Uses of Class
biolockj.module.report.taxa.TaxaLevelTable

Packages that use TaxaLevelTable

Package	Description
biolockj.module.diversity
biolockj.module.report.taxa
biolockj.util	Static utilities centralize and organize reusable core methods.

Uses of TaxaLevelTable in biolockj.module.diversity

Methods in biolockj.module.diversity that return TaxaLevelTable

Modifier and Type	Method and Description
protected TaxaLevelTable	ShannonDiversity.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs)

Methods in biolockj.module.diversity with parameters of type TaxaLevelTable

Modifier and Type	Method and Description
protected List<String>	ShannonDiversity.filterTaxa(TaxaLevelTable inputData)
protected TaxaLevelTable	ShannonDiversity.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs)

Uses of TaxaLevelTable in biolockj.module.report.taxa

Methods in biolockj.module.report.taxa that return TaxaLevelTable

Modifier and Type	Method and Description
protected TaxaLevelTable	AddPseudoCount.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs)
protected TaxaLevelTable	LogTransformTaxaTables.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Log transform the data
protected abstract TaxaLevelTable	TransformTaxaTables.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Transform a table of values.
protected TaxaLevelTable	NormalizeByReadsPerMillion.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs)
protected TaxaLevelTable	NormalizeTaxaTables.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1

Methods in biolockj.module.report.taxa with parameters of type TaxaLevelTable

Modifier and Type	Method and Description
protected List<String>	TransformTaxaTables.filterSamples(TaxaLevelTable inputData) Filter out any samples in which all values are 0.
protected List<String>	TransformTaxaTables.filterTaxa(TaxaLevelTable inputData)
protected TaxaLevelTable	AddPseudoCount.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs)
protected TaxaLevelTable	LogTransformTaxaTables.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Log transform the data
protected abstract TaxaLevelTable	TransformTaxaTables.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Transform a table of values.
protected TaxaLevelTable	NormalizeByReadsPerMillion.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs)
protected TaxaLevelTable	NormalizeTaxaTables.transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1

Uses of TaxaLevelTable in biolockj.util

Methods in biolockj.util that return TaxaLevelTable

Modifier and Type	Method and Description
static TaxaLevelTable	TaxaUtil.readTaxaTable(File taxaTable) Read a table of counts, formatted with samples as rows (ids in first column) and taxa as columns (ids in header).

Methods in biolockj.util with parameters of type TaxaLevelTable

Modifier and Type	Method and Description
static void	TaxaUtil.writeDataToFile(File outFile, List<String> sampleNames, List<String> taxaNames, TaxaLevelTable taxaCounts) Write transformed data to file
static void	TaxaUtil.writeDataToFile(File outFile, TaxaLevelTable taxaCounts)