String totalIntensityVar
modulationTimeVar
String modulationTimeVar
scanRateVar
String scanRateVar
scanDurationVar
String scanDurationVar
secondColumnTimeVar
String secondColumnTimeVar
secondColumnScanIndexVar
String secondColumnScanIndexVar
totalIntensity1dVar
String totalIntensity1dVar
scanAcquisitionTimeVar
String scanAcquisitionTimeVar
scanAcquisitionTime1dVar
String scanAcquisitionTime1dVar
totalIntensity2dVar
String totalIntensity2dVar
modulationTime
double modulationTime
scanDuration
double scanDuration
scanRate
double scanRate
modulationIndex0Dimension
String modulationIndex0Dimension
modulationIndex1Dimension
String modulationIndex1Dimension
modulationTimeDimension
String modulationTimeDimension
scanRateDimension
String scanRateDimension
scanNumberDimension
String scanNumberDimension
estimateModulationTime
boolean estimateModulationTime
snrthreshold
double snrthreshold
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
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
totalIntensityVar
String totalIntensityVar
modulationTimeVar
String modulationTimeVar
scanRateVar
String scanRateVar
scanAcquisitionTimeVar
String scanAcquisitionTimeVar
scanIndexVar
String scanIndexVar
startModulation
int startModulation
endModulation
int endModulation
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 |
input
File input
numberOfScans
int numberOfScans
offset
int offset
Package maltcms.commands.fragments2d.testing |
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 |
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
colorrampLocation
String colorrampLocation
lowThreshold
double lowThreshold
totalIntensityVar
String totalIntensityVar
secondScanIndexVar
String secondScanIndexVar
scanRateVar
String scanRateVar
modulationTimeVar
String modulationTimeVar
colorrampLocation
String colorrampLocation
format
String format
doubleFillValue
double doubleFillValue
threshold
double threshold
distClass
String distClass
similarity
IArraySimilarity similarity
absolut
boolean absolut
modulationVar
String modulationVar
scanRateVar
String scanRateVar
indices
int[] indices
Package maltcms.commands.fragments2d.warp |
warpPathi
String warpPathi
warpPathj
String warpPathj
totalIntensity
String totalIntensity
modulationVar
String modulationVar
scanRateVar
String scanRateVar
secondColumnScanIndexVar
String secondColumnScanIndexVar
boundaryPeakListVar
String boundaryPeakListVar
regionIndexListVar
String regionIndexListVar
fillPeakArea
boolean fillPeakArea
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
totalIntensity
String totalIntensity
secondColumnScanIndexVar
String secondColumnScanIndexVar
transpose
boolean transpose
scale
boolean scale
k
int k
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
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
totalIntensity
String totalIntensity
secondColumnScanIndexVar
String secondColumnScanIndexVar
Package maltcms.commands.fragments2d.warp.visualization |
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
currentrasterline
int currentrasterline
Package maltcms.commands.scanners |
gsm
cross.datastructures.StatsMap gsm
ff
cross.datastructures.fragments.IFileFragment ff
vfs
cross.datastructures.fragments.IVariableFragment[] vfs
ignorePositiveInfinity
boolean ignorePositiveInfinity
ignoreNegativeInfinity
boolean ignoreNegativeInfinity
Package maltcms.datastructures |
Package maltcms.datastructures.array |
data
ArrayDouble.D2 data
defaultValue
double defaultValue
shape
Area shape
colStart
ArrayInt.D1 colStart
dataArray
ArrayDouble.D1 dataArray
defaultValue
double defaultValue
elemsToCalculate
float elemsToCalculate
log
org.slf4j.Logger log
neighborhoods
List<E> neighborhoods
nPartitions
int nPartitions
partitions
List<E> partitions
row
int row
rowLength
ArrayInt.D1 rowLength
rowOffset
ArrayInt.D1 rowOffset
totalNumElements
float totalNumElements
virtualCols
int virtualCols
virtualRows
int virtualRows
sdm
cern.colt.matrix.impl.SparseDoubleMatrix2D sdm
serialVersionUID: -3193556606479661979L
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 |
scanIndexVar
String scanIndexVar
maxRangeVar
String maxRangeVar
modulationVar
String modulationVar
scanRateVar
String scanRateVar
iff
cross.datastructures.fragments.IFileFragment iff
lastIndex
int lastIndex
scansPerModulation
int scansPerModulation
binSize
int binSize
cacheModulations
boolean cacheModulations
log
org.slf4j.Logger log
intensityValuesVar
String intensityValuesVar
scanIndexVar
String scanIndexVar
massValuesVar
String massValuesVar
useCache
boolean useCache
prefetch
boolean prefetch
cacheSize
int cacheSize
intensity
cross.datastructures.fragments.IVariableFragment intensity
mass
cross.datastructures.fragments.IVariableFragment mass
intensities
List<E> intensities
masses
List<E> masses
log
org.slf4j.Logger log
intensityValuesVar
String intensityValuesVar
scanIndexVar
String scanIndexVar
massValuesVar
String massValuesVar
maxRangeVar
String maxRangeVar
modulationVar
String modulationVar
scanRateVar
String scanRateVar
secondColumnIndexVar
String secondColumnIndexVar
xyToScanIndexMap
List<E> xyToScanIndexMap
scanIndex
cross.datastructures.fragments.IVariableFragment scanIndex
massValues
cross.datastructures.fragments.IVariableFragment massValues
massIntensities
cross.datastructures.fragments.IVariableFragment massIntensities
iff
cross.datastructures.fragments.IFileFragment iff
lastIndex
int lastIndex
scansPerModulation
int scansPerModulation
binSize
int binSize
cache
HashMap<K,V> cache
cachemiss
int cachemiss
cachehit
int cachehit
loads
int loads
loadnew
int loadnew
cacheModulations
boolean cacheModulations
log
org.slf4j.Logger log
intensityValuesVar
String intensityValuesVar
scanIndexVar
String scanIndexVar
massValuesVar
String massValuesVar
maxRangeVar
String maxRangeVar
modulationVar
String modulationVar
scanRateVar
String scanRateVar
scanIndex
cross.datastructures.fragments.IVariableFragment scanIndex
massValues
cross.datastructures.fragments.IVariableFragment massValues
massIntensities
cross.datastructures.fragments.IVariableFragment massIntensities
iff
cross.datastructures.fragments.IFileFragment iff
lastIndex
int lastIndex
scansPerModulation
int scansPerModulation
binSize
int binSize
cache
HashMap<K,V> cache
cachemiss
int cachemiss
cachehit
int cachehit
loads
int loads
loadnew
int loadnew
cacheModulations
boolean cacheModulations
log
org.slf4j.Logger log
intensityValuesVar
String intensityValuesVar
scanIndexVar
String scanIndexVar
massValuesVar
String massValuesVar
maxRangeVar
String maxRangeVar
modulationVar
String modulationVar
scanRateVar
String scanRateVar
secondColumnIndexVar
String secondColumnIndexVar
xyToScanIndexMap
List<E> xyToScanIndexMap
scanIndex
cross.datastructures.fragments.IVariableFragment scanIndex
massValues
cross.datastructures.fragments.IVariableFragment massValues
massIntensities
cross.datastructures.fragments.IVariableFragment massIntensities
iff
cross.datastructures.fragments.IFileFragment iff
lastIndex
int lastIndex
scansPerModulation
int scansPerModulation
binSize
int binSize
cache
HashMap<K,V> cache
cachemiss
int cachemiss
cachehit
int cachehit
loads
int loads
loadnew
int loadnew
cacheModulations
boolean cacheModulations
Package maltcms.datastructures.feature |
serialVersionUID: 4737942765869140810L
binned_mass_values
List<E> binned_mass_values
binned_intensity_values
List<E> binned_intensity_values
sat
ArrayDouble.D0 sat
tic
ArrayDouble.D0 tic
i
int i
iff
cross.datastructures.fragments.IFileFragment iff
serialVersionUID: -2245293151270164895L
featureToIndex
Map<K,V> featureToIndex
datalist
List<E> datalist
serialVersionUID: 2026476569387259118L
binnedMasses
Array binnedMasses
binnedIntens
Array binnedIntens
sat
ArrayDouble.D0 sat
tic
ArrayDouble.D0 tic
l
List<E> l
featureNames
List<E> featureNames
serialVersionUID: 1423070246312970401L
iff
cross.datastructures.fragments.IFileFragment iff
index
int index
Package maltcms.datastructures.fragments |
ff
cross.datastructures.fragments.IFileFragment ff
savePWDM
boolean savePWDM
saveCDM
boolean saveCDM
alignment
IArrayD2Double alignment
distance
IArrayD2Double distance
isMinimize
boolean isMinimize
refsize
int refsize
querysize
int querysize
cd
IRecurrence cd
result
ArrayDouble.D0 result
resultVector
ArrayDouble.D1 resultVector
pwd
PairwiseFeatureSimilarity pwd
ref
cross.datastructures.fragments.IFileFragment ref
target
cross.datastructures.fragments.IFileFragment target
path
List<E> path
creator
Class<T> creator
localPathOptima
List<E> localPathOptima
anchors
DefaultPairSet<T extends IAnchor> anchors
cumulativeDistanceVariableName
String cumulativeDistanceVariableName
pairwiseDistanceVariableName
String pairwiseDistanceVariableName
arrayComparatorVariableName
String arrayComparatorVariableName
arrayDistanceClassName
String arrayDistanceClassName
iw
cross.datastructures.workflow.IWorkflow iw
predecessors
byte[][] predecessors
normalizeAlignmentValueByMapWeights
boolean normalizeAlignmentValueByMapWeights
interppath
List<E> interppath
pwDistFileFragment
cross.datastructures.fragments.IFileFragment pwDistFileFragment
pairwiseDistances
ArrayDouble.D2 pairwiseDistances
pwDistMatrixVariableName
String pwDistMatrixVariableName
pwDistVariableName
String pwDistVariableName
pwDistAlignmentsVarName
String pwDistAlignmentsVarName
name
String name
minimize
boolean minimize
minArrayComp
String minArrayComp
names
ArrayChar.D2 names
alignments
cross.datastructures.tuple.TupleND<T extends Serializable> alignments
iw
cross.datastructures.workflow.IWorkflow iw
Package maltcms.datastructures.ms |
parent
cross.datastructures.fragments.IFileFragment parent
scanAcquisitionTimeUnit
String scanAcquisitionTimeUnit
scan_acquisition_time_var
String scan_acquisition_time_var
massValues
List<E> massValues
intensityValues
List<E> intensityValues
parent
cross.datastructures.fragments.IFileFragment parent
isl
IScanLine isl
scanAcquisitionTimeUnit
String scanAcquisitionTimeUnit
secondColumnScanAcquisitionTimeUnit
String secondColumnScanAcquisitionTimeUnit
md
double md
spm
int spm
slc
int slc
satOffset
double satOffset
log
org.slf4j.Logger log
cfg
org.apache.commons.configuration.Configuration cfg
readExternal
public void readExternal(ObjectInput in)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
writeExternal
public void writeExternal(ObjectOutput out)
throws IOException
- Throws:
IOException
readExternal
public void readExternal(ObjectInput in)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
writeExternal
public void writeExternal(ObjectOutput out)
throws IOException
- Throws:
IOException
serialVersionUID: 2937381605461829269L
scanNumber
ArrayInt.D0 scanNumber
scanAcquisitionTime
ArrayDouble.D0 scanAcquisitionTime
total_intensity
ArrayDouble.D0 total_intensity
masses
Array masses
intensities
Array intensities
serialVersionUID: -5785157824205744680L
fctime
double fctime
sctime
double sctime
fcind
int fcind
scind
int scind
Package maltcms.datastructures.peak |
serialVersionUID: -4337180586706400884L
scanIndex
int scanIndex
msIntensities
Array msIntensities
sat
double sat
sims
HashMap<K,V> sims
sortedPeaks
HashMap<K,V> sortedPeaks
name
String name
peakIndex
int peakIndex
association
String association
storeOnlyBestSimilarities
boolean storeOnlyBestSimilarities
serialVersionUID: -8878754902179218064L
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
serialVersionUID: 6343209775465424292L
peakArea
PeakArea2D peakArea
scanIndex
int scanIndex
index
int index
firstRetTime
double firstRetTime
secondRetTime
double secondRetTime
identification
List<E> identification
reference
Peak2D reference
Package maltcms.datastructures.quadTree |
serialVersionUID: 7864374322427340984L
Package maltcms.db.predicates.metabolite |
serialVersionUID: -2688853916226964219L
mpl
Collection<E> mpl
serialVersionUID: 4401086253537298137L
im
IMatchPredicate<T> im
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
serialVersionUID: 4384503672151011994L
lB
Number lB
uB
Number uB
serialVersionUID: -3684834963267981958L
s
MetaboliteSimilarity s
serialVersionUID: -8108747283945214056L
serialVersionUID: 7126522681487993030L
match
String match
matchCaseInsensitive
boolean matchCaseInsensitive
serialVersionUID: -2284912996792720438L
serialVersionUID: 8174435563633316055L
mvm
MetaboliteViewModel mvm
ap
com.db4o.query.Predicate<ExtentType> ap
jtf
JTextField jtf
filter
String filter
af
IAggregatePredicateFactory<T> af
serialVersionUID: -3658654429470080006L
jtf
JTextField jtf
sb
JButton sb
spb
JButton spb
mvm
MetaboliteViewModel mvm
serialVersionUID: 1L
mvm
MetaboliteViewModel mvm
textFields
HashMap<K,V> textFields
panels
HashMap<K,V> panels
submitFilterButton
JButton submitFilterButton
buttonPanel
JPanel buttonPanel
error
boolean error
serialVersionUID: -38817321732051832L
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
serialVersionUID: 5980514459833450228L
Package maltcms.experimental.bipace |
fragment
cross.datastructures.fragments.IFileFragment fragment
peaks
List<E> peaks
index
int index
Package maltcms.experimental.bipace.api |
uniqueId
UUID uniqueId
peakListA
List<E> peakListA
peakListB
List<E> peakListB
similarityFunction
IScalarArraySimilarity similarityFunction
storeOnlyBestSimilarities
boolean storeOnlyBestSimilarities
Package maltcms.experimental.bipace.datastructures.api |
result
Serializable result
producerId
UUID producerId
Package maltcms.experimental.bipace.datastructures.spi |
retentionTime1
double retentionTime1
retentionTime2
double retentionTime2
Package maltcms.experimental.bipace.spi |
maxRtDifference
double maxRtDifference
maxRt1Difference
double maxRt1Difference
maxRt2Difference
double maxRt2Difference
Package maltcms.experimental.operations |
mass_values
String mass_values
intensity_values
String intensity_values
Package maltcms.experimental.ui |
serialVersionUID: 4300139196647706338L
bi
BufferedImage bi
Package maltcms.io.andims |
log
org.slf4j.Logger log
fileEnding
String[] fileEnding
updateAttributes
boolean updateAttributes
useNetcdfFileCache
boolean useNetcdfFileCache
- Deprecated.
saveNCML
boolean saveNCML
scanDimensionVars
List<E> scanDimensionVars
scanDimensionName
String scanDimensionName
pointDimensionVars
List<E> pointDimensionVars
pointDimensionName
String pointDimensionName
fileEnding
String[] fileEnding
scanDimensionVars
List<E> scanDimensionVars
scanDimensionName
String scanDimensionName
pointDimensionVars
List<E> pointDimensionVars
pointDimensionName
String pointDimensionName
ndf
NetcdfDataSource ndf
dataFieldToRead
int dataFieldToRead
Package maltcms.io.xml.mzData |
log
org.slf4j.Logger log
fileEnding
String[] fileEnding
mass_values
String mass_values
intensity_values
String intensity_values
total_intensity
String total_intensity
scan_acquisition_time
String scan_acquisition_time
scan_index
String scan_index
mass_range_min
String mass_range_min
mass_range_max
String mass_range_max
ndf
NetcdfDataSource ndf
source_files
String source_files
Package maltcms.io.xml.mzML |
log
org.slf4j.Logger log
fileEnding
String[] fileEnding
mass_values
String mass_values
intensity_values
String intensity_values
total_intensity
String total_intensity
scan_acquisition_time
String scan_acquisition_time
scan_index
String scan_index
mass_range_min
String mass_range_min
mass_range_max
String mass_range_max
ndf
NetcdfDataSource ndf
source_files
String source_files
Package maltcms.io.xml.mzXML |
ds
List<E> ds
log
org.slf4j.Logger log
fragmentToValidReaderMap
WeakHashMap<K,V> fragmentToValidReaderMap
log
org.slf4j.Logger log
fileEnding
String[] fileEnding
mass_values
String mass_values
intensity_values
String intensity_values
total_intensity
String total_intensity
scan_acquisition_time
String scan_acquisition_time
scan_index
String scan_index
mass_range_min
String mass_range_min
mass_range_max
String mass_range_max
ndf
NetcdfDataSource ndf
source_files
String source_files
mslevel
int mslevel
parser
org.systemsbiology.jrap.MSXMLParser parser
variableToArrayCache
cross.datastructures.ehcache.ICacheDelegate<K,V> variableToArrayCache
log
org.slf4j.Logger log
fileEnding
String[] fileEnding
mass_values
String mass_values
intensity_values
String intensity_values
total_intensity
String total_intensity
scan_acquisition_time
String scan_acquisition_time
scan_index
String scan_index
mass_range_min
String mass_range_min
mass_range_max
String mass_range_max
ndf
NetcdfDataSource ndf
source_files
String source_files
mslevel
int mslevel
parser
org.systemsbiology.jrap.stax.MSXMLParser parser
variableToArrayCache
cross.datastructures.ehcache.ICacheDelegate<K,V> variableToArrayCache
Package maltcms.math.functions |
expansionWeight
double expansionWeight
matchWeight
double matchWeight
compressionWeight
double compressionWeight
denseMassSpectraSimilarity
IArraySimilarity denseMassSpectraSimilarity
expansionWeight
double expansionWeight
matchWeight
double matchWeight
compressionWeight
double compressionWeight
retentionTimeSimilarity
IScalarSimilarity retentionTimeSimilarity
denseMassSpectraSimilarity
IArraySimilarity denseMassSpectraSimilarity
progress
net.sf.maltcms.execution.api.job.Progress progress
finished
long finished
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
serialVersionUID: 7611857256393422827L
pa
PartitionedArray pa
paSize
Dimension paSize
paIm
BufferedImage paIm
rr
maltcms.ui.TabbedPanel.RepaintRunnable rr
aps
AnchorPairSet aps
Package maltcms.ui.charts |
yaxis_min
double yaxis_min
yaxis_max
double yaxis_max
map
List<E> map
height
int height
title
String title
domain1
Array domain1
domain2
Array domain2
x_label
String x_label
log
org.slf4j.Logger log
stride
int stride
xlabel
String xlabel
ylabel
String ylabel
label
String label
title
String title
filename
String filename
xaxis
ArrayDouble.D1 xaxis
yaxis
ArrayDouble.D1 yaxis
title
String title
x_axis
String x_axis
subplots
List<E> subplots
cdxyp
org.jfree.chart.plot.CombinedDomainXYPlot cdxyp
gap
int gap
log
org.slf4j.Logger log
chart
org.jfree.chart.JFreeChart chart
serialVersionUID: 1121734275349109897L
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
hm
BufferedImage hm
xlabel
String xlabel
ylabel
String ylabel
label
String label
title
String title
xaxis
ArrayDouble.D1 xaxis
yaxis
ArrayDouble.D1 yaxis
serialVersionUID: -830245788879399345L
jtp
JTabbedPane jtp
lastOpenDir
File lastOpenDir
jmb
JMenuBar jmb
fileMenu
JMenu fileMenu
status
JLabel status
serialVersionUID: 425194552644224115L
jfc
org.jfree.chart.JFreeChart jfc
serialVersionUID: 5547094237664337509L
serialVersionUID: -8133108907581040380L
parent
Component parent
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
plot
org.jfree.chart.plot.Plot plot
title
String title
filetype
String filetype
filename
String filename
outputDir
File outputDir
fontFamily
String fontFamily
imgwidth
int imgwidth
imgheight
int imgheight
sizeOverride
boolean sizeOverride
headless
boolean headless
stop
boolean stop
file
File file
targetContainer
JFrame targetContainer
log
org.slf4j.Logger log
serializeJFreeChart
boolean serializeJFreeChart
saveGraphics
boolean saveGraphics
title
String title
cd
org.jfree.data.category.CategoryDataset cd
serialVersionUID: -1731263966310777412L
jCheckBox1
JCheckBox jCheckBox1
jComboBox1
JComboBox jComboBox1
jComboBox3
JComboBox jComboBox3
jLabel1
JLabel jLabel1
jLabel4
JLabel jLabel4
jSeparator1
JSeparator jSeparator1
serialVersionUID: 1311452000544833279L
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
maxUpperXAxisBound
Double maxUpperXAxisBound
maxUpperYAxisBound
Double maxUpperYAxisBound
minLowerXAxisBound
Double minLowerXAxisBound
minLowerYAxisBound
Double minLowerYAxisBound
backgroundImageFilename
String backgroundImageFilename
xaxis
String xaxis
yaxis
String yaxis
labels
List<E> labels
annotations
List<E> annotations
arrays
List<E> arrays
domains
Array[] domains
title
String title
annotation_positions_x
Array annotation_positions_x
annotation_positions_y
Array annotation_positions_y
renderArea
boolean renderArea
fgAlpha
float fgAlpha
diffRender
boolean diffRender
log
org.slf4j.Logger log
logScale
boolean logScale
x
Array x
y
ArrayList<E> y
z
ArrayList<E> z
name
String name
xaxis
String xaxis
yaxis
String yaxis
title
String title
log
org.slf4j.Logger log
Package maltcms.ui.renderer |
serialVersionUID: 7297064254819024794L
Package maltcms.ui.wizard |
serialVersionUID: -5324638127680705898L
dcbm
DefaultComboBoxModel dcbm
jComboBox1
JComboBox jComboBox1
jLabel1
JLabel jLabel1
jLabel2
JLabel jLabel2
jLabel3
JLabel jLabel3
jLabel4
JLabel jLabel4
jTextField1
JTextField jTextField1
jTextField2
JTextField jTextField2
jTextField3
JTextField jTextField3
serialVersionUID: 4887167150661489442L
dtm
DefaultTableModel dtm
longestString
String longestString
files
HashSet<E> files
dlm
DefaultComboBoxModel dlm
activeFile
String activeFile
anchorID
int anchorID
cwd
File cwd
hasSaved
boolean hasSaved
hasLoaded
boolean hasLoaded
fileToAnchorsMap
HashMap<K,V> fileToAnchorsMap
jButton1
JButton jButton1
jButton2
JButton jButton2
jButton3
JButton jButton3
jButton4
JButton jButton4
jButton5
JButton jButton5
jComboBox1
JComboBox jComboBox1
jLabel6
JLabel jLabel6
jScrollPane2
JScrollPane jScrollPane2
jTable1
JTable jTable1
serialVersionUID: 8468582599008051433L
cwd
File cwd
cod
File cod
dlm
DefaultListModel dlm
jButton1
JButton jButton1
jButton3
JButton jButton3
jButton4
JButton jButton4
jCheckBox1
JCheckBox jCheckBox1
jLabel1
JLabel jLabel1
jLabel6
JLabel jLabel6
jLabel7
JLabel jLabel7
jList1
JList jList1
jPanel2
JPanel jPanel2
jPanel3
JPanel jPanel3
jScrollPane1
JScrollPane jScrollPane1
jTextField5
JTextField jTextField5
jTextField6
JTextField jTextField6
serialVersionUID: -6216223747360194482L
pw
PipelineWizard pw
serialVersionUID: -4941454703967935783L
pw
PipelineWizard pw
serialVersionUID: -3371831501616427849L
jf
Container jf
serialVersionUID: 7614497705493470346L
c
Container c
cfg
org.apache.commons.configuration.PropertiesConfiguration cfg
serialVersionUID: 4992924104511397101L
dlm1
DefaultListModel dlm1
jButton2
JButton jButton2
jButton5
JButton jButton5
jCheckBox1
JCheckBox jCheckBox1
jLabel1
JLabel jLabel1
jLabel8
JLabel jLabel8
jList2
JList jList2
jScrollPane2
JScrollPane jScrollPane2
jTextField7
JTextField jTextField7
serialVersionUID: 1009564289591217777L
jCheckBox1
JCheckBox jCheckBox1
jCheckBox2
JCheckBox jCheckBox2
jCheckBox3
JCheckBox jCheckBox3
jCheckBox4
JCheckBox jCheckBox4
jCheckBox5
JCheckBox jCheckBox5
jCheckBox6
JCheckBox jCheckBox6
jComboBox1
JComboBox jComboBox1
jLabel1
JLabel jLabel1
jLabel2
JLabel jLabel2
jLabel3
JLabel jLabel3
jLabel4
JLabel jLabel4
jLabel5
JLabel jLabel5
jTextField1
JTextField jTextField1
jTextField2
JTextField jTextField2
jTextField3
JTextField jTextField3
jTextField4
JTextField jTextField4
Package net.sf.maltcms.apps |
serialVersionUID: 6217168349675106268L
selectTableHeaders
HashMap<K,V> selectTableHeaders
mvm
MetaboliteViewModel mvm
qpanel
JPanel qpanel
Package net.sf.maltcms.evaluation.api |
serialVersionUID: -5936343655074144856L
rt
ArrayDouble.D0 rt
Package net.sf.maltcms.evaluation.api.alignment |
serialVersionUID: -5936343655074144856L
values
ArrayDouble.D1 values
Package net.sf.maltcms.evaluation.api.tasks |
Package net.sf.maltcms.evaluation.spi.classification |
groundTruthFile
File groundTruthFile
delta
double delta
oc
com.db4o.ObjectContainer oc
toolFileName
String toolFileName
serialVersionUID: -5936343655074144856L
rt
ArrayDouble.D0 rt
Package net.sf.maltcms.evaluation.spi.hohenheim |
serialVersionUID: -6754630453106703429L
p
com.db4o.query.Predicate<ExtentType>[] p
serialVersionUID: -3389850465308219316L
rt
double rt
maxrtdev
double maxrtdev
name
String name
chromname
String chromname
serialVersionUID: 6463510990923985730L
name
String name
peakName
String peakName
serialVersionUID: 1L
name
String name
serialVersionUID: 4469891680424542881L
file
String file
creator
String creator
peakname
String peakname
serialVersionUID: 5009287857661674974L
file
String file
creator
String creator
serialVersionUID: -2493853621255366827L
name
String name
serialVersionUID: 5009287857661674974L
file
String file
serialVersionUID: -55691937902127499L
serialVersionUID: -3734257468780932748L
creator
String creator
serialVersionUID: -3543269480153995134L
name
String name
serialVersionUID: -1948551337371019623L
Package net.sf.maltcms.evaluation.spi.tasks |
serialVersionUID: 986719239076016L
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 |
pipelines
List<E> pipelines
name
String name
ics
net.sf.maltcms.execution.api.ICompletionService<T> ics
Package net.sf.maltcms.evaluation.spi.tasks.maltcms |
taskInputs
List<E> taskInputs
taskOutputs
List<E> taskOutputs
serialVersionUID: -4395347427746465402L
workflow
File workflow
Package net.sf.maltcms.evaluation.spi.xcalibur |
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
pairsWithFirst
boolean pairsWithFirst
log
org.slf4j.Logger log
minArrayComp
String minArrayComp
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