doe

package
v0.0.0-...-040724e Latest Latest
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 Go to latest Published: Jun 6, 2019 License: BSD-3-Clause, GPL-2.0, BSD-3-Clause, + 1 more Imports: 17 Imported by: 2

Documentation

Overview

Package doe facilitates DOE methodology in antha

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func AddWelllocations 

func AddWelllocations(DXORJMP string, xlsxfile string, oldsheet int, runnumbertowellcombos []string, nameappendage string, pathtosave string, extracolumnheaders []string, extracolumnvalues []interface{}) error

func AllComboCount 

func AllComboCount(pairs []DOEPair) (numberofuniquecombos int)

func AssemblyParametersFromRuns 

func AssemblyParametersFromRuns(runs []Run, enzymename string) (assemblyparameters []enzymes.Assemblyparameters)

func DNASequencetoInterface 

func DNASequencetoInterface(genes []wtype.DNASequence) (geneseqs []interface{})

func DXXLSXFilefromRuns 

func DXXLSXFilefromRuns(runs []Run, outputfilename string) (xlsxfile *xlsx.File)

func FixedAndNonFixed 

func FixedAndNonFixed(factors []DOEPair) (fixedfactors []DOEPair, nonfixed []DOEPair)

func HandleComponentWithConcentration 

func HandleComponentWithConcentration(ctx context.Context, header string, value interface{}) (component *wtype.Liquid, concentration wunit.Concentration, err error)

HandleComponentWithConcentration returns both LHComponent and Concentration from a component name with concentration in a DOE design. If no valid concentration is found or an invalid component name is specifed an error is returned.

func HandleConcFactor 

func HandleConcFactor(header string, value interface{}) (anthaConc wunit.Concentration, err error)

HandleConcFactor parses a factor name and value and returns an antha concentration. If the value cannot be converted to a valid concentration an error is returned. If the header contains a valid concentration unit a number can be specified as the value.

func HandleLHComponentFactor 

func HandleLHComponentFactor(ctx context.Context, header string, value interface{}) (*wtype.Liquid, error)

HandleLHComponentFactor parses a factor name and value and returns an LHComponent.

If the value cannot be converted to a valid component an error is returned.

func HandleLHPlateFactor 

func HandleLHPlateFactor(ctx context.Context, header string, value interface{}) (*wtype.Plate, error)

HandleLHPlateFactor parses a factor name and value and returns an LHComponent.

If the value cannot be converted to a valid component an error is returned.

func HandleRPMFactor 

func HandleRPMFactor(header string, value interface{}) (anthaRate wunit.Rate, err error)

HandleRPMFactor parses a factor name and value and returns an antha Rate. If the value cannot be converted to a valid Rate an error is returned. A float or int value with no unit is assumed to be in /min.

func HandleStringFactor 

func HandleStringFactor(header string, value interface{}) (string, error)

HandleStringFactor converts the value of a factor with an interface value to a string.

func HandleTemperatureFactor 

func HandleTemperatureFactor(header string, value interface{}) (anthaTemp wunit.Temperature, err error)

HandleTemperatureFactor parses a factor name and value and returns an antha Temperature. If the value cannot be converted to a valid Temperature an error is returned. A float or int value with no unit is assumed to be in C.

func HandleTimeFactor 

func HandleTimeFactor(header string, value interface{}) (anthaTime wunit.Time, err error)

HandleTimeFactor parses a factor name and value and returns an antha Time. If the value cannot be converted to a valid Time an error is returned. A float or int value with no unit is assumed to be in s.

func HandleVolumeFactor 

func HandleVolumeFactor(header string, value interface{}) (anthaVolume wunit.Volume, err error)

HandleVolumeFactor parses a factor name and value and returns an antha Volume. If the value cannot be converted to a valid Volume an error is returned.

func IsFixedFactor 

func IsFixedFactor(factor DOEPair) (yesorno bool)

func JMPXLSXFilefromRuns 

func JMPXLSXFilefromRuns(runs []Run, outputfilename string) (xlsxfile *xlsx.File)

func LowestLevelValue 

func LowestLevelValue(runs []Run, factor string) (value interface{}, err error)

LowestLevelValue returns the lowest level value for a specified factor name from an array of runs

func MergeFactorNames 

func MergeFactorNames(factorNames []string) (combinedFactor string)

func XLSXFileFromRuns 

func XLSXFileFromRuns(runs []Run, outputfilename string, dxorjmp string) (xlsxfile *xlsx.File)

Types

type DOEPair 

type DOEPair struct {
	Factor string
	Levels []interface{}
}

func MakePair 

func MakePair(runs []Run, factor string) (allfactorPairs DOEPair, err error)

MakePair pairs a factor with all levels found in runs

func Pair 

func Pair(factordescription string, levels []interface{}) (doepair DOEPair)

func RemoveDuplicateLevels 

func RemoveDuplicateLevels(pair DOEPair) (reducedpair DOEPair, err error)

RemoveDuplicateLevels creates a copy of the pair with reduced factors if an error occurs the orginal pair is returned

func (DOEPair) LevelCount 

func (pair DOEPair) LevelCount() (numberoflevels int)

func (DOEPair) MaxLevel 

func (pair DOEPair) MaxLevel() (maxlevel interface{}, err error)

MaxLevel returns the maximum level of a DOEPair if the factor is numeric, if the factor is not numeric an error is returned

func (DOEPair) MinLevel 

func (pair DOEPair) MinLevel() (minlevel interface{}, err error)

MinLevel returns the minimum level of a DOEPair if the factor is numeric, if the factor is not numeric an error is returned unless the factor is a MergedLevel comprising of concentration values

func (DOEPair) RoundLevels 

func (pair DOEPair) RoundLevels() (newpair DOEPair, err error)

RoundLevels round floats and concs

type MergeOption 

type MergeOption string

MergeOption is an option to control the position in the factors of a run at which the merged factor will be added. Valid options are MoveToFront, MoveToBack and UsePositionOfLastFactorInFactorList. The default if no option is set is UsePositionOfLastFactorInFactorList. 

var (
	// MoveToFront specifies that the merged factor should be moved to the front of the factor list
	MoveToFront MergeOption = "MoveToFront"

	// MoveToBack specifies that the merged factor should be moved to the back of the factor list
	MoveToBack MergeOption = "MoveToBack"

	// UsePositionOfLastFactorInFactorList specifies that the merged factor should be moved to the position of the last factor in the merged list.
	UsePositionOfLastFactorInFactorList MergeOption = "UsePositionOfLastFactorInFactorList"

	// Default will use UsePositionOfLastFactorInFactorList.
	DefaultMergeOption MergeOption = UsePositionOfLastFactorInFactorList
)

type MergedLevel 

type MergedLevel struct {
	OriginalFactorPairs map[string]interface{} `json:"OriginalFactorPairs"` // map of original factor names to levels e.g. "Glucose":"10uM", "Glycerol mM": 0
}

A MergedLevel is the product of merging two factor levels and retaining the original merged factor level pairs in a map

func MakeMergedLevel 

func MakeMergedLevel(factorsInOrder []string, levelsInOrder []interface{}) (m MergedLevel, err error)

MakeMergedLevel merges an array of factors into a single merged level type using arrays of factor names and levels in order

func ToMergedLevel 

func ToMergedLevel(level interface{}) (m MergedLevel, err error)

ToMergedLevel casts a valid interface into a MergedLevel. Independent of serialisation history. If the value cannot be cast into a merged level an error is returned.

func (MergedLevel) EqualTo 

func (m MergedLevel) EqualTo(e MergedLevel) (bool, error)

EqualTo evaluates whether two merged levels are equal

func (MergedLevel) EqualToMergeConcs 

func (m MergedLevel) EqualToMergeConcs(e MergedLevel) (bool, error)

EqualToMergeConcs evaluates whether two merged levels are equal

func (MergedLevel) Sort 

func (m MergedLevel) Sort() (orderedKeys []string)

Sort returns keys in alphabetical order; values are returned in the order corresponding to the key order

func (MergedLevel) UnMerge 

func (m MergedLevel) UnMerge() (factors []string, setpoints []interface{})

UnMerge returns keys in alphabetical order; values are returned in the order corresponding to the key order

type Run 

type Run struct {
	RunNumber            int
	StdNumber            int
	Factordescriptors    []string
	Setpoints            []interface{}
	Responsedescriptors  []string
	ResponseValues       []interface{}
	AdditionalHeaders    []string // could represent a class e.g. Environment variable, processed, raw, location
	AdditionalSubheaders []string // e.g. well ID, Ambient Temp, order,
	AdditionalValues     []interface{}
}

func AddAdditionalHeaderandValue 

func AddAdditionalHeaderandValue(run Run, additionalheader string, additionalsubheader string, additionalvalue interface{}) (newrun Run)

func AddAdditionalHeaders 

func AddAdditionalHeaders(run Run, additionalheader string, additionalsubheader string) (newrun Run)

func AddAdditionalValue 

func AddAdditionalValue(run Run, additionalsubheader string, additionalvalue interface{}) (newrun Run)

func AddFixedFactors 

func AddFixedFactors(runs []Run, fixedfactors []DOEPair) (runswithfixedfactors []Run)

func AddNewFactorFieldandValue 

func AddNewFactorFieldandValue(run Run, factordescriptor string, factorvalue interface{}) (newrun Run)

func AddNewResponseField 

func AddNewResponseField(run Run, responsedescriptor string) (newrun Run)

AddNewResponseField adds a new response field. The response field will be added with a blank response value. The field will only be added if the response is not already present.

func AddNewResponseFieldandValue 

func AddNewResponseFieldandValue(run Run, responsedescriptor string, responsevalue interface{}) (newrun Run)

func AllCombinations 

func AllCombinations(factors []DOEPair) (runs []Run)

AllCombinations combines all factor pairs to make all possible combinations of runs

func Copy 

func Copy(run Run) (newrun Run)

func DeleteAllResponses 

func DeleteAllResponses(run Run) (newrun Run)

func DeleteFactorField 

func DeleteFactorField(run Run, factorDescriptor string) (newrun Run)

func DeleteResponseField 

func DeleteResponseField(run Run, responsedescriptor string) (newrun Run)

func MergeRunsFromAllCombos 

func MergeRunsFromAllCombos(originalRuns []Run, allcombos []Run, factors []string, options ...MergeOption) (mergedRuns []Run, err error)

MergeRunsFromAllCombos will make a set of runs based on the original runs which merges all factors specified in factors and finds a valid merged run from all combos to inject in as the set point. MergeOptions can be specified to control the position in the factors of a run at which the merged factor will be added. Valid options are MoveToFront, MoveToBack and UsePositionOfLastFactorInFactorList. The default if no option is set is UsePositionOfLastFactorInFactorList.

func ReplaceAdditionalValue 

func ReplaceAdditionalValue(run Run, additionalsubheader string, additionalvalue interface{}) (newrun Run)

func ReplaceFactorField 

func ReplaceFactorField(run Run, factorToReplace, factorToReplaceWith string, setPointToReplaceWith interface{}) (newrun Run)

ReplaceFactorField will replace the factorToReplace with factorToReplaceWith with Set point setPointToReplaceWith. The index of the factor to replace will be the same as the replaced factor.

func ReplaceResponseValue 

func ReplaceResponseValue(run Run, responsedescriptor string, responsevalue interface{}) (newrun Run)

func RunsFromDXDesign 

func RunsFromDXDesign(filename string, intfactors []string) (runs []Run, err error)

func RunsFromDXDesignContents 

func RunsFromDXDesignContents(bytes []byte, intfactors []string) (runs []Run, err error)

func RunsFromDesign 

func RunsFromDesign(contents []byte, intfactors []string, dxorjmp string) (runs []Run, err error)

func RunsFromDesignPreResponses 

func RunsFromDesignPreResponses(designfile string, intfactors []string, dxorjmp string) (runs []Run, err error)

func RunsFromDesignPreResponsesContents 

func RunsFromDesignPreResponsesContents(designfileContents []byte, intfactors []string, dxorjmp string) (runs []Run, err error)

func RunsFromFixedFactors 

func RunsFromFixedFactors(fixedfactors []DOEPair) (runswithfixedfactors []Run)

func RunsFromJMPDesign 

func RunsFromJMPDesign(xlsx string, factorcolumns []int, responsecolumns []int, intfactors []string) (runs []Run, err error)

func RunsFromJMPDesignContents 

func RunsFromJMPDesignContents(bytes []byte, factorcolumns []int, responsecolumns []int, intfactors []string) (runs []Run, err error)

func UnMergeRuns 

func UnMergeRuns(mergedRuns []Run) (originalRuns []Run)

UnMergeRuns turns mergedlevels into original factors and levels

func (Run) AddResponseValue 

func (run Run) AddResponseValue(responsedescriptor string, responsevalue interface{})

func (Run) AllFactors 

func (run Run) AllFactors() (headers []string, values []interface{})

func (Run) AllResponses 

func (run Run) AllResponses() (headers []string, values []interface{})

func (Run) CheckAdditionalInfo 

func (run Run) CheckAdditionalInfo(subheader string, value interface{}) bool

func (Run) EqualTo 

func (run Run) EqualTo(run2 Run) (bool, error)

EqualTo compares Runs but ignores run order, std order and additional information but checks all other properties for identical matches

func (Run) GetAdditionalInfo 

func (run Run) GetAdditionalInfo(subheader string) (value interface{}, err error)

func (Run) GetFactorValue 

func (run Run) GetFactorValue(factordescriptor string) (factorvalue interface{}, err error)

GetFactorValue searches for a factor descriptor in the list of factors in a Run. Exact matches will be searched first, followed by matches once any unit is removed (e.g. TotalVolume (ul) to TotalVolume)

func (Run) GetResponseValue 

func (run Run) GetResponseValue(responsedescriptor string) (responsevalue interface{}, err error)

Source Files

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