wtype

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: 26 Imported by: 55

Documentation

Overview

defines types for dealing with liquid handling requests

defines types for dealing with liquid handling requests

defines types for dealing with liquid handling requests

solutions is a utility package for working with solutions of LHComponents

Package wtype contains core Antha types

Index

Constants

View Source 
const (
	ORF           = "ORF"
	CDS           = "CDS"
	GENE          = "gene"
	MISC_FEATURE  = "misc_feature"
	PROMOTER      = "promoter"
	TRNA          = "tRNA"
	RRNA          = "rRNA"
	NCRNA         = "ncRNA"
	REGULATORY    = "regulatory"
	REPEAT_REGION = "repeat_region"
)

feature class options based on genbank conventions

View Source 
const (
	// Option to feed into coordinates method.
	// HUMANFRIENDLY returns a sequence PositionPair's start and end positions in a human friendly format
	// i.e. in a Sequence "ATGTGTTG" position 1 is A, 2 is T.
	HUMANFRIENDLY = "humanFriendly"

	// Option to feed into coordinates method.
	// CODEFRIENDLY returns a sequence PositionPair's start and end positions in a code friendly format
	// i.e. in a Sequence "ATGTGTTG" position 0 is A, 1 is T.
	CODEFRIENDLY = "codeFriendly"

	// Option to feed into coordinates method.
	// IGNOREDIRECTION is a constant to specify that direction of a feature position
	// should be ignored when returning start and end positions of a feature.
	// If selected, the start position will be the first position at which the feature is encountered regardless of orientation.
	IGNOREDIRECTION = "ignoreDirection"
)
View Source 
const (
	// PolicyNameField returns the map entry of a liquid policy corresponding to the name of the policy.
	PolicyNameField string = "POLICYNAME"

	// PolicyNameField returns the map entry of a liquid policy corresponding to the name of the policy.
	PolicyDescriptionField string = "DESCRIPTION"

	// LiquidClass is the name of the liquid type checked at instruction generation.
	// Currently this is analogous to the POLICYNAME
	LiquidClass string = "LIQUIDCLASS"

	// This value will be used for aspirating, dispensing and mixing.
	DefaultPipetteSpeed string = "DEFAULTPIPETTESPEED"
)
View Source 
const (
	NEITHER = 0
	// Top strand, or coding strand
	TOP = 1
	// Bottom strand, or complimentary strand.
	BOTTOM = 2
)

Options for Strand choice

View Source 
const (
	LH_OK = iota
	LH_ERR_NO_DECK_SPACE
	LH_ERR_NO_TIPS
	LH_ERR_NOT_IMPLEMENTED
	LH_ERR_CONC
	LH_ERR_DRIV
	LH_ERR_POLICY
	LH_ERR_VOL
	LH_ERR_DIRE
	LH_ERR_OTHER
	LH_ERR_TIP_WASTE
)
View Source 
const (
	LHIMIX = iota
	LHIPRM
	LHISPL
)
View Source 
const (
	LHP_AND int = iota
	LHP_OR
)
View Source 
const (
	BYROW    = true
	BYCOLUMN = false
)
View Source 
const DefaultLHPolicy = LTDefault

DefaultLHPolicy which will be used if no policy is set.

View Source 
const (
	FORCE bool = true // Optional parameter to use in AddDNASequence method to override error check preventing addition of a duplicate sequence.
)
View Source 
const InPlaceMarker = "-INPLACE"
View Source 
const SEQSKEY = "DNASequences"
View Source 
const SubComponentsHeader = "SubComponents"

SubComponentsHeader is the header found to be used in the plate CSV files to specify Sub components of liquids.

Variables

View Source 
var (
	TAXLINE = regexp.MustCompile(`^taxid\s+(\d+)`)
	CODLINE = regexp.MustCompile(`^([ACTG]{3,3})\s+([A-Z*])\s+(\d+)\s+([0-9.]+)`)
)
View Source 
var (
	Globals = LHGlobals{
		MIN_REASONABLE_VOLUME_UL: 0.01,
		VOL_RESOLUTION_DIGITS:    2,
	}

	MAGICBARRIERPROMPTSTRING = "___BARRIER___"
)
View Source 
var (
	OnSmartMix  = categoricCondition{"LIQUIDCLASS", "SmartMix"}
	OnPostMix   = categoricCondition{"LIQUIDCLASS", "PostMix"}
	OnPreMix    = categoricCondition{"LIQUIDCLASS", "PreMix"}
	OnNeedToMix = categoricCondition{"LIQUIDCLASS", "NeedToMix"}
	OnMegaMix   = categoricCondition{"LIQUIDCLASS", "MegaMix"}
)

Conditions to apply to LHpolicyRules based on liquid policy used

View Source 
var (
	IntoEmpty                 = numericCondition{Class: "WELLTOVOLUME", Range: conditionRange{Lower: 0.0, Upper: 0.009}}
	IntoLessThan20ul          = numericCondition{Class: "WELLTOVOLUME", Range: conditionRange{Lower: 0.01, Upper: 20.0}}
	IntoBetween20ulAnd50ul    = numericCondition{Class: "WELLTOVOLUME", Range: conditionRange{20.1, 50.0}}
	IntoBetween50ulAnd100ul   = numericCondition{Class: "WELLTOVOLUME", Range: conditionRange{50.1, 100.0}}
	IntoBetween100ulAnd200ul  = numericCondition{Class: "WELLTOVOLUME", Range: conditionRange{100.1, 200.0}}
	IntoBetween200ulAnd1000ul = numericCondition{Class: "WELLTOVOLUME", Range: conditionRange{200.1, 1000.0}}
)

Conditions to apply to LHpolicyRules based on volume of liquid that a sample is being pipetted into at the destination well

View Source 
var (
	LessThan20ul        = numericCondition{Class: "VOLUME", Range: conditionRange{0.0, 20.0}}
	GreaterThan20ul     = numericCondition{Class: "VOLUME", Range: conditionRange{20.1, 1000.0}}
	Between20ulAnd200ul = numericCondition{Class: "VOLUME", Range: conditionRange{20.01, 200.0}}
)

Conditions to apply to LHpolicyRules based on volume of liquid being transferred

View Source 
var (
	FromBetween100ulAnd200ul  = numericCondition{Class: "WELLFROMVOLUME", Range: conditionRange{100.0, 200.0}}
	FromBetween200ulAnd1000ul = numericCondition{Class: "WELLFROMVOLUME", Range: conditionRange{200.1, 1000.0}}
)

Conditions to apply to LHpolicyRules based on volume of liquid in source well from which a sample is taken

View Source 
var (
	UnknownShape   = (*shapeType)(nil)
	CylinderShape  = newShapeType("cylinder", true)
	CircleShape    = newShapeType("circle", true)
	RoundShape     = newShapeType("round", true)
	SphereShape    = newShapeType("sphere", true)
	SquareShape    = newShapeType("square", false)
	BoxShape       = newShapeType("box", false)
	RectangleShape = newShapeType("rectangle", false)
	TrapezoidShape = newShapeType("trapezoid", false)
)
View Source 
var (
	CONSTRAINTMARKER = "constraint-"
)
View Source 
var DefaultPolicies map[string]LHPolicy = MakePolicies()
View Source 
var GLOBALCARRYVOLUME wunit.Volume = wunit.NewVolume(0.5, "ul")
View Source 
var InsNames = []string{"MIX", "PROMPT", "SPLIT"}
View Source 
var NotFoundError = errors.New("not found")
View Source 
var SBSFootprint = Coordinates2D{X: 127.76, Y: 85.48}

SBSFootprint the size of standard SBS format plates

View Source 
var WellBottomNames []string = []string{"flat", "U", "V"}

Functions

func A1ArrayFromWellCoords 

func A1ArrayFromWellCoords(arr []WellCoords) []string

func A1ArrayFromWells 

func A1ArrayFromWells(wells []*LHWell) []string

func AddSubComponent 

func AddSubComponent(component *Liquid, subcomponent *Liquid, conc wunit.Concentration) error

AddSubComponent adds a subcomponent with concentration to a component. An error is returned if subcomponent is already found.

func AddSubComponents 

func AddSubComponents(component *Liquid, allsubComponents ComponentList) error

AddSubComponents adds a component list to a component. If a conflicting sub component concentration is already present then an error will be returned. To overwrite all subcomponents ignoring conficts, use OverWriteSubComponents.

func ChannelWells 

func ChannelWells(prm LHChannelParameter, plt Plate, wellsfrom []string) []string

func ChannelsUsed 

func ChannelsUsed(wf []string) []bool

func ClassOf 

func ClassOf(o interface{}) string

ClassOf

func Comp 

func Comp(s string) string

func CompareStringWellCoordsCol 

func CompareStringWellCoordsCol(sw1, sw2 string) int

func CompareStringWellCoordsRow 

func CompareStringWellCoordsRow(sw1, sw2 string) int

func CompareWellCoordsCol 

func CompareWellCoordsCol(w1, w2 WellCoords) int

func CompareWellCoordsRow 

func CompareWellCoordsRow(w1, w2 WellCoords) int

func CopyRulesFromPolicy 

func CopyRulesFromPolicy(ruleSet *LHPolicyRuleSet, policyToCopyRulesFrom, policyToCopyRulesTo string) (err error)

CopyRulesFromPolicy will copy all instances of rules which mention tthe liquid class policyToCopyRulesFrom into duplicate rules set on policyToCopyRulesTo.

func EqualLists 

func EqualLists(list1, list2 ComponentList) error

EqualLists compares two ComponentLists and returns an error if the lists are not identical.

func EquivalentPolicies 

func EquivalentPolicies(policy1, policy2 LHPolicy) bool

EquivalentPolicies checks for equality of two policies. We're being conservative here. It's possible that at the point at which low level instructions are generated that two policies of different length will be actioned in exactly the same way. Since we cannot guarantee this at this point, we'll say they're not equivalent.

func ErrorDesc 

func ErrorDesc(code int) string

func ErrorName 

func ErrorName(code int) string

func FirstIndexInStrArray 

func FirstIndexInStrArray(s string, a []string) int

func GetUUID 

func GetUUID() string

this package wraps the uuid library appropriately by generating a V4 UUID

func HumanizeWellCoords 

func HumanizeWellCoords(coords []WellCoords) string

HumanizeWellCoords convenience function to make displaying a slice of WellCoords more human readable

func IDOf 

func IDOf(o interface{}) string

IDOf

func IndexOfString 

func IndexOfString(query string, pa *[]string) int

func IndexOfStringArray 

func IndexOfStringArray(s string, a []string) int

func Initialize_Wells 

func Initialize_Wells(plate *Plate)

func InsType 

func InsType(i int) string

func IsNotFound 

func IsNotFound(err error) bool

IsNotFound returns true if the underlying error is NotFoundError

func LHError 

func LHError(code int, detail string) error

func LHErrorCodeFromErr 

func LHErrorCodeFromErr(err error) int

func LHErrorIsInternal 

func LHErrorIsInternal(err error) bool

func LHErrorf 

func LHErrorf(code int, format string, values ...interface{}) error

LHErrorf convenience method for formatting error messages

func MakePolicies 

func MakePolicies() map[string]LHPolicy

func MakeTGraph 

func MakeTGraph(inss []*LHInstruction) (tGraph, error)

func Makeseq 

func Makeseq(dir string, seq BioSequence) string

creates a fasta file containing the sequence

func MarshalDeckObject 

func MarshalDeckObject(object LHObject) ([]byte, error)

MarshalDeckObject marshals any object which can be placed on a deck into valid JSON in a way such that it can be unmarshalled by UnMarshalDeckObject

func MatchString 

func MatchString(s1, s2 string) bool

func NameOf 

func NameOf(o interface{}) string

NameOf

func NewSTip 

func NewSTip(tip *LHTip) *sTip

func NewUUID 

func NewUUID() string

func NormaliseComponentName 

func NormaliseComponentName(component *Liquid) error

NormaliseComponentName will change the name of the component to the normalised form returned by ReturnNormalisedComponentName. If sub components exist the name will be changed to the list of sub components with concentrations. e.g. a solution called LB with a concentration of 10X and components 10g/L Yeast Extract and 5g/L Tryptone will be normalised to 10g/L Yeast Extract + 5g/L Tryptone. An LB solution with concentration 1 X and no components is returned as 1X LB. An LB solution with no concentration and no components is returned as LB.

func NormaliseName 

func NormaliseName(name string) (normalised string)

NormaliseName evaluates whether a string contains a concentration and attempts to normalise the name in a standardised format. e.g. 10ng/ul glucose will be normalised to 10 mg/l glucose or 10mM glucose to 10 mM/l glucose or 10mM/l glucose to 10 mM/l glucose or glucose 10mM/l to 10 mM/l glucose A concatanenated name such as 10g/L glucose + 10g/L yeast extract will be returned with no modifications

func Normalize 

func Normalize(tx []string) []string

TODO -- fill in some normalizations - water + salt = saline might be an eg but unlikely to be useful

func Prefix 

func Prefix(seq string, lengthofprefix int) (prefix string)

func ReturnNormalisedComponentName 

func ReturnNormalisedComponentName(component *Liquid) string

ReturnNormalisedComponentName will return the component name in a normalised form. If sub components exist the name will be changed to the list of sub components with concentrations. e.g. a solution called LB with a concentration of 10X and components 10g/L Yeast Extract and 5g/L Tryptone will be normalised to 10g/L Yeast Extract + 5g/L Tryptone. An LB solution with concentration 1 X and no components is returned as 1X LB. An LB solution with no concentration and no components is returned as LB.

func Rev 

func Rev(s string) string

func RevComp 

func RevComp(s string) string

Reverse Complement

func ShapeTypeFromName 

func ShapeTypeFromName(name string) *shapeType

shapeTypeFromName get a shape type by string name, required for deserialisation returns nil if the name is unknown

func SimulateMix 

func SimulateMix(samples ...*Liquid) (newComponentList ComponentList, mixSteps []ComponentListSample, warning error)

SimulateMix simulates the resulting list of components and concentrations which would be generated by mixing the samples together. This will only add the component name itself to the new component list if the sample has no components this is to prevent potential duplication since if a component has a list of sub components the name is considered to be an alias and the component list the true meaning of what the component is. If any sample concentration of zero is found the component list will be made but an error returned.

func Suffix 

func Suffix(seq string, lengthofsuffix int) (suffix string)

func TipsPerWell 

func TipsPerWell(prm LHChannelParameter, p Plate) (int, int)

func TypeOf 

func TypeOf(o interface{}) string

TypeOf

func UpdateComponentDetails 

func UpdateComponentDetails(productOfMixes *Liquid, mixes ...*Liquid) error

UpdateComponentDetails corrects the sub component list and normalises the name of a component with the details of all sample mixes which are specified to be the source of that component. This must currently be updated manually using this function.

func ValidAA 

func ValidAA(seq string) error

ValidAA checks a sequence given as a string for validity as a ProteinSequence. All standard single letter AminoAcids are valid as well as * indicating stop.

func ValidDNA 

func ValidDNA(seq string) error

ValidDNA checks a sequence given as a string for validity as a DNASequence. Any IUPAC nucleotide is considered valid, not just ACTG.

func ValidRNA 

func ValidRNA(seq string) error

ValidRNA checks a sequence given as a string for validity as an RNASequence. ACGU are valid entries.

func WCArrayCols 

func WCArrayCols(wcA []WellCoords) []int

func WCArrayRows 

func WCArrayRows(wcA []WellCoords) []int

Types

type AParam 

type AParam struct {
	Name string
	Type reflect.Type
	Desc string
}

a typed parameter, with description

func (AParam) TypeName 

func (alhpi AParam) TypeName() string

type AParamSet 

type AParamSet map[string]AParam

func GetLHPolicyOptions 

func GetLHPolicyOptions() AParamSet

func GetPolicyConsequents 

func GetPolicyConsequents() AParamSet

func MakeInstructionParameters 

func MakeInstructionParameters() AParamSet

func MakePolicyItems 

func MakePolicyItems() AParamSet

func (AParamSet) CodeForIt 

func (alhpis AParamSet) CodeForIt() string

func (AParamSet) OrderedList 

func (alhpis AParamSet) OrderedList() []string

func (AParamSet) TypeList 

func (alhpis AParamSet) TypeList() string

type Absorbance 

type Absorbance struct {
	WellLocation WellCoords
	Reading      float64
	Wavelength   float64
	Pathlength   wunit.Length
	Reader       string
	// Annotations is a field to add custom user labels
	Annotations []string
}

func (*Absorbance) BlankCorrect 

func (sample *Absorbance) BlankCorrect(blank Absorbance)

func (*Absorbance) PathlengthCorrect 

func (sample *Absorbance) PathlengthCorrect(pathlength wunit.Length)

func (Absorbance) WavelengthAsInt 

func (a Absorbance) WavelengthAsInt() int

WavelengthAsInt will return the Wavelength field as an int. Whilst it is possible that the wavelength used may be a decimal, Wavelength would typically be expected to be in the form of an integer of the wavelength in nm. In some platereader data sets this is stored as a float so this method is intended to take the safest representation, as a float, and return the more common representation, as an int, for parsers where it is known that the wavelength is stored as an int. This method would therefore not be safe to use for situations where the wavelength may in fact be represented by a decimal.

type AddressIterator 

type AddressIterator interface {
	Next() WellCoords
	Curr() WellCoords
	MoveTo(WellCoords)
	Reset()
	GetAddressable() Addressable
	Valid() bool
}

AddressIterator iterates through the addresses in an Addressable

func NewAddressIterator 

func NewAddressIterator(addr Addressable, order MajorOrder, ver VerticalDirection, hor HorizontalDirection, repeat bool) AddressIterator

NewAddressIterator iterates through the addresses in addr in order order, moving in directions ver and hor when all addresses are returned, resets to the first address if repeat is true, otherwise Valid() returns false

type AddressSliceIterator 

type AddressSliceIterator interface {
	Next() []WellCoords
	Curr() []WellCoords
	MoveTo(WellCoords)
	Reset()
	GetAddressable() Addressable
	Valid() bool
}

AddressSliceIterator iterates through slices of addresses

func NewColumnIterator 

func NewColumnIterator(addr Addressable, ver VerticalDirection, hor HorizontalDirection, repeat bool) AddressSliceIterator

NewColumnIterator get an iterator which iterates through the columns of the addressible, optionally repeating

func NewRowIterator 

func NewRowIterator(addr Addressable, ver VerticalDirection, hor HorizontalDirection, repeat bool) AddressSliceIterator

NewRowIterator get an iterator which iterates through the columns of the addressible, optionally repeating

func NewTickingIterator 

func NewTickingIterator(addr Addressable, order MajorOrder, ver VerticalDirection, hor HorizontalDirection, repeat bool, chunkSize, stepSize, repeatAddresses int) AddressSliceIterator

GetTickingIterator iterates through the addresses in addr in order order, moving in directions ver and hor, returning the output in slices of length chunkSize. In the direction specified by order, steps are of size stepSize (which is assumed to a factor of the number of adresses in that direction), and repeat such that every address is returned. Each address is repeated repeatAddresses times. For example, if addr is of size 4x4, then the iterator returned by 

NewTickingIterator(addr, RowOrder, TopToBottom, LeftToRight, false, 4, 2, 2)

returns 

[[A1,A1,C1,C2],[B1,B1,D1,D1],[A2,A2, ...

type Addressable 

type Addressable interface {
	//AddressExists Do the given coordinates exist in the object?
	AddressExists(WellCoords) bool
	NRows() int
	NCols() int
	//GetChildByAddress Returns the object at the given well coords
	//nil if empty or position doesn't exist
	GetChildByAddress(WellCoords) LHObject
	//CoordsToWellCoords Convert Real world coordinates
	//(relative to the object origin) to WellCoords.
	//The returned WellCoords should be the closest
	//addressable location to the coorinates, and shold only be
	//invalid if the object has no adressable locations (e.g. wells
	//or tips). The second return value gives the offset from the top
	//of the center of the well/tip to the given coordinate
	//(this leaves the caller to ascertain whether any mis-alignment
	//is acceptable)
	CoordsToWellCoords(Coordinates3D) (WellCoords, Coordinates3D)
	//WellCoordsToCoords Get the physical location of an addressable
	//position relative to the object origin.
	//WellCoords should be valid in the object, or the bool will
	//return false and Coordinates are undefined.
	//WellReference is the position within a well.
	//Requesting LiquidReference on a LHTipbox will return false
	WellCoordsToCoords(WellCoords, WellReference) (Coordinates3D, bool)
}

Addressable unifies the interface to objects which have sub-components that can be addressed by WellCoords (e.g. "A1") for example tip-boxes, plates, etc

type AlignedBioSequence 

type AlignedBioSequence struct {
	Query   string
	Subject string
	Score   float64
}

type AlignedSequence 

type AlignedSequence struct {
	Qstrand string
	Sstrand string
	Qstart  int
	Qend    int
	Sstart  int
	Send    int
	Qseq    string
	Sseq    string
	ID      float64
}

struct for holding an aligned sequence

func NewAlignedSequence 

func NewAlignedSequence() AlignedSequence

constructor for an AlignedSequence object, makes an empty structure

func (AlignedSequence) CentreToQuery 

func (aln AlignedSequence) CentreToQuery(q string) (string, string)

CentreToQuery trims aligned (subject) sequences to only those residues/nucleotides aligned to those in the query. This removes inserts (with respect to the query) from aligned sequences. Gaps within the interior of the aligned sequence are already represented by '-' characters, however gaps at the ends of the aligned sequence must be added here as well. The resulting aligned sequences will have the same length as the query.

type AminoAcid 

type AminoAcid string

AminoAcid is a single letter format amino acid in string form. It can be validated as a valid AminoAcid using the SetAminoAcid function.

func SetAminoAcid 

func SetAminoAcid(aa string) (AminoAcid, error)

SetAminoAcid creates an AminoAcid from a string input and returns an error if the string is not a valid amino acid.

type Annotatable 

type Annotatable interface {
	GetData(k string) (AnthaData, error)
	AddData(k string, d AnthaData) error
	ClearData(k string) error
}

type AnthaData 

type AnthaData struct {
	Name string
	Data string
}

type BBox 

type BBox struct {
	Position Coordinates3D
	Size     Coordinates3D
}

BBox is a simple LHObject representing a bounding box, useful for checking if there's stuff in the way

func NewBBox 

func NewBBox(pos, Size Coordinates3D) *BBox

func NewBBox6f 

func NewBBox6f(pos_x, pos_y, pos_z, Size_x, Size_y, Size_z float64) *BBox

func NewXBox4f 

func NewXBox4f(pos_y, pos_z, Size_y, Size_z float64) *BBox

func NewYBox4f 

func NewYBox4f(pos_x, pos_z, Size_x, Size_z float64) *BBox

func NewZBox4f 

func NewZBox4f(pos_x, pos_y, Size_x, Size_y float64) *BBox

func (BBox) Contains 

func (self BBox) Contains(rhs Coordinates3D) bool

func (BBox) ContainsBox 

func (self BBox) ContainsBox(rhs BBox) bool

func (*BBox) Dup 

func (self *BBox) Dup() *BBox

Dup duplicate the bounding box

func (BBox) Equals 

func (bb BBox) Equals(bb2 BBox) bool

Equals defines an equivalence relation over bounding boxes returns true iff position and size are both equal

func (BBox) GetPosition 

func (self BBox) GetPosition() Coordinates3D

func (BBox) GetSize 

func (self BBox) GetSize() Coordinates3D

func (BBox) IntersectsBox 

func (self BBox) IntersectsBox(rhs BBox) bool

IntersectsBox checks for bounding box intersection

func (BBox) IntersectsPoint 

func (self BBox) IntersectsPoint(rhs Coordinates3D) bool

IntersectsPoint

func (*BBox) SetPosition 

func (self *BBox) SetPosition(c Coordinates3D)

func (*BBox) SetSize 

func (self *BBox) SetSize(c Coordinates3D)

func (BBox) String 

func (self BBox) String() string

String gets a string representation of the box

func (BBox) ZMax 

func (self BBox) ZMax() float64

type BLASTSearchParameters 

type BLASTSearchParameters struct {
	Evalthreshold float64
	Matrix        string
	Filter        bool
	Open          int
	Extend        int
	DBSeqs        int
	DBAlns        int
	GCode         int
}

func DefaultBLASTSearchParameters 

func DefaultBLASTSearchParameters() BLASTSearchParameters

type BioSequence 

type BioSequence interface {
	Name() string
	Sequence() string
	Append(string) error
	Prepend(string) error
	Blast() ([]Hit, error)
	MolecularWeight() float64
}

defines things which have biosequences... useful for operations valid on biosequences such as BLASTing / other alignment methods

type BlastHit 

type BlastHit struct {
	Name       string
	Score      float64
	Eval       float64
	Alignments []AlignedSequence
}

struct for holding a particular hit

func NewBlastHit 

func NewBlastHit() BlastHit

constructor, makes an empty BlastHit structure

type BlastResults 

type BlastResults struct {
	Program       string
	DBname        string
	DBSizeSeqs    int
	DBSizeLetters int
	Query         string
	Hits          []BlastHit
}

struct for holding results of a blast search

func NewBlastResults 

func NewBlastResults() BlastResults

constructor, makes an empty BlastResults structure

func (BlastResults) QueryCentredAlignment 

func (res BlastResults) QueryCentredAlignment() []AlignedBioSequence

type BlockID 

type BlockID struct {
	Value string
}

A block of instructions associated with a particular job, etc.

func NewBlockID 

func NewBlockID(id string) BlockID

func (BlockID) String 

func (a BlockID) String() string

type ByColumn 

type ByColumn []*LHInstruction

func (ByColumn) Len 

func (bg ByColumn) Len() int

func (ByColumn) Less 

func (bg ByColumn) Less(i, j int) bool

func (ByColumn) Swap 

func (bg ByColumn) Swap(i, j int)

type ByResultComponent 

type ByResultComponent []*LHInstruction

Optimally - order by component.

func (ByResultComponent) Len 

func (bg ByResultComponent) Len() int

func (ByResultComponent) Less 

func (bg ByResultComponent) Less(i, j int) bool

func (ByResultComponent) Swap 

func (bg ByResultComponent) Swap(i, j int)

type CentrifugeParameters 

type CentrifugeParameters map[string]interface{}

type ChannelOrientation 

type ChannelOrientation bool
const (
	LHVChannel ChannelOrientation = iota%2 == 1 // vertical orientation
	LHHChannel                                  // horizontal orientation
)

func (ChannelOrientation) String 

func (o ChannelOrientation) String() string

type ChannelPositions 

type ChannelPositions []Coordinates2D

A list of 2d coordinates of the channels of an adaptor in channel order

func (ChannelPositions) Add 

func (self ChannelPositions) Add(rhs Coordinates2D) ChannelPositions

Add return a new set of channel positions with the offset added

func (ChannelPositions) GetCenter 

func (self ChannelPositions) GetCenter() Coordinates2D

GetCenter return the center of the channel coordinates

func (ChannelPositions) Size 

func (self ChannelPositions) Size(channelRadius float64) Coordinates2D

Size get the total footprint size of the channel positions including the radius

func (ChannelPositions) Subtract 

func (self ChannelPositions) Subtract(rhs Coordinates2D) ChannelPositions

Subtract return a new set of channel positions with the offset subtracted

type Classy 

type Classy interface {
	GetClass() string
}

the class of thing it is, mainly for more helpful errors

type Codon 

type Codon string

Codon is a triplet of valid nucleotides which encodes an amino acid or stop codon. It can be validated using the SetCodon function.

func SetCodon 

func SetCodon(dna string) (Codon, error)

SetCodon creates a Codon from a string input and returns an error if the string is not a valid codon.

type CodonSet 

type CodonSet map[string]float64

func (CodonSet) ChooseWeighted 

func (cs CodonSet) ChooseWeighted() string

func (CodonSet) Codons 

func (cs CodonSet) Codons() []string

type CodonTable 

type CodonTable struct {
	TaxID     string
	CodonByAA map[string]CodonSet // maps amino acid to set of codons
	AAByCodon map[string]string   // maps codon to amino acid
}

func NewCodonTable 

func NewCodonTable() CodonTable

func ParseCodonTableSimpleFormat 

func ParseCodonTableSimpleFormat(sa []string) CodonTable

these are tables devised by wholesale analysis of CDS sets

func (CodonTable) ChooseWeighted 

func (ct CodonTable) ChooseWeighted(aa string) string

type ComponentList 

type ComponentList struct {
	Components map[string]wunit.Concentration `json:"Components"`
}

List of the components and corresponding concentrations contained within an LHComponent

func GetSubComponents 

func GetSubComponents(component *Liquid) (componentMap ComponentList, err error)

GetSubComponents returns a component list from a component

func MixComponentLists 

func MixComponentLists(sample1, sample2 ComponentListSample) (newList ComponentList, err error)

MixComponentLists merges two componentListSamples. When two ComponentListSamples are mixed a new diluted ComponentList is generated. An error may be generated if two components with the same name exist within the two lists with incompatible concentration units. In this instance, the molecular weight for that component will be looked up in pubchem in order to change the units in both lists to g/l, which will be able to be added.

func (ComponentList) Add 

func (c ComponentList) Add(component *Liquid, conc wunit.Concentration) (newlist ComponentList)

add a single entry to a component list

func (ComponentList) AllComponents 

func (c ComponentList) AllComponents() []string

Returns all component names present in component list, sorted in alphabetical order.

func (ComponentList) Dup 

func (c ComponentList) Dup() ComponentList

func (ComponentList) Get 

func (c ComponentList) Get(component *Liquid) (conc wunit.Concentration, err error)

Get a single concentration set point for a named component present in a component list. An error will be returned if the component is not present.

func (ComponentList) GetByName 

func (c ComponentList) GetByName(component string) (conc wunit.Concentration, err error)

Get a single concentration set point using just the name of a component present in a component list. An error will be returned if the component is not present.

func (ComponentList) List 

func (c ComponentList) List(options ...bool) string

List all Components and concentration set points present in a component list. if verbose is set to true the field annotations for each component and concentration will be included for each component. option1 is verbose, option2 is use mixdelimiter

func (ComponentList) RemoveConcsFromSubComponentNames 

func (c ComponentList) RemoveConcsFromSubComponentNames() (nc ComponentList)

type ComponentListSample 

type ComponentListSample struct {
	ComponentList
	Volume wunit.Volume
}

ComponentListSample is a sample of a Component list at a specified volume when two ComponentListSamples are mixed a new diluted ComponentList is generated

type ComponentMatch 

type ComponentMatch struct {
	Matches []Match
}

type ComponentVector 

type ComponentVector []*Liquid

func (ComponentVector) Dup 

func (cv ComponentVector) Dup() ComponentVector

func (ComponentVector) Equal 

func (cv1 ComponentVector) Equal(cv2 ComponentVector) bool

func (ComponentVector) Filter 

func (cv ComponentVector) Filter(filters ...func(*Liquid) bool) ComponentVector

Filter returns the subset of the liquids in cv for which every filter returns true does not guarantee to call every filter on every liquid

func (ComponentVector) GetNames 

func (cv ComponentVector) GetNames() []string

func (ComponentVector) GetPlateIds 

func (cv ComponentVector) GetPlateIds() []string

func (ComponentVector) GetVols 

func (cv ComponentVector) GetVols() []wunit.Volume

func (ComponentVector) GetWellCoords 

func (cv ComponentVector) GetWellCoords() []string

func (ComponentVector) IsEmpty 

func (cv ComponentVector) IsEmpty() bool

IsEmpty returns true if there is no volume in the component vector

func (ComponentVector) Map 

func (cv ComponentVector) Map(maps ...func(*Liquid) *Liquid) ComponentVector

Map return a new componentvector which is the result calling each function in maps sequentially on each element

func (ComponentVector) String 

func (cv ComponentVector) String() string

func (ComponentVector) SubtractVolume 

func (cv ComponentVector) SubtractVolume(vol wunit.Volume)

func (ComponentVector) Volume 

func (cv ComponentVector) Volume() wunit.Volume

Volume get the total volume of liquid in the component vector

type ConfigItem 

type ConfigItem map[string]interface{}

type Coordinates2D 

type Coordinates2D struct {
	X float64
	Y float64
}

func (Coordinates2D) Abs 

func (self Coordinates2D) Abs() float64

Abs return the L2 norm of the coordinate

func (Coordinates2D) Add 

func (self Coordinates2D) Add(rhs Coordinates2D) Coordinates2D

Add return a new coordinate which is the sum of the two

func (Coordinates2D) Divide 

func (self Coordinates2D) Divide(factor float64) Coordinates2D

Divide return a new coordinate scaled by the reciprocal of factor if factor is zero, inf will be returned

func (Coordinates2D) Equals 

func (self Coordinates2D) Equals(rhs Coordinates2D) bool

Equals return true if the two coordinates are equal

func (Coordinates2D) Multiply 

func (self Coordinates2D) Multiply(factor float64) Coordinates2D

Multiply return a new coordinate scaled by factor

func (Coordinates2D) String 

func (self Coordinates2D) String() string

String string representation of the coordinate

func (Coordinates2D) Subtract 

func (self Coordinates2D) Subtract(rhs Coordinates2D) Coordinates2D

Subtract return a new coordinate which is self minus rhs

type Coordinates3D 

type Coordinates3D struct {
	X float64
	Y float64
	Z float64
}

func OriginOf 

func OriginOf(o LHObject) Coordinates3D

get the origin for the objects coordinate system

func (Coordinates3D) Abs 

func (self Coordinates3D) Abs() float64

Abs L2-Norm

func (Coordinates3D) AbsXY 

func (self Coordinates3D) AbsXY() float64

AbsXY L2-Norm in XY only

func (Coordinates3D) Add 

func (self Coordinates3D) Add(rhs Coordinates3D) Coordinates3D

Add Addition returns a new wtype.Coordinates

func (Coordinates3D) Dim 

func (a Coordinates3D) Dim(x int) float64

Dim Value for dimension

func (Coordinates3D) Divide 

func (self Coordinates3D) Divide(v float64) Coordinates3D

Divide returns a new wtype.Coordinates divided by v. If v is zero, inf will be returned

func (Coordinates3D) Dot 

func (self Coordinates3D) Dot(rhs Coordinates3D) float64

Dot product

func (Coordinates3D) Equals 

func (c Coordinates3D) Equals(c2 Coordinates3D) bool

func (Coordinates3D) Multiply 

func (self Coordinates3D) Multiply(v float64) Coordinates3D

Multiply returns a new wtype.Coordinates

func (Coordinates3D) String 

func (self Coordinates3D) String() string

String implements Stringer

func (Coordinates3D) StringXY 

func (self Coordinates3D) StringXY() string

func (Coordinates3D) Subtract 

func (self Coordinates3D) Subtract(rhs Coordinates3D) Coordinates3D

Subtract returns a new wtype.Coordinates

func (Coordinates3D) To2D 

func (self Coordinates3D) To2D() Coordinates2D

To2D return a two dimensional coordinate by dropping z dimension

func (Coordinates3D) Unit 

func (self Coordinates3D) Unit() Coordinates3D

Unit return a Unit vector in the same direction as the coordinates

type DNA 

type DNA struct {
	Seq DNASequence
}

defines something as physical DNA hence it is physical and has a DNASequence

type DNASeqSet 

type DNASeqSet []*DNASequence

func (DNASeqSet) AsBioSequences 

func (dss DNASeqSet) AsBioSequences() []BioSequence

type DNASequence 

type DNASequence struct {
	Nm             string    `json:"nm"`
	Seq            string    `json:"seq"`
	Plasmid        bool      `json:"plasmid"`
	Singlestranded bool      `json:"single_stranded"`
	Overhang5prime Overhang  `json:"overhang_5_prime"`
	Overhang3prime Overhang  `json:"overhang_3_prime"`
	Methylation    string    `json:"methylation"` // add histones etc?
	Features       []Feature `json:"features"`
}

DNAsequence is a type of Biosequence

func Annotate 

func Annotate(dnaseq DNASequence, features []Feature) (annotated DNASequence)

func MakeDNASequence 

func MakeDNASequence(name string, seqstring string, properties []string) (seq DNASequence, err error)

func MakeLinearDNASequence 

func MakeLinearDNASequence(name string, seqstring string) (seq DNASequence)

func MakePlasmidDNASequence 

func MakePlasmidDNASequence(name string, seqstring string) (seq DNASequence)

func MakeSingleStrandedDNASequence 

func MakeSingleStrandedDNASequence(name string, seqstring string) (seq DNASequence)

func Phosphorylate 

func Phosphorylate(dnaseq DNASequence) (phosphorylateddna DNASequence, err error)

func (*DNASequence) AddBluntEnd 

func (seq *DNASequence) AddBluntEnd(end int) (err error)

AddBluntOverhang adds a blunt overhang to a specified end. Valid options are either 5 (for 5 prime/upstream end) or 3 (for 3 prime/upstream end).

func (*DNASequence) AddOverhang 

func (seq *DNASequence) AddOverhang(end int, sequence string) (err error)

AddOverhang adds an overhang to a specified end. Valid options are either 5 (for 5 prime/upstream end) or 3 (for 3 prime/upstream end).

func (*DNASequence) AddUnderhang 

func (seq *DNASequence) AddUnderhang(end int, sequence string) (err error)

AddUnderhang adds an underhang to a specified end. Valid options are either 5 (for 5 prime/upstream end) or 3 (for 3 prime/upstream end).

func (*DNASequence) Append 

func (dna *DNASequence) Append(s string) error

Append appends the existing dna sequence with the upper case of the string added

func (*DNASequence) Blast 

func (seq *DNASequence) Blast() (hits []Hit, err error)

Blast performs a blast search on the sequence and returns any hits found. An error is returned if a problem interacting with the blast server occurs.

func (DNASequence) Dup 

func (seq DNASequence) Dup() DNASequence

func (DNASequence) FeatureNames 

func (annotated DNASequence) FeatureNames() (featurenames []string)

FeatureNames returns a list of all feature names in the sequence

func (DNASequence) GetFeatureByName 

func (annotated DNASequence) GetFeatureByName(featureName string) (returnedFeatures []Feature)

GetFeatureByName returns all features found which match the specified feature name. Searches are not case sensitive.

func (*DNASequence) MolecularWeight 

func (seq *DNASequence) MolecularWeight() float64

MolecularWeight calculates the molecular weight of the specified DNA sequence. For accuracy it is important to specify if the DNA is single stranded or doublestranded along with phosphorylation.

func (*DNASequence) Name 

func (dna *DNASequence) Name() string

Name returns the name of the DNASequence

func (*DNASequence) Prepend 

func (dna *DNASequence) Prepend(s string) error

Preprend adds the requested sequence to the beginning of the existing sequence.

func (*DNASequence) RevComp 

func (dna *DNASequence) RevComp() string

RevComp returns the reverse complement of the DNASequence.

func (*DNASequence) Sequence 

func (dna *DNASequence) Sequence() string

Sequence returns the sequence of the DNA Sequence

func (*DNASequence) Set3PrimeEnd 

func (seq *DNASequence) Set3PrimeEnd(overhang Overhang) (err error)

Set3PrimeEnd adds a 3 prime overhang to a sequence. Validation is performed on the compatibility of the overhang with the sequence.

func (*DNASequence) Set5PrimeEnd 

func (seq *DNASequence) Set5PrimeEnd(overhang Overhang) (err error)

Set5PrimeEnd adds a 5 prime overhang to a sequence. Validation is performed on the compatibility of the overhang with the sequence.

func (*DNASequence) SetName 

func (dna *DNASequence) SetName(name string)

SetName sets the names of the dna sequence

func (*DNASequence) SetSequence 

func (dna *DNASequence) SetSequence(seq string) error

SetSequence checks the validity of sequence given as an argument and if all characters are present in ValidNucleotides If invalid characters are found an error returned listing all invalid characters and their positions in human friendly form. i.e. the first position is 1 and not 0.

type ElectroshockParameters 

type ElectroshockParameters map[string]interface{}

type Entity 

type Entity interface {
	IsEntity() bool
}

type Enzyme 

type Enzyme struct {
	Properties map[string]wunit.Measurement
	Nm         string
}

structure which defines an enzyme -- solutions containing enzymes need careful handling as they can be quite delicate

func (Enzyme) Name 

func (enzyme Enzyme) Name() string

type Feature 

type Feature struct {
	Name          string `json:"name"`
	Class         string `json:"class	"` //  defined by constants above
	Reverse       bool   `json:"reverse"`
	StartPosition int    `json:"start_position"` // in human friendly format
	EndPosition   int    `json:"end_position"`   // in human friendly format
	DNASeq        string `json:"dna_seq"`
	Protseq       string `json:"prot_seq"`
}

Feature describes a feature within a sequence, it's position in the sequence, in human friendly format, a protein sequence if applicablae and a class. Use the MakeFeature and AddFeature functions from the sequences packages. valid class fields are: 

ORF = "ORF"
CDS = "CDS"
GENE = "gene"
MISC_FEATURE = "misc_feature"
PROMOTER = "promoter"
TRNA = "tRNA"
RRNA = "rRNA"
NCRNA = "ncRNA"
REGULATORY = "regulatory"
REPEAT_REGION = "repeat_region"

func (*Feature) Coordinates 

func (feat *Feature) Coordinates(options ...string) (start, end int)

Coordinates returns the start and end positions of the feature by default this will return the start position followed by the end position in human friendly format Available options are: HUMANFRIENDLY returns a sequence PositionPair's start and end positions in a human friendly format i.e. in a Sequence "ATGTGTTG" position 1 is A, 2 is T. CODEFRIENDLY returns a sequence PositionPair's start and end positions in a code friendly format i.e. in a Sequence "ATGTGTTG" position 0 is A, 1 is T. IGNOREDIRECTION is a constant to specify that direction of a feature position should be ignored when returning start and end positions of a feature. If selected, the start position will be the first position at which the feature is encountered regardless of orientation.

func (Feature) DNASequence 

func (f Feature) DNASequence() DNASequence

DNASequence returns the linear DNA sequence of the feature.

func (*Feature) End 

func (f *Feature) End(options ...string) int

End returns the end position of the Feature by default this will return a directional human friendly position

func (*Feature) Start 

func (f *Feature) Start(options ...string) int

Start returns the start position of the Feature by default this will return a directional human friendly position

type File 

type File struct {
	Name string
	// contains filtered or unexported fields
}

Representation of a file.

func AutoExportPlateCSV 

func AutoExportPlateCSV(outputFileName string, plate *Plate) (file File, err error)

AutoExportPlateCSV exports an LHPlate and its contents as a csv file. This is not 100% safe to use in elements since, currently, at the time of running an element, the scheduler will not have allocated positions for the components so, for example, accurate well information cannot currently be obtained with this function. If allocating wells manually use the ExportPlateCSV function and explicitely set the sample locations and volumes.

func ExportPlateCSV 

func ExportPlateCSV(outputFileName string, plate *Plate, plateName string, wells []string, liquids []*Liquid, volumes []wunit.Volume) (file File, err error)

ExportPlateCSV a exports an LHPlate and its contents as a csv file. The caller is required to set the well locations and volumes explicitely with this function.

func (File) MarshalJSON 

func (a File) MarshalJSON() ([]byte, error)

func (*File) ReadAll 

func (a *File) ReadAll() ([]byte, error)

ReadAll returns contents of file.

func (*File) UnmarshalBlob 

func (a *File) UnmarshalBlob(blob *api.Blob) error

func (*File) UnmarshalJSON 

func (a *File) UnmarshalJSON(data []byte) error

func (*File) WriteAll 

func (a *File) WriteAll(data []byte) error

WriteAll replaces contents of file with data.

type FileSeries 

type FileSeries struct {
	Files []File
}

FileSeries is a datatype representing a set of files for data processing usecases: - the files are related to the same entity (likely to the same device); - the files implicitly form a single dataset - i.e. they likely have the same data schema; A parameter of type FileSeries signals to the UI that it should be set using a special query dialog (rather than manually filling the list of files).

type FromFactory 

type FromFactory struct {
	String string
}

func (*FromFactory) MarshalJSON 

func (f *FromFactory) MarshalJSON() ([]byte, error)

func (*FromFactory) UnmarshalJSON 

func (f *FromFactory) UnmarshalJSON(b []byte) error

type Haswelladdress 

type Haswelladdress interface {
	PlateID() string
	WellCoords() WellCoords
}

type HorizontalDirection 

type HorizontalDirection int
const (
	LeftToRight HorizontalDirection = 1
	RightToLeft HorizontalDirection = -1
)

func (HorizontalDirection) String 

func (s HorizontalDirection) String() string

type IChain 

type IChain struct {
	Parent *IChain
	Child  *IChain
	Values []*LHInstruction
	Depth  int
}

func MakeNewIChain 

func MakeNewIChain(vals ...[]*LHInstruction) *IChain

MakeNewIChain return a chain containing one node for each argument, linked in sequence skip any empty sets

func NewIChain 

func NewIChain(parent *IChain) *IChain

func (*IChain) AsList 

func (it *IChain) AsList(ica []*IChain) []*IChain

func (*IChain) AssertInstructionsSeparate 

func (self *IChain) AssertInstructionsSeparate() error

AssertInstructionsSeparate check that there's only one type of instruction in each link of the chain

func (*IChain) FindEnd 

func (it *IChain) FindEnd() *IChain

func (*IChain) FlattenInstructionIDs 

func (it *IChain) FlattenInstructionIDs() []string

FlattenInstructionIDs returns a slice containing the IDs of each instruction in the chain in order

func (*IChain) GetOrderedLHInstructions 

func (it *IChain) GetOrderedLHInstructions() []*LHInstruction

GetOrderedLHInstructions get the instructions in order

func (*IChain) Height 

func (it *IChain) Height() int

depth from here

func (*IChain) Print 

func (it *IChain) Print()

func (*IChain) PruneOut 

func (it *IChain) PruneOut(Remove map[string]bool) *IChain

func (*IChain) Reverse 

func (it *IChain) Reverse()

func (*IChain) SortInstructions 

func (ic *IChain) SortInstructions(byComponent bool)

SortInstructions sort the instructions within each link of the chain

func (*IChain) SplitMixedNodes 

func (it *IChain) SplitMixedNodes() *IChain

func (*IChain) SwapForChain 

func (ch *IChain) SwapForChain(newch *IChain) *IChain

SwapForChain replace node ch with the node chain starting with newch 

if ch is the head of the chain, return newch as the new head
otherwise return nil

func (*IChain) ValueIDs 

func (it *IChain) ValueIDs() []string

type Identifiable 

type Identifiable interface {
	GetID() string
}

type Kind 

type Kind uint8
const (
	Float64 Kind = iota
	Int
	String
	Volume
	Bool
)

type LHAdaptor 

type LHAdaptor struct {
	Name         string
	ID           string
	Manufacturer string
	Params       *LHChannelParameter
	Tips         []*LHTip
}

adaptor

func NewLHAdaptor 

func NewLHAdaptor(name, mf string, params *LHChannelParameter) *LHAdaptor

NewLHAdaptor make a new adaptor

func (*LHAdaptor) AdaptorType 

func (lha *LHAdaptor) AdaptorType() string

AdaptorType the manufacturer and name of the adaptor

func (*LHAdaptor) AddTip 

func (lha *LHAdaptor) AddTip(channelNumber int, tip *LHTip)

AddTip Load a tip to the specified channel, overwriting any tip already present

func (*LHAdaptor) Dup 

func (lha *LHAdaptor) Dup() *LHAdaptor

Dup duplicate the adaptor and any loaded tips with new IDs

func (*LHAdaptor) DupKeepIDs 

func (lha *LHAdaptor) DupKeepIDs() *LHAdaptor

DupKeepIDs duplicate the adaptor and any loaded tips keeping the same IDs

func (*LHAdaptor) GetLargestChannelSpacing 

func (self *LHAdaptor) GetLargestChannelSpacing() Coordinates2D

GetLargestChannelSpacing get the largest possible distance between successive channels

func (*LHAdaptor) GetMostCompactChannelPositions 

func (self *LHAdaptor) GetMostCompactChannelPositions() ChannelPositions

GetMostCompactChannelPositions get the relative channel positions for the adaptor in the most tightly bunched layout supported

func (*LHAdaptor) GetParams 

func (lha *LHAdaptor) GetParams() *LHChannelParameter

GetParams get the channel parameters for the adaptor, combined with any loaded tips

func (*LHAdaptor) GetSmallestChannelSpacing 

func (self *LHAdaptor) GetSmallestChannelSpacing() Coordinates2D

GetSmallestChannelSpacing get the smallest possible distance between successive channels

func (*LHAdaptor) GetTip 

func (lha *LHAdaptor) GetTip(channelNumber int) *LHTip

GetTip Return the tip at channelNumber, nil otherwise

func (*LHAdaptor) GetWellTargets 

func (self *LHAdaptor) GetWellTargets(well *LHWell) []Coordinates2D

GetWellTargets get the offset from the center of the well for each channel that can access the well simultaneously returns nil if the well cannot fit multiple channels

func (*LHAdaptor) IsTipLoaded 

func (lha *LHAdaptor) IsTipLoaded(channelNumber int) bool

IsTipLoaded Is there a tip loaded on channelNumber

func (*LHAdaptor) NumTipsLoaded 

func (lha *LHAdaptor) NumTipsLoaded() int

NumTipsLoaded the number of tips currently loaded

func (*LHAdaptor) RemoveTip 

func (lha *LHAdaptor) RemoveTip(channelNumber int) *LHTip

RemoveTip Remove a tip from the specified channel and return it

func (*LHAdaptor) RemoveTips 

func (lha *LHAdaptor) RemoveTips() []*LHTip

RemoveTips Return all previously loaded tips, with nils removed

type LHCategoryCondition 

type LHCategoryCondition struct {
	Category string
}

func (LHCategoryCondition) IsEqualTo 

func (lhcc LHCategoryCondition) IsEqualTo(other LHCondition) bool

func (LHCategoryCondition) Match 

func (lhcc LHCategoryCondition) Match(v interface{}) bool

func (LHCategoryCondition) Type 

func (lhcc LHCategoryCondition) Type() string

type LHChannelParameter 

type LHChannelParameter struct {
	ID          string
	Platform    string
	Name        string
	Minvol      wunit.Volume
	Maxvol      wunit.Volume
	Minspd      wunit.FlowRate
	Maxspd      wunit.FlowRate
	Multi       int
	Independent bool
	Orientation ChannelOrientation
	Head        int
}

describes sets of parameters which can be used to create a configuration

func NewLHChannelParameter 

func NewLHChannelParameter(name, platform string, minvol, maxvol wunit.Volume, minspd, maxspd wunit.FlowRate, multi int, independent bool, orientation ChannelOrientation, head int) *LHChannelParameter

func (LHChannelParameter) CanMove 

func (lhcp LHChannelParameter) CanMove(v wunit.Volume, oneshot bool) bool

can you move this much? If oneshot is true it's strictly Minvol <= v <= Maxvol otherwise it's just Minvol <= v

func (*LHChannelParameter) Dup 

func (lhcp *LHChannelParameter) Dup() *LHChannelParameter

func (*LHChannelParameter) DupKeepIDs 

func (lhcp *LHChannelParameter) DupKeepIDs() *LHChannelParameter

func (*LHChannelParameter) Equals 

func (lhcprm *LHChannelParameter) Equals(prm2 *LHChannelParameter) bool

func (LHChannelParameter) GetConstraint 

func (lhcp LHChannelParameter) GetConstraint(n int) LHMultiChannelConstraint

given the dimension of the plate, what is the constraint on multichannel access?

func (*LHChannelParameter) MergeWithTip 

func (lhcp *LHChannelParameter) MergeWithTip(tip *LHTip) *LHChannelParameter

func (LHChannelParameter) String 

func (lhcp LHChannelParameter) String() string

func (LHChannelParameter) VolumeLimitString 

func (lhcp LHChannelParameter) VolumeLimitString() string

type LHComponent 

type LHComponent = Liquid

LHComponent is an alias for Liquid to preserve backwards compatibility Liquid describes a liquid component and its desired properties

type LHCondition 

type LHCondition interface {
	Match(interface{}) bool
	Type() string
	IsEqualTo(LHCondition) bool
}

type LHContainer 

type LHContainer interface {
	Contents() *Liquid
	CurrentVolume() wunit.Volume
	ResidualVolume() wunit.Volume
	//WorkingVolume = CurrentVolume - ResidualVolume
	CurrentWorkingVolume() wunit.Volume
	//Add to the container
	AddComponent(*Liquid) error
	//Set the contents of the container
	SetContents(*Liquid) error
	//Remove from the container
	RemoveVolume(wunit.Volume) (*Liquid, error)
}

LHContainer a tip or a well or something that holds liquids

type LHDeck 

type LHDeck struct {
	// contains filtered or unexported fields
}

LHDeck Represents a robot deck

func NewLHDeck 

func NewLHDeck(name, mfg, decktype string) *LHDeck

NewLHDeck make a new deck

func (*LHDeck) Accepts 

func (self *LHDeck) Accepts(name string, child LHObject) bool

func (*LHDeck) AddSlot 

func (self *LHDeck) AddSlot(name string, position Coordinates3D, size Coordinates2D)

func (*LHDeck) Clear 

func (self *LHDeck) Clear(name string) error

func (*LHDeck) ClearParent 

func (self *LHDeck) ClearParent()

@implement LHObject

func (*LHDeck) DimensionsString 

func (self *LHDeck) DimensionsString() string

DimensionsString returns a string description of the position and size of the object and its children.

func (*LHDeck) Duplicate 

func (self *LHDeck) Duplicate(keepIDs bool) LHObject

Duplicate copy the LHObject, optionally keeping IDs unchanged

func (*LHDeck) GetBoxIntersections 

func (self *LHDeck) GetBoxIntersections(box BBox) []LHObject

func (*LHDeck) GetChild 

func (self *LHDeck) GetChild(name string) (LHObject, bool)

@implements LHParent

func (*LHDeck) GetChildBelow 

func (self *LHDeck) GetChildBelow(point Coordinates3D) LHObject

Return the nearest object below the point, nil if none. The base of the object is used as reference, so e.g. a point within a well will return the plate

func (*LHDeck) GetClass 

func (self *LHDeck) GetClass() string

func (*LHDeck) GetID 

func (self *LHDeck) GetID() string

func (*LHDeck) GetManufacturer 

func (self *LHDeck) GetManufacturer() string

func (*LHDeck) GetName 

func (self *LHDeck) GetName() string

func (*LHDeck) GetParent 

func (self *LHDeck) GetParent() LHObject

func (*LHDeck) GetPointIntersections 

func (self *LHDeck) GetPointIntersections(point Coordinates3D) []LHObject

func (*LHDeck) GetPosition 

func (self *LHDeck) GetPosition() Coordinates3D

func (*LHDeck) GetSize 

func (self *LHDeck) GetSize() Coordinates3D

zero size

func (*LHDeck) GetSlotContaining 

func (self *LHDeck) GetSlotContaining(obj LHObject) string

func (*LHDeck) GetSlotNames 

func (self *LHDeck) GetSlotNames() []string

func (*LHDeck) GetSlotNamesBelow 

func (self *LHDeck) GetSlotNamesBelow(point Coordinates3D) []string

func (*LHDeck) GetSlotPosition 

func (self *LHDeck) GetSlotPosition(name string) Coordinates3D

func (*LHDeck) GetSlotSize 

func (self *LHDeck) GetSlotSize(name string) Coordinates2D

func (*LHDeck) GetType 

func (self *LHDeck) GetType() string

func (*LHDeck) GetVChildren 

func (self *LHDeck) GetVChildren(point Coordinates3D) []LHObject

get all objects above and below the point

func (*LHDeck) SetChild 

func (self *LHDeck) SetChild(name string, child LHObject) error

func (*LHDeck) SetOffset 

func (self *LHDeck) SetOffset(o Coordinates3D) error

func (*LHDeck) SetParent 

func (self *LHDeck) SetParent(o LHObject) error

func (*LHDeck) SetSlotAccepts 

func (self *LHDeck) SetSlotAccepts(name string, class string)

type LHDevice 

type LHDevice struct {
	ID   string
	Name string
	Mnfr string
}

func NewLHDevice 

func NewLHDevice(name, mfr string) *LHDevice

func (*LHDevice) Dup 

func (lhd *LHDevice) Dup() *LHDevice

type LHGlobals 

type LHGlobals struct {
	MIN_REASONABLE_VOLUME_UL float64
	VOL_RESOLUTION_DIGITS    int
}

type LHHead 

type LHHead struct {
	Name         string
	Manufacturer string
	ID           string
	Adaptor      *LHAdaptor
	Params       *LHChannelParameter
	TipLoading   TipLoadingBehaviour // defines the way in which tips are loaded into the head
}

head

func NewLHHead 

func NewLHHead(name, mf string, params *LHChannelParameter) *LHHead

NewLHHead constructor for liquid handling heads

func (*LHHead) CanReach 

func (head *LHHead) CanReach(plate *LHPlate, addresses WellCoordSlice) bool

CanReach return true if the head can service the given addresses in the given object simultaneously. addresses is a slice of well addresses which should be serviced by successive channels of the head, eg. ["A1", "B1", "", "D1",] means channels 0, 1, and 3 should address wells A1, B1, and D1 respectively and channels 2 and 4-7 should not be used. Repeated addresses (e.g. ["A1", "A1", "A1"]) imply multiple tips per well, with exact positioning for each tip calculated with LHHead.GetWellTargets(). Addresses are not reordered, and so ["A1", "B1"] != ["B1", "A1"].

func (*LHHead) Dup 

func (head *LHHead) Dup() *LHHead

Dup duplicate the head and adaptor, changing the IDs

func (*LHHead) DupKeepIDs 

func (head *LHHead) DupKeepIDs() *LHHead

DupKeepIDs duplicate the head and adaptor, keeping the IDs the same

func (*LHHead) GetParams 

func (lhh *LHHead) GetParams() *LHChannelParameter

GetParams get the channel parameters of the head or the adaptor if one is loaded

type LHHeadAssembly 

type LHHeadAssembly struct {
	Positions      []*LHHeadAssemblyPosition
	MotionLimits   *BBox          //the limits on range of motion of the head assembly, nil if unspecified
	VelocityLimits *VelocityRange // the range of valid velocities for the head, nil if unspecified
}

LHHeadAssembly represent a set of LHHeads which are constrained to move together

func NewLHHeadAssembly 

func NewLHHeadAssembly(MotionLimits *BBox) *LHHeadAssembly

NewLHHeadAssembly build a new head assembly

func (*LHHeadAssembly) AddPosition 

func (self *LHHeadAssembly) AddPosition(Offset Coordinates3D)

AddPosition add a position to the head assembly with the given offset

func (*LHHeadAssembly) CountHeadsLoaded 

func (self *LHHeadAssembly) CountHeadsLoaded() int

GetNumHeadsLoaded get the number of heads that are loaded into the assembly

func (*LHHeadAssembly) CountPositions 

func (self *LHHeadAssembly) CountPositions() int

GetNumPositions get the number of positions added to the head assembly

func (*LHHeadAssembly) DupWithoutHeads 

func (self *LHHeadAssembly) DupWithoutHeads() *LHHeadAssembly

DupWithoutHeads copy the headassembly leaving all positions in the new assembly unloaded

func (*LHHeadAssembly) GetLoadedHeads 

func (self *LHHeadAssembly) GetLoadedHeads() []*LHHead

GetLoadedHeads get an ordered slice of all the heads that have been loaded into the assembly

func (*LHHeadAssembly) LoadHead 

func (self *LHHeadAssembly) LoadHead(head *LHHead) error

LoadHead load a head into the next available position in the assembly, returns error if no positions are available

func (*LHHeadAssembly) UnloadAllHeads 

func (self *LHHeadAssembly) UnloadAllHeads()

UnloadAllHeads unload all heads from the assembly

func (*LHHeadAssembly) UnloadHead 

func (self *LHHeadAssembly) UnloadHead(head *LHHead) error

UnloadHead unload a head from the assembly, return an error if the head is not loaded

type LHHeadAssemblyPosition 

type LHHeadAssemblyPosition struct {
	Offset Coordinates3D
	Head   *LHHead
}

LHHeadAssemblyPosition a position within a head assembly

type LHInstruction 

type LHInstruction struct {
	ID               string
	BlockID          BlockID
	Inputs           []*Liquid
	Outputs          []*Liquid
	ContainerType    string
	Welladdress      string
	PlateID          string
	Platetype        string
	Vol              float64
	Type             int
	Conc             float64
	Tvol             float64
	Majorlayoutgroup int

	PlateName string
	OutPlate  *Plate
	Message   string
	WaitTime  time.Duration
	// contains filtered or unexported fields
}

high-level instruction to a liquid handler

func NewLHMixInstruction 

func NewLHMixInstruction() *LHInstruction

func NewLHPromptInstruction 

func NewLHPromptInstruction() *LHInstruction

func NewLHSplitInstruction 

func NewLHSplitInstruction() *LHInstruction

func (*LHInstruction) AddInput 

func (inst *LHInstruction) AddInput(cmp *Liquid)

func (*LHInstruction) AddOutput 

func (inst *LHInstruction) AddOutput(cmp *Liquid)

func (*LHInstruction) AdjustVolumesBy 

func (ins *LHInstruction) AdjustVolumesBy(r float64)

func (*LHInstruction) ComponentsMoving 

func (ins *LHInstruction) ComponentsMoving() []*Liquid

func (*LHInstruction) DupLiquids 

func (ins *LHInstruction) DupLiquids()

func (*LHInstruction) Generation 

func (ins *LHInstruction) Generation() int

func (*LHInstruction) GetID 

func (inst *LHInstruction) GetID() string

GetID returns the ID of the instruction, useful for interfaces

func (*LHInstruction) HasAnyParent 

func (ins *LHInstruction) HasAnyParent() bool

func (*LHInstruction) HasParent 

func (ins *LHInstruction) HasParent(id string) bool

func (*LHInstruction) InputVolumeMap 

func (ins *LHInstruction) InputVolumeMap(addition wunit.Volume) map[string]wunit.Volume

func (*LHInstruction) InsType 

func (inst *LHInstruction) InsType() string

func (*LHInstruction) IsDummy 

func (ins *LHInstruction) IsDummy() bool

IsDummy return true if the instruction has no effect

func (*LHInstruction) IsMixInPlace 

func (ins *LHInstruction) IsMixInPlace() bool

func (*LHInstruction) NamesOfComponentsMoving 

func (ins *LHInstruction) NamesOfComponentsMoving() string

func (*LHInstruction) ParentString 

func (ins *LHInstruction) ParentString() string

func (*LHInstruction) SetGeneration 

func (ins *LHInstruction) SetGeneration(i int)

func (*LHInstruction) SetPlateID 

func (ins *LHInstruction) SetPlateID(pid string)

func (LHInstruction) String 

func (ins LHInstruction) String() string

func (*LHInstruction) Summarize 

func (ins *LHInstruction) Summarize(indent int) string

Summarize get a string summary of the instruction for end users

func (*LHInstruction) Wellcoords 

func (ins *LHInstruction) Wellcoords() WellCoords

type LHInstructions 

type LHInstructions map[string]*LHInstruction

func (LHInstructions) AssertDestinationsSet 

func (insts LHInstructions) AssertDestinationsSet() error

AssertDestinationsSet make certain that a destination has been set for each instruction, returning a descriptive error if not

func (LHInstructions) AssertMixResultsCorrect 

func (insts LHInstructions) AssertMixResultsCorrect() error

assertMixResultsCorrect checks that volumes of the mix result matches either the sum of the input, or the total volume if specified

func (LHInstructions) AssertNoPointerReuse 

func (insts LHInstructions) AssertNoPointerReuse() error

AssertNoPointerReuse make certain that inputs and outputs are not shared among LHInstructions as should be ensured by calling DupLiquids()

func (LHInstructions) AssertTotalVolumesMatch 

func (insts LHInstructions) AssertTotalVolumesMatch() error

assertTotalVolumesMatch checks that component total volumes are all the same in mix instructions

func (LHInstructions) AssertVolumesNonNegative 

func (insts LHInstructions) AssertVolumesNonNegative() error

assertVolumesNonNegative tests that the volumes within the LHRequest are zero or positive

func (LHInstructions) DupLiquids 

func (insts LHInstructions) DupLiquids()

DupLiquids duplicate the input and output liquids for each LHInstruction, thereby making certain that there can be no pointer-reuse between the instructions

type LHMultiChannelConstraint 

type LHMultiChannelConstraint struct {
	X int
	Y int
	M int
}

what constraints apply to adjacent channels

func (LHMultiChannelConstraint) Equals 

func (lhmcc LHMultiChannelConstraint) Equals(lhmcc2 LHMultiChannelConstraint) bool

func (LHMultiChannelConstraint) Satisfied 

func (lhmcc LHMultiChannelConstraint) Satisfied(wc1, wc2 WellCoords) bool

func (LHMultiChannelConstraint) SatisfiedV 

func (lhmcc LHMultiChannelConstraint) SatisfiedV(awc1, awc2 []WellCoords) bool

type LHNumericCondition 

type LHNumericCondition struct {
	Upper float64
	Lower float64
}

func (LHNumericCondition) IsEqualTo 

func (lhnc LHNumericCondition) IsEqualTo(other LHCondition) bool

func (LHNumericCondition) Match 

func (lhnc LHNumericCondition) Match(v interface{}) bool

func (LHNumericCondition) Type 

func (lhnc LHNumericCondition) Type() string

type LHObject 

type LHObject interface {
	//GetPosition get the absolute position of the object (mm)
	GetPosition() Coordinates3D
	//GetSize get the size of the object (mm)
	GetSize() Coordinates3D
	//GetBoxIntersections get a list of LHObjects (can be this object or children) which intersect with the BBox
	GetBoxIntersections(BBox) []LHObject
	//GetPointIntersections get a list of LHObjects (can be this object or children) which intersect with the given point
	GetPointIntersections(Coordinates3D) []LHObject
	//SetOffset set the offset of the object relative to its parent (global if parent is nil)
	SetOffset(Coordinates3D) error
	//SetParent Store the offset of the object
	SetParent(LHObject) error
	//ClearParent Clear the parent of the object
	ClearParent()
	//GetParent
	GetParent() LHObject
	//GetID
	GetID() string
	//Dup duplicate the object, optionally keeping the IDs identical
	Duplicate(bool) LHObject
	//DimensionsString returns a string description of the position and size of the object and its children.
	//useful for debugging
	DimensionsString() string
}

LHObject Provides a unified interface to physical size and location of objects that exist within a liquid handler

func GetObjectRoot 

func GetObjectRoot(o LHObject) LHObject

GetObjectRoot get the highest parent

func UnmarshalDeckObject 

func UnmarshalDeckObject(data []byte) (LHObject, error)

UnmarshalDeckObject unmarshal an on-deck object serialised with MarshalDeckObject retaining the correct underlying type

type LHParent 

type LHParent interface {
	//GetChild get the child in the specified slot, nil if none. bool is false if the slot doesn't exists
	GetChild(string) (LHObject, bool)
	//GetSlotNames get a list of the slots
	GetSlotNames() []string
	//SetChild put the object in the slot
	SetChild(string, LHObject) error
	//Accepts test if slot can accept a certain class
	Accepts(string, LHObject) bool
	//GetSlotSize
	GetSlotSize(string) Coordinates2D
}

LHParent An LHObject that can hold other LHObjects

type LHPlate 

type LHPlate = Plate

LHPlate is an alias for Plate to preserve backwards compatibility. Plate is the principle type for Liquid handling Plates in Antha. The structure describing a microplate.

type LHPolicy 

type LHPolicy map[string]interface{}

LHPolicy defines parameters for a liquid handling policy. Valid key and value pairs are found aparam.go

func AdjustPostMixVolume 

func AdjustPostMixVolume(mixToVol wunit.Volume) LHPolicy

func AdjustPreMixVolume 

func AdjustPreMixVolume(mixToVol wunit.Volume) LHPolicy

func DupLHPolicy 

func DupLHPolicy(in LHPolicy) LHPolicy

func GetPolicyByName 

func GetPolicyByName(policyname PolicyName) (lhpolicy LHPolicy, err error)

func GetPolicyByType 

func GetPolicyByType(liquidType LiquidType) (lhpolicy LHPolicy, err error)

GetPolicyByType will return the default LHPolicy corresponding to a LiquidType. An error is returned if an invalid liquidType is specified.

func MakeCarbonSourcePolicy 

func MakeCarbonSourcePolicy() LHPolicy

func MakeColonyMixPolicy 

func MakeColonyMixPolicy() LHPolicy

func MakeColonyPolicy 

func MakeColonyPolicy() LHPolicy

func MakeCulturePolicy 

func MakeCulturePolicy() LHPolicy

func MakeCultureReusePolicy 

func MakeCultureReusePolicy() LHPolicy

func MakeDNACELLSMixMultiPolicy 

func MakeDNACELLSMixMultiPolicy() LHPolicy

func MakeDNACELLSMixPolicy 

func MakeDNACELLSMixPolicy() LHPolicy

func MakeDNAMixMultiPolicy 

func MakeDNAMixMultiPolicy() LHPolicy

func MakeDNAMixPolicy 

func MakeDNAMixPolicy() LHPolicy

func MakeDNAPolicy 

func MakeDNAPolicy() LHPolicy

func MakeDefaultPolicy 

func MakeDefaultPolicy() LHPolicy

func MakeDetergentPolicy 

func MakeDetergentPolicy() LHPolicy

func MakeDispenseAboveLiquidMultiPolicy 

func MakeDispenseAboveLiquidMultiPolicy() LHPolicy

func MakeDispenseAboveLiquidPolicy 

func MakeDispenseAboveLiquidPolicy() LHPolicy

func MakeGlycerolPolicy 

func MakeGlycerolPolicy() LHPolicy

func MakeHVFlowRatePolicy 

func MakeHVFlowRatePolicy() LHPolicy

func MakeHVOffsetPolicy 

func MakeHVOffsetPolicy() LHPolicy

func MakeJBPolicy 

func MakeJBPolicy() LHPolicy

func MakeLVDNAMixPolicy 

func MakeLVDNAMixPolicy() LHPolicy

func MakeLVExtraPolicy 

func MakeLVExtraPolicy() LHPolicy

func MakeLoadPolicy 

func MakeLoadPolicy() LHPolicy

func MakeLoadWaterPolicy 

func MakeLoadWaterPolicy() LHPolicy

func MakeMultiWaterPolicy 

func MakeMultiWaterPolicy() LHPolicy

func MakeNeedToMixPolicy 

func MakeNeedToMixPolicy() LHPolicy

func MakeNitrogenSourcePolicy 

func MakeNitrogenSourcePolicy() LHPolicy

func MakePEGPolicy 

func MakePEGPolicy() LHPolicy

func MakePaintPolicy 

func MakePaintPolicy() LHPolicy

func MakePlateOutPolicy 

func MakePlateOutPolicy() LHPolicy

func MakeProteinPolicy 

func MakeProteinPolicy() LHPolicy

func MakeProtoplastPolicy 

func MakeProtoplastPolicy() LHPolicy

func MakeSingleChannelPolicy 

func MakeSingleChannelPolicy() LHPolicy

func MakeSmartMixSingleChannelPolicy 

func MakeSmartMixSingleChannelPolicy() LHPolicy

func MakeSolventPolicy 

func MakeSolventPolicy() LHPolicy

func MakeTOPolicy 

func MakeTOPolicy() LHPolicy

func MakeViscousPolicy 

func MakeViscousPolicy() LHPolicy

func MakeWaterPolicy 

func MakeWaterPolicy() LHPolicy

func MakeXYOffsetTestPolicy 

func MakeXYOffsetTestPolicy() LHPolicy

func MegaMixPolicy 

func MegaMixPolicy() LHPolicy

func NewLHPolicy 

func NewLHPolicy() LHPolicy

NewLHPolicy generates an empty LHPolicy

func PostMixPolicy 

func PostMixPolicy() LHPolicy

func PreMixPolicy 

func PreMixPolicy() LHPolicy

func SmartMixPolicy 

func SmartMixPolicy() LHPolicy

3 post mixes of the sample being transferred. Volume is adjusted based upon the volume of liquid in the destination well. No tip reuse permitted. Rules added to adjust post mix volume based on volume of the destination well. volume now capped at max for tip type (MIX_VOLUME_OVERRIDE_TIP_MAX)

func TurnOffBlowoutPolicy 

func TurnOffBlowoutPolicy() LHPolicy

func TurnOffPostMix 

func TurnOffPostMix() LHPolicy

func TurnOffPostMixAndPermitTipReUse 

func TurnOffPostMixAndPermitTipReUse() LHPolicy

func (LHPolicy) IsEqualTo 

func (lhp LHPolicy) IsEqualTo(lh2 LHPolicy) bool

func (LHPolicy) MergeWith 

func (lhp LHPolicy) MergeWith(other LHPolicy) LHPolicy

clobber everything in here with the other policy then return the merged copy

func (LHPolicy) Name 

func (policy LHPolicy) Name() string

Name returns the name of an LHPolicy as a string

func (*LHPolicy) Set 

func (plhp *LHPolicy) Set(item string, value interface{}) error

func (*LHPolicy) SetName 

func (policy *LHPolicy) SetName(name string) error

SetName sets the name of an LHPolicy.

func (*LHPolicy) UnmarshalJSON 

func (plhp *LHPolicy) UnmarshalJSON(data []byte) error

type LHPolicyRule 

type LHPolicyRule struct {
	Name       string
	Conditions []LHVariableCondition
	Priority   int
	Type       int // AND =0 OR = 1
}

conditions are ANDed together there is no chaining

func NewLHPolicyRule 

func NewLHPolicyRule(name string) LHPolicyRule

func (*LHPolicyRule) AddCategoryConditionOn 

func (lhpr *LHPolicyRule) AddCategoryConditionOn(variable, category string) error

func (*LHPolicyRule) AddNumericConditionOn 

func (lhpr *LHPolicyRule) AddNumericConditionOn(variable string, low, up float64) error

func (LHPolicyRule) HasCondition 

func (lhpr LHPolicyRule) HasCondition(cond LHVariableCondition) bool

func (LHPolicyRule) IsEqualTo 

func (lhpr LHPolicyRule) IsEqualTo(other LHPolicyRule) bool

this just looks for the same conditions, doesn't matter if the rules lead to different outcomes... not sure if this quite gives us the right behaviour but let's plough on for now

type LHPolicyRuleSet 

type LHPolicyRuleSet struct {
	Policies map[string]LHPolicy
	Rules    map[string]LHPolicyRule
	Options  map[string]interface{}
}

func AddUniversalRules 

func AddUniversalRules(originalRuleSet *LHPolicyRuleSet, policies map[string]LHPolicy) (lhpr *LHPolicyRuleSet, err error)

func CloneLHPolicyRuleSet 

func CloneLHPolicyRuleSet(parent *LHPolicyRuleSet) *LHPolicyRuleSet

func GetLHPolicyForTest 

func GetLHPolicyForTest() (*LHPolicyRuleSet, error)

GetLHPolicyForTest gets a set of Test LHPolicies for unit tests. This is not guaranteed to be consistent with the default system policies returned from GetSystemLHPolicies().

func GetSystemLHPolicies 

func GetSystemLHPolicies() (*LHPolicyRuleSet, error)

GetSystemLHPolicies is used to set the default System Policies.

func NewLHPolicyRuleSet 

func NewLHPolicyRuleSet() *LHPolicyRuleSet

func (*LHPolicyRuleSet) AddRule 

func (lhpr *LHPolicyRuleSet) AddRule(rule LHPolicyRule, consequent LHPolicy)

func (LHPolicyRuleSet) GetEquivalentRuleTo 

func (lhpr LHPolicyRuleSet) GetEquivalentRuleTo(rule LHPolicyRule) string

func (*LHPolicyRuleSet) IsEqualTo 

func (lhpr *LHPolicyRuleSet) IsEqualTo(lhp2 *LHPolicyRuleSet) bool

func (*LHPolicyRuleSet) MergeWith 

func (lhpr *LHPolicyRuleSet) MergeWith(policyToMerge *LHPolicyRuleSet)

MergeWith merges the policyToMerge with the current LHPolicyRuleSet. if equivalent rules are found in the policyToMerge these are given priority over the existing rules.

func (*LHPolicyRuleSet) SetOption 

func (lhpr *LHPolicyRuleSet) SetOption(optname string, value interface{}) error

type LHPosition 

type LHPosition struct {
	Name     string        // human readable name of the position chosen by device driver
	Location Coordinates3D // absolute position of read left corner of the position
	Size     Coordinates2D // size of the position - equal to the footprint of objects which can be accepted
}

describes a position on the liquid handling deck

func NewLHPosition 

func NewLHPosition(name string, location Coordinates3D, size Coordinates2D) *LHPosition

NewLHPosition constructs a new position on a liquidhandling deck

type LHSolution 

type LHSolution struct {
	ID               string
	BlockID          BlockID
	Inst             string
	SName            string
	Order            int
	Components       []*Liquid
	ContainerType    string
	Welladdress      string
	Plateaddress     string
	PlateID          string
	Platetype        string
	Vol              float64 // in S.I units only for now
	Type             string
	Conc             float64
	Tvol             float64
	Majorlayoutgroup int
	Minorlayoutgroup int
}

structure describing a solution: a combination of liquid components deprecated and no longer used... may well need to be deleted

func NewLHSolution 

func NewLHSolution() *LHSolution

func New_Solution 

func New_Solution() *LHSolution

func (*LHSolution) GetAssignment 

func (lhs *LHSolution) GetAssignment() string

func (LHSolution) GetComponentVolume 

func (sol LHSolution) GetComponentVolume(key string) float64

func (LHSolution) String 

func (sol LHSolution) String() string

type LHTip 

type LHTip struct {
	ID              string
	Type            string
	Mnfr            string
	Dirty           bool
	MaxVol          wunit.Volume
	MinVol          wunit.Volume
	Shape           *Shape
	Bounds          BBox
	EffectiveHeight float64

	Filtered bool
	// contains filtered or unexported fields
}

TODO remove BBox once shape implements LHObject

func CopyTip 

func CopyTip(tt LHTip) *LHTip

func NewLHTip 

func NewLHTip(mfr, ttype string, minvol, maxvol float64, volunit string, filtered bool, shape *Shape, effectiveHeightMM float64) *LHTip

func (*LHTip) AddComponent 

func (self *LHTip) AddComponent(v *Liquid) error

@implement LHContainer

func (*LHTip) ClearParent 

func (self *LHTip) ClearParent()

@implement LHObject

func (*LHTip) Contents 

func (self *LHTip) Contents() *Liquid

@implement LHContainer

func (*LHTip) CurrentVolume 

func (self *LHTip) CurrentVolume() wunit.Volume

@implement LHContainer

func (*LHTip) CurrentWorkingVolume 

func (self *LHTip) CurrentWorkingVolume() wunit.Volume

@implement LHContainer

func (*LHTip) DimensionsString 

func (self *LHTip) DimensionsString() string

DimensionsString returns a string description of the position and size of the object and its children.

func (*LHTip) Dup 

func (tip *LHTip) Dup() *LHTip

Dup copy the tip generating a new ID

func (*LHTip) DupKeepID 

func (tip *LHTip) DupKeepID() *LHTip

Dup copy the tip keeping the previous ID

func (*LHTip) Duplicate 

func (self *LHTip) Duplicate(keepIDs bool) LHObject

Duplicate copies an LHObject

func (*LHTip) GetBoxIntersections 

func (self *LHTip) GetBoxIntersections(box BBox) []LHObject

@implement LHObject

func (*LHTip) GetClass 

func (self *LHTip) GetClass() string

@implement Classy

func (*LHTip) GetEffectiveHeight 

func (self *LHTip) GetEffectiveHeight() float64

GetEffectiveHeight get the height of the tip when actually loaded onto a channel

func (*LHTip) GetID 

func (self *LHTip) GetID() string

func (*LHTip) GetName 

func (self *LHTip) GetName() string

@implement Named

func (*LHTip) GetParams 

func (tip *LHTip) GetParams() *LHChannelParameter

func (*LHTip) GetParent 

func (self *LHTip) GetParent() LHObject

@implement LHObject

func (*LHTip) GetPointIntersections 

func (self *LHTip) GetPointIntersections(point Coordinates3D) []LHObject

@implement LHObject

func (*LHTip) GetPosition 

func (self *LHTip) GetPosition() Coordinates3D

@implement LHObject

func (*LHTip) GetSize 

func (self *LHTip) GetSize() Coordinates3D

@implement LHObject

func (*LHTip) GetType 

func (self *LHTip) GetType() string

@implement Typed

func (*LHTip) IsEmpty 

func (self *LHTip) IsEmpty() bool

func (*LHTip) IsNil 

func (tip *LHTip) IsNil() bool

func (*LHTip) MarshalJSON 

func (self *LHTip) MarshalJSON() ([]byte, error)

func (*LHTip) RemoveVolume 

func (self *LHTip) RemoveVolume(v wunit.Volume) (*Liquid, error)

@implement LHContainer

func (*LHTip) ResidualVolume 

func (self *LHTip) ResidualVolume() wunit.Volume

@implement LHContainer

func (*LHTip) SetContents 

func (self *LHTip) SetContents(v *Liquid) error

SetContents set the contents of the tip, returns an error if the tip is overfilled

func (*LHTip) SetOffset 

func (self *LHTip) SetOffset(point Coordinates3D) error

@implement LHObject

func (*LHTip) SetParent 

func (self *LHTip) SetParent(o LHObject) error

@implement LHObject

func (*LHTip) UnmarshalJSON 

func (self *LHTip) UnmarshalJSON(data []byte) error

type LHTipbox 

type LHTipbox struct {
	ID         string
	Boxname    string
	Type       string
	Mnfr       string
	Nrows      int
	Ncols      int
	Height     float64
	Tiptype    *LHTip
	AsWell     *LHWell
	NTips      int
	Tips       [][]*LHTip // Tips[row][col]
	TipXOffset float64
	TipYOffset float64
	TipXStart  float64
	TipYStart  float64
	TipZStart  float64

	Bounds BBox
	// contains filtered or unexported fields
}

func NewLHTipbox 

func NewLHTipbox(nrows, ncols int, size Coordinates3D, manufacturer, boxtype string, tiptype *LHTip, well *LHWell, tipxoffset, tipyoffset, tipxstart, tipystart, tipzstart float64) *LHTipbox

func (*LHTipbox) AddressExists 

func (tb *LHTipbox) AddressExists(c WellCoords) bool

func (*LHTipbox) ClearParent 

func (self *LHTipbox) ClearParent()

@implement LHObject

func (*LHTipbox) CoordsToWellCoords 

func (tb *LHTipbox) CoordsToWellCoords(r Coordinates3D) (WellCoords, Coordinates3D)

func (*LHTipbox) DimensionsString 

func (self *LHTipbox) DimensionsString() string

DimensionsString returns a string description of the position and size of the object and its children. useful for debugging

func (*LHTipbox) Dup 

func (tb *LHTipbox) Dup() *LHTipbox

func (*LHTipbox) DupKeepIDs 

func (tb *LHTipbox) DupKeepIDs() *LHTipbox

func (*LHTipbox) Duplicate 

func (self *LHTipbox) Duplicate(keepIDs bool) LHObject

Duplicate copies an LHObject

func (*LHTipbox) GetBoxIntersections 

func (self *LHTipbox) GetBoxIntersections(box BBox) []LHObject

func (*LHTipbox) GetChildByAddress 

func (tb *LHTipbox) GetChildByAddress(c WellCoords) LHObject

func (*LHTipbox) GetClass 

func (self *LHTipbox) GetClass() string

func (LHTipbox) GetID 

func (tb LHTipbox) GetID() string

func (*LHTipbox) GetName 

func (tb *LHTipbox) GetName() string

func (*LHTipbox) GetParent 

func (self *LHTipbox) GetParent() LHObject

func (*LHTipbox) GetPointIntersections 

func (self *LHTipbox) GetPointIntersections(point Coordinates3D) []LHObject

func (*LHTipbox) GetPosition 

func (self *LHTipbox) GetPosition() Coordinates3D

func (*LHTipbox) GetSize 

func (self *LHTipbox) GetSize() Coordinates3D

func (*LHTipbox) GetTipBounds 

func (self *LHTipbox) GetTipBounds() BBox

func (*LHTipbox) GetTips 

func (tb *LHTipbox) GetTips(mirror bool, multi int, orient ChannelOrientation) []string

deprecated shortly

func (*LHTipbox) GetTipsMasked 

func (tb *LHTipbox) GetTipsMasked(mask []bool, ori ChannelOrientation, canTrim bool) ([]string, error)

find tips that fit the pattern and return in the same format

func (*LHTipbox) GetType 

func (tb *LHTipbox) GetType() string

func (*LHTipbox) HasEnoughTips 

func (tb *LHTipbox) HasEnoughTips(requested int) bool

HasEnoughTips returns true if the tipbox has at least requested tips equivalent to tb.N_clean_tips() > requested

func (*LHTipbox) HasTipAt 

func (tb *LHTipbox) HasTipAt(c WellCoords) bool

HasTipAt

func (*LHTipbox) MarshalJSON 

func (tb *LHTipbox) MarshalJSON() ([]byte, error)

func (*LHTipbox) NCols 

func (self *LHTipbox) NCols() int

func (*LHTipbox) NRows 

func (self *LHTipbox) NRows() int

func (*LHTipbox) N_clean_tips 

func (tb *LHTipbox) N_clean_tips() int

func (LHTipbox) Output 

func (tb LHTipbox) Output() string

func (*LHTipbox) PutTip 

func (tb *LHTipbox) PutTip(c WellCoords, tip *LHTip) bool

PutTip

func (*LHTipbox) Refill 

func (tb *LHTipbox) Refill()

func (*LHTipbox) Refresh 

func (tb *LHTipbox) Refresh()

func (*LHTipbox) Remove 

func (tb *LHTipbox) Remove(sa []string) bool

func (*LHTipbox) RemoveTip 

func (tb *LHTipbox) RemoveTip(c WellCoords) *LHTip

RemoveTip

func (*LHTipbox) SetOffset 

func (self *LHTipbox) SetOffset(o Coordinates3D) error

func (*LHTipbox) SetParent 

func (self *LHTipbox) SetParent(p LHObject) error

func (LHTipbox) String 

func (tb LHTipbox) String() string

func (*LHTipbox) UnmarshalJSON 

func (tb *LHTipbox) UnmarshalJSON(data []byte) error

func (*LHTipbox) WellCoordsToCoords 

func (tb *LHTipbox) WellCoordsToCoords(wc WellCoords, r WellReference) (Coordinates3D, bool)

type LHTipwaste 

type LHTipwaste struct {
	Name       string
	ID         string
	Type       string
	Mnfr       string
	Capacity   int
	Contents   int
	Height     float64
	WellXStart float64
	WellYStart float64
	WellZStart float64
	AsWell     *LHWell
	Bounds     BBox
	// contains filtered or unexported fields
}

func NewLHTipwaste 

func NewLHTipwaste(capacity int, typ, mfr string, size Coordinates3D, w *LHWell, wellxstart, wellystart, wellzstart float64) *LHTipwaste

func (*LHTipwaste) AddressExists 

func (self *LHTipwaste) AddressExists(c WellCoords) bool

func (*LHTipwaste) ClearParent 

func (self *LHTipwaste) ClearParent()

@implement LHObject

func (*LHTipwaste) CoordsToWellCoords 

func (self *LHTipwaste) CoordsToWellCoords(r Coordinates3D) (WellCoords, Coordinates3D)

func (*LHTipwaste) DimensionsString 

func (self *LHTipwaste) DimensionsString() string

DimensionsString returns a string description of the position and size of the object and its children.

func (*LHTipwaste) Dispose 

func (lht *LHTipwaste) Dispose(channels []*LHChannelParameter) ([]WellCoords, bool)

Dispose attempt to eject the tips from non-nil channels into the tipwaste. Returns a slice of well coordinates which specify where each tip should be ejected (undefined for nil channels), and a bool which is true if the tips were disposed of successfully, false if the tipbox is over capacity

func (*LHTipwaste) DisposeNum 

func (lht *LHTipwaste) DisposeNum(num int) bool

func (*LHTipwaste) Dup 

func (tw *LHTipwaste) Dup() *LHTipwaste

func (*LHTipwaste) DupKeepIDs 

func (tw *LHTipwaste) DupKeepIDs() *LHTipwaste

func (*LHTipwaste) Duplicate 

func (self *LHTipwaste) Duplicate(keepIDs bool) LHObject

Duplicate copies an LHObject

func (*LHTipwaste) Empty 

func (lht *LHTipwaste) Empty()

func (*LHTipwaste) GetBoxIntersections 

func (self *LHTipwaste) GetBoxIntersections(box BBox) []LHObject

func (*LHTipwaste) GetChildByAddress 

func (self *LHTipwaste) GetChildByAddress(c WellCoords) LHObject

func (*LHTipwaste) GetClass 

func (self *LHTipwaste) GetClass() string

func (*LHTipwaste) GetID 

func (tw *LHTipwaste) GetID() string

func (*LHTipwaste) GetName 

func (tw *LHTipwaste) GetName() string

func (*LHTipwaste) GetParent 

func (self *LHTipwaste) GetParent() LHObject

func (*LHTipwaste) GetPointIntersections 

func (self *LHTipwaste) GetPointIntersections(point Coordinates3D) []LHObject

func (*LHTipwaste) GetPosition 

func (self *LHTipwaste) GetPosition() Coordinates3D

func (*LHTipwaste) GetSize 

func (self *LHTipwaste) GetSize() Coordinates3D

func (*LHTipwaste) GetTargetOffset 

func (self *LHTipwaste) GetTargetOffset(adaptorName string, channel int) Coordinates3D

GetTargetOffset get the offset for addressing a well with the named adaptor and channel

func (*LHTipwaste) GetTargets 

func (self *LHTipwaste) GetTargets(adaptorName string) []Coordinates3D

GetTargets return all the defined targets for the named adaptor

func (*LHTipwaste) GetType 

func (tw *LHTipwaste) GetType() string

func (*LHTipwaste) MarshalJSON 

func (tw *LHTipwaste) MarshalJSON() ([]byte, error)

func (*LHTipwaste) NCols 

func (self *LHTipwaste) NCols() int

func (*LHTipwaste) NRows 

func (self *LHTipwaste) NRows() int

func (*LHTipwaste) SetOffset 

func (self *LHTipwaste) SetOffset(o Coordinates3D) error

func (*LHTipwaste) SetParent 

func (self *LHTipwaste) SetParent(p LHObject) error

func (LHTipwaste) SpaceLeft 

func (tw LHTipwaste) SpaceLeft() int

func (LHTipwaste) String 

func (te LHTipwaste) String() string

func (*LHTipwaste) UnmarshalJSON 

func (tw *LHTipwaste) UnmarshalJSON(data []byte) error

func (*LHTipwaste) WellCoordsToCoords 

func (self *LHTipwaste) WellCoordsToCoords(wc WellCoords, r WellReference) (Coordinates3D, bool)

type LHVariableCondition 

type LHVariableCondition struct {
	TestVariable string
	Condition    LHCondition
}

func NewLHVariableCondition 

func NewLHVariableCondition(testvariable string) LHVariableCondition

func (LHVariableCondition) IsEqualTo 

func (lhvc LHVariableCondition) IsEqualTo(other LHVariableCondition) bool

func (*LHVariableCondition) SetCategoric 

func (lhvc *LHVariableCondition) SetCategoric(category string) error

func (*LHVariableCondition) SetNumeric 

func (lhvc *LHVariableCondition) SetNumeric(low, up float64) error

func (*LHVariableCondition) UnmarshalJSON 

func (lh *LHVariableCondition) UnmarshalJSON(data []byte) error

type LHWell 

type LHWell struct {
	ID        string
	Inst      string
	Crds      WellCoords
	MaxVol    float64 //Maximum total capacity of the well
	WContents *Liquid
	Rvol      float64 //Residual volume which can't be removed from the well
	WShape    *Shape
	Bottom    WellBottomType
	Bounds    BBox
	Bottomh   float64
	Extra     map[string]interface{}
	Plate     LHObject `gotopb:"-" json:"-"`
}

structure representing a well on a microplate - description of a destination

func Get_Next_Well 

func Get_Next_Well(plate *Plate, component *Liquid, curwell *LHWell) (*LHWell, bool)

this function is somewhat buggy... need to define its responsibilities better

func NewLHWell 

func NewLHWell(vunit string, vol, rvol float64, shape *Shape, bott WellBottomType, xdim, ydim, zdim, bottomh float64, dunit string) *LHWell

make a new well structure

func (*LHWell) AddComponent 

func (w *LHWell) AddComponent(c *Liquid) error

AddComponent add some liquid to the well

func (*LHWell) CDup 

func (lhw *LHWell) CDup() *LHWell

copy of type

func (*LHWell) CalculateMaxCrossSectionArea 

func (lhw *LHWell) CalculateMaxCrossSectionArea() (ca wunit.Area, err error)

func (*LHWell) CalculateMaxVolume 

func (lhw *LHWell) CalculateMaxVolume() (vol wunit.Volume, err error)

func (LHWell) CheckExtraKey 

func (w LHWell) CheckExtraKey(s string) error

CheckExtraKey checks if the key is a reserved name

func (*LHWell) Clean 

func (w *LHWell) Clean()

Clean resets the volume in the well so that it's empty

func (*LHWell) Clear 

func (w *LHWell) Clear()

func (*LHWell) ClearParent 

func (self *LHWell) ClearParent()

@implement LHObject

func (*LHWell) ClearUserAllocated 

func (w *LHWell) ClearUserAllocated()

func (*LHWell) ContainerType 

func (w *LHWell) ContainerType() string

func (*LHWell) Contains 

func (w *LHWell) Contains(cmp *Liquid) bool

func (*LHWell) Contents 

func (w *LHWell) Contents() *Liquid

func (*LHWell) CurrentVolume 

func (w *LHWell) CurrentVolume() wunit.Volume

CurrentVolume return the volume of the component currently in the well

func (*LHWell) CurrentWorkingVolume 

func (w *LHWell) CurrentWorkingVolume() wunit.Volume

CurrentWorkingVolume return the available working volume in the well - i.e. current volume minus residual volume

func (*LHWell) DeclareAutoallocated 

func (well *LHWell) DeclareAutoallocated()

func (*LHWell) DeclareNotAutoallocated 

func (well *LHWell) DeclareNotAutoallocated()

func (*LHWell) DimensionsString 

func (self *LHWell) DimensionsString() string

DimensionsString returns a string description of the position and size of the object and its children.

func (*LHWell) Dup 

func (lhw *LHWell) Dup() *LHWell

copy of instance

func (*LHWell) DupKeepIDs 

func (lhw *LHWell) DupKeepIDs() *LHWell

func (*LHWell) Duplicate 

func (self *LHWell) Duplicate(keepIDs bool) LHObject

Duplicate copies an LHObject

func (*LHWell) GetAfVFunc 

func (lhw *LHWell) GetAfVFunc() wutil.Func1Prm

func (*LHWell) GetBoxIntersections 

func (self *LHWell) GetBoxIntersections(box BBox) []LHObject

@implement LHObject

func (*LHWell) GetClass 

func (self *LHWell) GetClass() string

@implement Classy

func (*LHWell) GetID 

func (self *LHWell) GetID() string

func (*LHWell) GetName 

func (self *LHWell) GetName() string

@implement Named

func (*LHWell) GetParent 

func (self *LHWell) GetParent() LHObject

@implement LHObject

func (*LHWell) GetPointIntersections 

func (self *LHWell) GetPointIntersections(point Coordinates3D) []LHObject

@implement LHObject

func (*LHWell) GetPosition 

func (self *LHWell) GetPosition() Coordinates3D

@implement LHObject

func (*LHWell) GetSize 

func (self *LHWell) GetSize() Coordinates3D

@implement LHObject

func (*LHWell) GetType 

func (self *LHWell) GetType() string

@implement Typed

func (*LHWell) GetVolumeUnit 

func (self *LHWell) GetVolumeUnit() string

func (*LHWell) GetWellCoords 

func (self *LHWell) GetWellCoords() WellCoords

func (*LHWell) GetWellTargets 

func (w *LHWell) GetWellTargets(adaptor string) []Coordinates3D

GetWellTargets return the well targets for the given adaptor if the adaptor has no defined targets, simply returns the well center

func (*LHWell) IsAutoallocated 

func (well *LHWell) IsAutoallocated() bool

func (*LHWell) IsEmpty 

func (w *LHWell) IsEmpty() bool

IsEmpty returns true if the well contains nothing, though this does not mean that the working volume is greater than zero

func (*LHWell) IsUserAllocated 

func (w *LHWell) IsUserAllocated() bool

func (*LHWell) IsVolumeValid 

func (w *LHWell) IsVolumeValid() bool

IsVolumeValid tests whether the volume in the well is within the allowable range

func (*LHWell) ListAdaptorsWithTargets 

func (w *LHWell) ListAdaptorsWithTargets() []string

GetAdaptorsWithTargets gets the list of the names of adaptors which have targets defined for the well

func (*LHWell) Location_ID 

func (lhw *LHWell) Location_ID() string

func (*LHWell) Location_Name 

func (lhw *LHWell) Location_Name() string

func (*LHWell) MaxVolume 

func (w *LHWell) MaxVolume() wunit.Volume

MaxVolume get the maximum working volume of the well

func (*LHWell) MaxWorkingVolume 

func (w *LHWell) MaxWorkingVolume() wunit.Volume

MaxWorkingVolume get the total maximum working volume in the well, i.e. the max volume minus residual volume

func (*LHWell) PlateLocation 

func (w *LHWell) PlateLocation() PlateLocation

func (*LHWell) RemoveCarry 

func (w *LHWell) RemoveCarry(v wunit.Volume)

RemoveCarry Remove the carry volume

func (*LHWell) RemoveVolume 

func (w *LHWell) RemoveVolume(v wunit.Volume) (*Liquid, error)

RemoveVolume remove some liquid from the well

func (*LHWell) ResetPlateID 

func (w *LHWell) ResetPlateID(newID string)

func (*LHWell) ResidualVolume 

func (w *LHWell) ResidualVolume() wunit.Volume

func (*LHWell) SetAfVFunc 

func (lhw *LHWell) SetAfVFunc(f string)

func (*LHWell) SetContents 

func (w *LHWell) SetContents(newContents *Liquid) error

func (*LHWell) SetOffset 

func (self *LHWell) SetOffset(point Coordinates3D) error

@implement LHObject

func (*LHWell) SetParent 

func (self *LHWell) SetParent(p LHObject) error

@implement LHObject

func (*LHWell) SetUserAllocated 

func (w *LHWell) SetUserAllocated()

func (*LHWell) SetWellTargets 

func (w *LHWell) SetWellTargets(adaptor string, offsets []Coordinates3D)

SetWellTargets sets the targets for each channel when accessing the well using adaptor. offsets is a list of coordinates which specify the offset in mm from the well center for each channel. len(offsets) specifies the maximum number of channels which can access the well simultaneously using adaptor

func (*LHWell) Shape 

func (lhw *LHWell) Shape() *Shape

func (LHWell) String 

func (w LHWell) String() string

func (*LHWell) UpdateContentID 

func (w *LHWell) UpdateContentID(IDBefore string, after *Liquid) bool

func (*LHWell) ValidateVolume 

func (w *LHWell) ValidateVolume() error

ValidateVolume validates that the volume in the well is within allowable range

func (*LHWell) XDim 

func (w *LHWell) XDim() float64

func (*LHWell) YDim 

func (w *LHWell) YDim() float64

func (*LHWell) ZDim 

func (w *LHWell) ZDim() float64

type Liquid 

type Liquid struct {
	ID                 string
	BlockID            BlockID
	DaughtersID        map[string]struct{}
	ParentID           string
	Inst               string
	Order              int
	CName              string
	Type               LiquidType
	Vol                float64
	Conc               float64
	Vunit              string
	Cunit              string
	Tvol               float64
	Smax               float64 // maximum solubility
	Visc               float64
	StockConcentration float64
	SubComponents      ComponentList // List of all sub components in the LHComponent.
	Extra              map[string]interface{}
	Loc                string // refactor to PlateLocation
	Destination        string
	Policy             LHPolicy // Policy is where a custom liquid policy is stored
}

Liquid is the principle liquid handling type in Antha. A liquid describes a liquid component and its desired properties

func CopyComponentArray 

func CopyComponentArray(arin []*Liquid) []*Liquid

func NewLHComponent 

func NewLHComponent() *Liquid

func (*Liquid) AddDNASequence 

func (lhc *Liquid) AddDNASequence(seq DNASequence, options ...bool) error

AddDNASequence adds DNASequence to the LHComponent. If a Sequence already exists an error is returned and the sequence is not added unless an additional boolean argument (FORCEADD or true) is specified to ignore duplicates. A warning will be returned in either case if a duplicate sequence is already found.

func (*Liquid) AddDaughterComponent 

func (cmp *Liquid) AddDaughterComponent(cmp2 *Liquid)

func (*Liquid) AddParentComponent 

func (cmp *Liquid) AddParentComponent(cmp2 *Liquid)

func (*Liquid) AddPolicy 

func (lhc *Liquid) AddPolicy(pol LHPolicy) error

func (*Liquid) AddSubComponent 

func (cmp *Liquid) AddSubComponent(subcomponent *Liquid, conc wunit.Concentration) error

AddSubComponent adds a subcomponent with concentration to a component. An error is returned if subcomponent is already found.

func (*Liquid) AddSubComponents 

func (cmp *Liquid) AddSubComponents(allsubComponents ComponentList) error

AddSubComponents adds a component list to a component. If a conflicting sub component concentration is already present then an error will be returned. To overwrite all subcomponents ignoring conficts, use OverWriteSubComponents.

func (*Liquid) AddVolumeRule 

func (lhc *Liquid) AddVolumeRule(minvol, maxvol float64, pol LHPolicy) error

func (*Liquid) CNID 

func (lhc *Liquid) CNID() string

func (*Liquid) Clean 

func (cmp *Liquid) Clean()

Clean the component to its initial state

func (*Liquid) Concentration 

func (lhc *Liquid) Concentration() (conc wunit.Concentration)

Concentration returns the Concentration of the LHComponent

func (*Liquid) Cp 

func (lhc *Liquid) Cp() *Liquid

func (*Liquid) DNASequences 

func (lhc *Liquid) DNASequences() ([]DNASequence, error)

DNASequences returns DNA Sequences asociated with an LHComponent. An error is also returned indicating whether a sequence was found.

func (*Liquid) DeclareInstance 

func (lhc *Liquid) DeclareInstance()

func (*Liquid) DeclareNotInstance 

func (lhc *Liquid) DeclareNotInstance()

func (*Liquid) Dup 

func (lhc *Liquid) Dup() *Liquid

func (*Liquid) EqualTypeVolume 

func (l1 *Liquid) EqualTypeVolume(l2 *Liquid) bool

func (*Liquid) EqualTypeVolumeID 

func (l1 *Liquid) EqualTypeVolumeID(l2 *Liquid) bool

func (*Liquid) FindDNASequence 

func (lhc *Liquid) FindDNASequence(seq DNASequence) (seqs []DNASequence, positions []int, err error)

FindDNASequence searches for the presence of a DNASequence in the LHComponent. Search is based upon both name of the sequence and sequence. If multiple copies of the sequence exists and error is returned. If a Sequence does not exist, the sequence is added and an error is returned.

func (Liquid) FullyQualifiedName 

func (cmp Liquid) FullyQualifiedName() string

func (*Liquid) Generation 

func (lhc *Liquid) Generation() int

func (*Liquid) GetClass 

func (lhc *Liquid) GetClass() string

GetClass return the class of the object

func (*Liquid) GetConc 

func (lhc *Liquid) GetConc() float64

func (*Liquid) GetConcentrationOf 

func (c *Liquid) GetConcentrationOf(subComponentName string) (wunit.Concentration, error)

GetConcentrationOf attempts to retrieve the concentration of subComponentName in component. If the component name is equal to subComponentName, the concentration of the component itself is returned.

func (*Liquid) GetCunit 

func (lhc *Liquid) GetCunit() string

func (*Liquid) GetExtra 

func (lhc *Liquid) GetExtra() map[string]interface{}

func (Liquid) GetID 

func (lhc Liquid) GetID() string

func (*Liquid) GetName 

func (lhc *Liquid) GetName() string

GetName the component's name

func (*Liquid) GetPolicies 

func (lhc *Liquid) GetPolicies() (*LHPolicyRuleSet, error)

func (*Liquid) GetSmax 

func (lhc *Liquid) GetSmax() float64

func (*Liquid) GetSubComponents 

func (cmp *Liquid) GetSubComponents() (ComponentList, error)

GetSubComponents returns a component list from a component

func (*Liquid) GetType 

func (lhc *Liquid) GetType() string

func (*Liquid) GetVisc 

func (lhc *Liquid) GetVisc() float64

func (*Liquid) GetVunit 

func (lhc *Liquid) GetVunit() string

func (*Liquid) HasAnyParent 

func (cmp *Liquid) HasAnyParent() bool

func (*Liquid) HasConcentration 

func (lhc *Liquid) HasConcentration() bool

HasConcentration checks whether a Concentration is set for the LHComponent

func (*Liquid) HasDaughter 

func (lhc *Liquid) HasDaughter(id string) bool

func (*Liquid) HasParent 

func (lhc *Liquid) HasParent(s string) bool

func (*Liquid) HasSubComponent 

func (c *Liquid) HasSubComponent(subComponentName string) bool

HasSubComponent evaluates if a sub component with subComponentName is found in component. If the component name is equal to subComponentName, true will be returned.

func (Liquid) IDOrName 

func (cmp Liquid) IDOrName() string

func (*Liquid) IsInstance 

func (lhc *Liquid) IsInstance() bool

func (*Liquid) IsSameKindAs 

func (lhc *Liquid) IsSameKindAs(c2 *Liquid) bool

func (*Liquid) IsSample 

func (cmp *Liquid) IsSample() bool

func (*Liquid) IsValuable 

func (lhc *Liquid) IsValuable() bool

func (*Liquid) IsZero 

func (lhc *Liquid) IsZero() bool

func (*Liquid) Kind 

func (lhc *Liquid) Kind() string

func (*Liquid) Matches 

func (cmp *Liquid) Matches(cmp2 *Liquid) bool

func (*Liquid) MeaningfulName 

func (l *Liquid) MeaningfulName() string

MeaningfulName returns the name of the liquid if one has been explicitly set (e.g. with SetName) or the empty string if only an autogenerated name is available

func (*Liquid) Mix 

func (cmp *Liquid) Mix(cmp2 *Liquid)

add cmp2 to cmp

func (*Liquid) MixPreserveTvol 

func (cmp *Liquid) MixPreserveTvol(cmp2 *Liquid)

func (*Liquid) ModifyLHPolicyParameter 

func (lhc *Liquid) ModifyLHPolicyParameter(parameter string, value interface{}) error

ModifyLHPolicyParameter specifies that this LHComponent or instance of the LHComponent should be handled with a modified LHPolicy parameter. e.g. to Change number of post mixes to 5: lhc.ModifyLHPolicyParameter("POST_MIX", 5) Valid parameters and value types are specified in aparam.go An error is returned if an invalid parameter or value type for that parameter is specified.

func (*Liquid) Name 

func (lhc *Liquid) Name() string

Name returns the component name as a string

func (*Liquid) OverwriteSubComponents 

func (cmp *Liquid) OverwriteSubComponents(allsubComponents ComponentList) error

OverwriteSubComponents Adds a component list to a component. Any existing component list will be overwritten. To add a ComponentList checking for duplicate entries, use AddSubComponents.

func (*Liquid) ParentTree 

func (cmp *Liquid) ParentTree() graph.StringGraph

func (*Liquid) ParentTreeString 

func (cmp *Liquid) ParentTreeString() string

graphviz format

func (*Liquid) PlateID 

func (lhc *Liquid) PlateID() string

PlateID returns the id of a plate or the empty string

func (*Liquid) PlateLocation 

func (lhc *Liquid) PlateLocation() PlateLocation

func (*Liquid) PolicyName 

func (lhc *Liquid) PolicyName() PolicyName

PolicyName returns the PolicyName of the LHComponent's LiquidType

func (*Liquid) Remove 

func (lhc *Liquid) Remove(v wunit.Volume) wunit.Volume

func (*Liquid) RemoveDNASequence 

func (lhc *Liquid) RemoveDNASequence(seq DNASequence) error

RemoveDNASequence removes an existing DNASequence from the LHComponent. Search is based upon both name of the sequence and sequence. If multiple copies of the sequence exists and error is returned. If a Sequence does not exist, the sequence is added and an error is returned.

func (*Liquid) RemoveDNASequenceAtPosition 

func (lhc *Liquid) RemoveDNASequenceAtPosition(position int) error

RemoveDNASequenceAtPosition removes a DNA sequence from a specific position. Designed for cases where FindDNASequnce() method returns multiple instances of the dna sequence.

func (*Liquid) RemoveDNASequences 

func (lhc *Liquid) RemoveDNASequences() error

RemoveDNASequences removes all DNASequences from the component.

func (*Liquid) ReplaceDaughterID 

func (cmp *Liquid) ReplaceDaughterID(ID1, ID2 string)

func (*Liquid) Sample 

func (lhc *Liquid) Sample(v wunit.Volume) (*Liquid, error)

func (*Liquid) SetConcentration 

func (lhc *Liquid) SetConcentration(conc wunit.Concentration)

SetConcentration sets a concentration to an LHComponent; assumes conc is valid; overwrites existing concentration

func (*Liquid) SetDNASequences 

func (lhc *Liquid) SetDNASequences(seqs []DNASequence, options ...bool) error

SetDNASequences adds a set of DNASequences to the LHComponent. If a Sequence already exists an error is returned and the sequence is not added unless an additional boolean argument (FORCEADD or true) is specified to ignore duplicates. A warning will be returned in either case if a duplicate sequence is already found.

func (*Liquid) SetGeneration 

func (lhc *Liquid) SetGeneration(i int)

func (*Liquid) SetName 

func (lhc *Liquid) SetName(name string)

SetName adds the specified component name to the component.

func (*Liquid) SetPolicies 

func (lhc *Liquid) SetPolicies(rs *LHPolicyRuleSet) error

in future this will be deprecated... should not let user completely reset policies

func (*Liquid) SetPolicyName 

func (lhc *Liquid) SetPolicyName(policy PolicyName, options ...PolicyOption) error

SetPolicyName adds the LiquidType associated with a PolicyName to the LHComponent. If the PolicyName is invalid and the DoNotPermitCustomPolicies option is used as an argument then an error is returned. By default, custom policyNames may be added and the validity of these will be checked later when robot instructions are generated, rather than in the element.

func (*Liquid) SetSample 

func (cmp *Liquid) SetSample(flag bool) bool

func (*Liquid) SetValue 

func (lhc *Liquid) SetValue(b bool)

func (*Liquid) SetVolume 

func (lhc *Liquid) SetVolume(v wunit.Volume)

SetVolume adds a volume to the component

func (*Liquid) SetWellLocation 

func (lhc *Liquid) SetWellLocation(wellLocation string) error

SetWellLocation sets the well location to an LHComponent in A1 format.

func (*Liquid) String 

func (cmp *Liquid) String() string

func (*Liquid) Summarize 

func (lhc *Liquid) Summarize() string

Summarize describe the component in a user friendly manner

func (*Liquid) TotalVolume 

func (lhc *Liquid) TotalVolume() wunit.Volume

func (*Liquid) TypeName 

func (lhc *Liquid) TypeName() string

TypeName returns the PolicyName of the LHComponent's LiquidType as a string

func (*Liquid) UpdateDNASequence 

func (lhc *Liquid) UpdateDNASequence(seq DNASequence) error

UpdateDNASequence replaces an existing DNASequence to the LHComponent. Search is based upon both name of the sequence and sequence. If multiple copies of the sequence exists and error is returned. If a Sequence does not exist, the sequence is added and an error is returned.

func (*Liquid) Volume 

func (lhc *Liquid) Volume() wunit.Volume

Volume returns the Volume of the LHComponent

func (*Liquid) WellLocation 

func (lhc *Liquid) WellLocation() string

WellLocation returns the well location in A1 format.

type LiquidType 

type LiquidType string

LiquidType represents the type of a Liquid 

const (
	LTNIL                   LiquidType = "nil"
	LTWater                 LiquidType = "water"
	LTDefault               LiquidType = "default"
	LTCulture               LiquidType = "culture"
	LTProtoplasts           LiquidType = "protoplasts"
	LTDNA                   LiquidType = "dna"
	LTDNAMIX                LiquidType = "dna_mix"
	LTProtein               LiquidType = "protein"
	LTMultiWater            LiquidType = "multiwater"
	LTLoad                  LiquidType = "load"
	LTVISCOUS               LiquidType = "viscous"
	LTPEG                   LiquidType = "peg"
	LTPAINT                 LiquidType = "paint"
	LTNeedToMix             LiquidType = "NeedToMix"
	LTPostMix               LiquidType = "PostMix"
	LTload                  LiquidType = "load"
	LTGlycerol              LiquidType = "glycerol"
	LTPLATEOUT              LiquidType = "plateout"
	LTDetergent             LiquidType = "detergent"
	LTCOLONY                LiquidType = "colony"
	LTNSrc                  LiquidType = "nitrogen_source"
	InvalidPolicyName       LiquidType = "InvalidPolicyName"
	LTEthanol               LiquidType = "ethanol"
	LTDoNotMix              LiquidType = "DoNotMix"
	LTloadwater             LiquidType = "loadwater"
	LTPreMix                LiquidType = "PreMix"
	LTDISPENSEABOVE         LiquidType = "DispenseAboveLiquid"
	LTDISPENSEABOVEMULTI    LiquidType = "DispenseAboveLiquidMulti"
	LTCulutureReuse         LiquidType = "culturereuse"
	LTDNAMIXMULTI           LiquidType = "dna_mix_multi"
	LTCOLONYMIX             LiquidType = "colonymix"
	LTDNACELLSMIX           LiquidType = "dna_cells_mix"
	LTDNACELLSMIXMULTI      LiquidType = "dna_cells_mix_multi"
	LTCSrc                  LiquidType = "carbon_source"
	LTMegaMix               LiquidType = "MegaMix"
	LTSolvent               LiquidType = "solvent"
	LTSmartMix              LiquidType = "SmartMix"
	LTSingleChannel         LiquidType = "SingleChannel"
	LTSmartMixSingleChannel LiquidType = "SmartMixSingleChannel"
	LTLiquidLevel           LiquidType = "LiquidLevel"
	LTSmartMixLiquidLevel   LiquidType = "SmartMixLiquidLevel"
)

Valid default LiquidTypes

func LiquidTypeFromString 

func LiquidTypeFromString(s PolicyName, options ...PolicyOption) (LiquidType, error)

LiquidTypeFromString returns a LiquidType from a PolicyName If the PolicyName is invalid and the DoNotPermitCustomPolicies option is used as an argument then an error is returned. By default, custom policyNames may be added and the validity of these will be checked later when robot instructions are generated, rather than in the element.

func (LiquidType) String 

func (l LiquidType) String() (PolicyName, error)

type MajorOrder 

type MajorOrder int
const (
	RowWise MajorOrder = iota
	ColumnWise
)

func (MajorOrder) String 

func (s MajorOrder) String() string

type Match 

type Match struct {
	IDs  []string       // PlateIDs in 'got' array
	WCs  []string       // Wellcoords in 'got' array
	Vols []wunit.Volume // vols (before suck) in 'got'
	M    []int          // offsets in 'got' array
	Sc   float64        // total score for this match
}

func MatchComponents 

func MatchComponents(want, got ComponentVector, independent, debug bool) (Match, error)

matchComponents takes one bite each time... the best it can find needs to be run repeatedly to pick everything up TODO: needs to supply more options

func (Match) Equals 

func (m Match) Equals(m2 Match) bool

type Named 

type Named interface {
	GetName() string
}

type Organism 

type Organism struct {
	Species *TOL // position on the TOL
}

structure which defines an organism. These need specific handling -- some detail is derived using the TOL structure

type OverHangType 

type OverHangType int

OverHangType represents the type of an overhang. Valid options are 

FALSE     OverHangType = 0
BLUNT     OverHangType = 1
OVERHANG  OverHangType = 2
UNDERHANG OverHangType = -1

const (
	// no overhang
	FALSE OverHangType = 0
	// A blunt overhang
	BLUNT OverHangType = 1
	// An overhang (5' sequence overhangs complementary strand)
	OVERHANG OverHangType = 2
	// an underhang (5' sequence underhangs complementary strand)
	UNDERHANG OverHangType = -1
)

Valid overhang types

type Overhang 

type Overhang struct {
	// Valid options are 5 (5 Prime end), 3 (3 prime end) or 0 (nul)
	End int `json:"end"`
	// Valid options are FALSE, BLUNT, OVERHANG, UNDERHANG
	Type OverHangType `json:"type"`
	// Overhang sequence
	Seq string `json:"sequence"`
	// Whether the overhang is phosphorylated.
	Phosphorylation bool `json:"phosphorylation"`
}

Overhang represents an end of a DNASequence.

func MakeOverHang 

func MakeOverHang(overhangSequence string, end int, toporbottom int, phosphorylated bool) (overhang Overhang, err error)

MakeOverHang is used to create an overhang.

func (Overhang) Length 

func (oh Overhang) Length() int

Length returns the length of the overhang.

func (Overhang) OverHang 

func (oh Overhang) OverHang() (sequence string)

Overhang returns the sequence if the overhang is of type OVERHANG.

func (Overhang) Sequence 

func (oh Overhang) Sequence() string

Sequence returns the sequence of the overhang.

func (Overhang) ToString 

func (oh Overhang) ToString() string

ToString returns a string summary of the overhang.

func (Overhang) TypeName 

func (oh Overhang) TypeName() string

TypeName returns the name of the overhang type as a string.

func (Overhang) UnderHang 

func (oh Overhang) UnderHang() (sequence string)

Overhang returns any sequence if the underhang is of type UNDERHANG.

type PRInstruction 

type PRInstruction struct {
	ID           string
	ComponentIn  *Liquid
	ComponentOut *Liquid
	Options      string
}

PRInstruction is a high-level instruction to a plate reader to measure a sample

func NewPRInstruction 

func NewPRInstruction() *PRInstruction

NewPRInstruction creates a new PRInstruction

func (PRInstruction) String 

func (ins PRInstruction) String() string

type Plasmid 

type Plasmid struct {
}

defines a plasmid

type Plate 

type Plate struct {
	ID          string
	Inst        string
	Loc         string             // location of plate
	PlateName   string             // user-definable plate name
	Type        string             // plate type
	Mnfr        string             // manufacturer
	WlsX        int                // wells along long axis
	WlsY        int                // wells along short axis
	Nwells      int                // total number of wells
	HWells      map[string]*LHWell // map of well IDs to well
	Rows        [][]*LHWell
	Cols        [][]*LHWell
	Welltype    *LHWell
	Wellcoords  map[string]*LHWell // map of coords in A1 format to wells
	WellXOffset float64            // distance (mm) between well centres in X direction
	WellYOffset float64            // distance (mm) between well centres in Y direction
	WellXStart  float64            // offset (mm) to first well in X direction
	WellYStart  float64            // offset (mm) to first well in Y direction
	WellZStart  float64            // offset (mm) to bottom of well in Z direction
	Bounds      BBox               // (relative) position of the plate (mm), set by parent
	// contains filtered or unexported fields
}

Plate is the principle type for Liquid handling Plates in Antha. The structure describing a microplate.

func NewLHPlate 

func NewLHPlate(platetype, mfr string, nrows, ncols int, size Coordinates3D, welltype *LHWell, wellXOffset, wellYOffset, wellXStart, wellYStart, wellZStart float64) *Plate

func (*Plate) AddComponent 

func (lhp *Plate) AddComponent(cmp *Liquid, overflow bool) (wc []WellCoords, err error)

func (*Plate) AddressExists 

func (self *Plate) AddressExists(c WellCoords) bool

func (*Plate) AllAutoallocated 

func (p *Plate) AllAutoallocated() bool

AllAutoallocated returns true if the plate only contains liquids which were autoallocated i.e. nothing user-defined

func (*Plate) AllContents 

func (p *Plate) AllContents() []*Liquid

AllContents returns all the components on the plate

func (*Plate) AllNonEmptyWells 

func (p *Plate) AllNonEmptyWells() []*LHWell

func (*Plate) AllWellPositions 

func (lhp *Plate) AllWellPositions(byrow bool) (wellpositionarray []string)

func (*Plate) AreWellTargetsEnabled 

func (p *Plate) AreWellTargetsEnabled(adaptorChannels int, channelSpacing float64) bool

AreaWellTargetsEnabled should well targets be set with this plate? aim is to deprecate IsSpecial

func (*Plate) AvailableContents 

func (lhp *Plate) AvailableContents(wv []WellCoords) ComponentVector

AvailableContents accepts a slice of well coordinates, wv, and returns the Liquids that could be taken from each well in subsequent steps. if any well coordinate in wv does not exist, a nil liquid is returned in that position

func (*Plate) BetterGetComponent 

func (lhp *Plate) BetterGetComponent(cmp *Liquid, mpv wunit.Volume, legacyVolume bool) ([]WellCoords, []wunit.Volume, bool)

this gets ONE component... possibly from several wells

func (Plate) CheckExtraKey 

func (p Plate) CheckExtraKey(k string) error

CheckExtraKey checks if the key is a reserved name

func (*Plate) Clean 

func (lhp *Plate) Clean()

Clean empty all the wells of the plate so that IsEmpty returns true

func (*Plate) ClearData 

func (p *Plate) ClearData(k string) error

ClearData removes data with the given name

func (*Plate) ClearParent 

func (self *Plate) ClearParent()

@implement LHObject

func (*Plate) ColVol 

func (p *Plate) ColVol() wunit.Volume

func (*Plate) CoordsToWellCoords 

func (self *Plate) CoordsToWellCoords(r Coordinates3D) (WellCoords, Coordinates3D)

func (*Plate) DeclareAutoallocated 

func (p *Plate) DeclareAutoallocated()

func (*Plate) DeclareSpecial 

func (p *Plate) DeclareSpecial()

func (*Plate) DimensionsString 

func (self *Plate) DimensionsString() string

DimensionsString returns a string description of the position and size of the object and its children.

func (*Plate) Dup 

func (lhp *Plate) Dup() *Plate

func (*Plate) DupKeepIDs 

func (lhp *Plate) DupKeepIDs() *Plate

func (*Plate) Duplicate 

func (self *Plate) Duplicate(keepIDs bool) LHObject

Duplicate copies an LHObject

func (*Plate) FindAndUpdateID 

func (p *Plate) FindAndUpdateID(before string, after *Liquid) bool

func (*Plate) GetA1WellCoordsFromOrdering 

func (lhp *Plate) GetA1WellCoordsFromOrdering(ordinals []int, byrow bool) []string

func (*Plate) GetAllConstraints 

func (p *Plate) GetAllConstraints() map[string][]string

func (*Plate) GetBoxIntersections 

func (self *Plate) GetBoxIntersections(box BBox) []LHObject

func (*Plate) GetChildByAddress 

func (self *Plate) GetChildByAddress(c WellCoords) LHObject

func (*Plate) GetClass 

func (self *Plate) GetClass() string

func (*Plate) GetComponent 

func (lhp *Plate) GetComponent(cmp *Liquid, mpv wunit.Volume) ([]WellCoords, []wunit.Volume, bool)

func (Plate) GetData 

func (p Plate) GetData(key string) ([]byte, error)

func (*Plate) GetID 

func (lhp *Plate) GetID() string

func (Plate) GetLayout 

func (plate Plate) GetLayout() string

func (*Plate) GetName 

func (lhp *Plate) GetName() string

func (*Plate) GetOrderingFromA1WellCoords 

func (lhp *Plate) GetOrderingFromA1WellCoords(wa1 []string, byrow bool) []int

func (*Plate) GetOrderingFromWellCoords 

func (lhp *Plate) GetOrderingFromWellCoords(wc []WellCoords, byrow bool) []int

func (*Plate) GetParent 

func (self *Plate) GetParent() LHObject

func (*Plate) GetPointIntersections 

func (self *Plate) GetPointIntersections(point Coordinates3D) []LHObject

func (*Plate) GetPosition 

func (self *Plate) GetPosition() Coordinates3D

func (*Plate) GetSize 

func (self *Plate) GetSize() Coordinates3D

func (*Plate) GetTargetOffset 

func (p *Plate) GetTargetOffset(adaptorName string, channel int) Coordinates3D

GetTargetOffset get the offset for addressing a well with the named adaptor and channel

func (*Plate) GetTargets 

func (p *Plate) GetTargets(adaptorName string) []Coordinates3D

GetTargets return all the defined targets for the named adaptor

func (*Plate) GetType 

func (lhp *Plate) GetType() string

@implement Typed

func (*Plate) GetWellBounds 

func (self *Plate) GetWellBounds() BBox

func (*Plate) GetWellCoordsFromOrdering 

func (lhp *Plate) GetWellCoordsFromOrdering(ordinals []int, byrow bool) []WellCoords

func (*Plate) GetWellCorner 

func (self *Plate) GetWellCorner() Coordinates3D

func (*Plate) GetWellOffset 

func (self *Plate) GetWellOffset() Coordinates3D

func (*Plate) GetWellSize 

func (self *Plate) GetWellSize() Coordinates3D

func (*Plate) Height 

func (p *Plate) Height() float64

func (*Plate) IsConstrainedOn 

func (p *Plate) IsConstrainedOn(platform string) ([]string, bool)

func (*Plate) IsEmpty 

func (lhp *Plate) IsEmpty() bool

func (*Plate) IsSpecial 

func (p *Plate) IsSpecial() bool

func (*Plate) IsUserAllocated 

func (p *Plate) IsUserAllocated() bool

func (*Plate) ListAdaptorsWithTargets 

func (p *Plate) ListAdaptorsWithTargets() []string

ListAdaptorsWithTargets get a list of the names of all the adaptors with targets set

func (*Plate) MarkNonEmptyWellsUserAllocated 

func (p *Plate) MarkNonEmptyWellsUserAllocated()

func (*Plate) MarshalJSON 

func (lhp *Plate) MarshalJSON() ([]byte, error)

func (*Plate) MergeWith 

func (p *Plate) MergeWith(p2 *Plate)

semantics are: put stuff from p2 into p unless the well in p is declared as user allocated

func (*Plate) NCols 

func (lhp *Plate) NCols() int

func (*Plate) NRows 

func (lhp *Plate) NRows() int

func (Plate) Name 

func (lhp Plate) Name() string

Name returns the name of the plate.

func (*Plate) NextEmptyWell 

func (lhp *Plate) NextEmptyWell(it AddressIterator) WellCoords

func (Plate) OutputLayout 

func (plate Plate) OutputLayout()

func (*Plate) RemoveComponent 

func (p *Plate) RemoveComponent(well string, vol wunit.Volume) *Liquid

func (*Plate) ResetID 

func (p *Plate) ResetID(newID string)

func (*Plate) SetConstrained 

func (p *Plate) SetConstrained(platform string, positions []string)

func (*Plate) SetData 

func (p *Plate) SetData(key string, data []byte) error

SetData implements Annotatable

func (*Plate) SetName 

func (lhp *Plate) SetName(name string)

Set name sets the name of the plate.

func (*Plate) SetOffset 

func (self *Plate) SetOffset(o Coordinates3D) error

func (*Plate) SetParent 

func (self *Plate) SetParent(p LHObject) error

func (Plate) String 

func (lhp Plate) String() string

func (*Plate) ToSLHPLate 

func (p *Plate) ToSLHPLate() SLHPlate

func (*Plate) UnmarshalJSON 

func (lhp *Plate) UnmarshalJSON(b []byte) error

func (*Plate) ValidateVolumes 

func (lhp *Plate) ValidateVolumes() error

func (*Plate) WellAt 

func (lhp *Plate) WellAt(wc WellCoords) (*LHWell, bool)

func (*Plate) WellAtString 

func (lhp *Plate) WellAtString(s string) (*LHWell, bool)

func (*Plate) WellCoordsToCoords 

func (self *Plate) WellCoordsToCoords(wc WellCoords, r WellReference) (Coordinates3D, bool)

func (*Plate) WellMap 

func (lhp *Plate) WellMap() map[string]*LHWell

func (*Plate) Wells 

func (lhp *Plate) Wells() [][]*LHWell

func (*Plate) WellsX 

func (lhp *Plate) WellsX() int

func (*Plate) WellsY 

func (lhp *Plate) WellsY() int

type PlateLocation 

type PlateLocation struct {
	ID     string
	Coords WellCoords
}

func PlateLocationFromString 

func PlateLocationFromString(s string) PlateLocation

func ZeroPlateLocation 

func ZeroPlateLocation() PlateLocation

func (PlateLocation) Equals 

func (pc PlateLocation) Equals(opc PlateLocation) bool

func (PlateLocation) IsZero 

func (pc PlateLocation) IsZero() bool

func (PlateLocation) ToString 

func (pc PlateLocation) ToString() string

type Platedestmap 

type Platedestmap [][][]*LHInstruction

func NewPlatedestmap 

func NewPlatedestmap() Platedestmap

func (Platedestmap) Print 

func (pdm Platedestmap) Print()

type PointSet 

type PointSet []Coordinates3D

func (PointSet) CentreTo 

func (ps PointSet) CentreTo(c Coordinates3D) PointSet

type PolicyName 

type PolicyName string

PolicyName represents the name of a liquid handling policy used to look up the details of that policy.

func LiquidTypeName 

func LiquidTypeName(lt LiquidType) (PolicyName, error)

LiquidTypeName returns a PolicyName from a LiquidType

func PolicyNameFromString 

func PolicyNameFromString(s string) PolicyName

func (PolicyName) String 

func (l PolicyName) String() string

type PolicyOption 

type PolicyOption string

PolicyOption allows specification of advanced options to feed into the SetPolicyName method. 

var DoNotPermitCustomPolicies PolicyOption = "DoNotPermitCustomPolicies"

DoNotPermitCustomPolicies is an option to pass into SetPolicyName to ensure only valid system policies are specified. With this flag set, custom user policies are not permitted.

type Population 

type Population struct {
}

a set of organisms, can be mixed or homogeneous

type Protein 

type Protein struct {
	Seq ProteinSequence
}

physical protein sample has a ProteinSequence

type ProteinSequence 

type ProteinSequence struct {
	Nm  string
	Seq string
}

ProteinSequence object is a type of Biosequence

func (*ProteinSequence) Append 

func (prot *ProteinSequence) Append(s string) error

func (*ProteinSequence) Blast 

func (seq *ProteinSequence) Blast() (hits []Hit, err error)

func (*ProteinSequence) Molecularweight 

func (seq *ProteinSequence) Molecularweight() (daltons float64)

Estimate molecular weight of protein product

func (*ProteinSequence) Name 

func (prot *ProteinSequence) Name() string

func (*ProteinSequence) Prepend 

func (prot *ProteinSequence) Prepend(s string) error

func (*ProteinSequence) Sequence 

func (prot *ProteinSequence) Sequence() string

func (*ProteinSequence) SetName 

func (prot *ProteinSequence) SetName(name string)

func (*ProteinSequence) SetSequence 

func (prot *ProteinSequence) SetSequence(seq string) error

type RNA 

type RNA struct {
	Seq RNASequence
}

RNA sample: physical RNA, has an RNASequence object

type RNASequence 

type RNASequence struct {
	Nm  string
	Seq string
}

RNASequence object is a type of Biosequence

func (*RNASequence) Append 

func (rna *RNASequence) Append(s string) error

func (*RNASequence) Blast 

func (seq *RNASequence) Blast() (hits []Hit, err error)

func (*RNASequence) Name 

func (rna *RNASequence) Name() string

func (*RNASequence) Prepend 

func (rna *RNASequence) Prepend(s string) error

func (*RNASequence) Sequence 

func (rna *RNASequence) Sequence() string

func (*RNASequence) SetName 

func (rna *RNASequence) SetName(name string)

func (*RNASequence) SetSequence 

func (rna *RNASequence) SetSequence(seq string) error

type Rational 

type Rational struct {
	N int
	D int
}

type ReadEMParameters 

type ReadEMParameters map[string]interface{}

type Reading 

type Reading interface {
	BlankCorrect(blank Absorbance)
	PathlengthCorrect(pathlength wunit.Length)
	NormaliseTo(target Absorbance)
	CorrecttoRefStandard()
}

type ReallySimpleAlignment 

type ReallySimpleAlignment []string

no guarantees... it's just some strings

func (ReallySimpleAlignment) Column 

func (aln ReallySimpleAlignment) Column(i int) string

func (ReallySimpleAlignment) MultiColumn 

func (aln ReallySimpleAlignment) MultiColumn(i, j int) []string

find column of length j slices at pos i

func (ReallySimpleAlignment) TrimToFrame 

func (aln ReallySimpleAlignment) TrimToFrame(frame int) ReallySimpleAlignment

type Rectangle 

type Rectangle struct {
	// contains filtered or unexported fields
}

a rectangle

func NewBoundingRectangle 

func NewBoundingRectangle(coords []Coordinates2D) Rectangle

NewBoundingRectangle create a new rectangle which is the smallest rectangle to include all the given coordinates

func NewRectangle 

func NewRectangle(firstCorner, secondCorner Coordinates2D) Rectangle

NewRectangle create a new rectangle from any two opposing corners

func (Rectangle) Center 

func (self Rectangle) Center() Coordinates2D

Center the central point of the rectangle

func (Rectangle) Contains 

func (self Rectangle) Contains(pos Coordinates2D) bool

Contains return true if the given coordinate is within the rectangle

func (Rectangle) Expand 

func (self Rectangle) Expand(amount float64) Rectangle

Expand return a new Rectangle with the same center point but whose width and height is increased by the given positive amount

func (Rectangle) Height 

func (self Rectangle) Height() float64

Height the height of the rectangle

func (Rectangle) Width 

func (self Rectangle) Width() float64

Width the width of the rectangle

type RestrictionEnzyme 

type RestrictionEnzyme struct {
	Enzyme
	// sequence
	RecognitionSequence               string
	EndLength                         int
	Prototype                         string
	Topstrand3primedistancefromend    int
	Bottomstrand5primedistancefromend int
	MethylationSite                   string   //"attr, <4>"
	CommercialSource                  []string //string "attr, <5>"
	References                        []int
	Class                             string
	Isoschizomers                     []string
}

RestrictionEnzyme is an enzyme which cleaves DNA

type SLHPlate 

type SLHPlate struct {
	ID          string
	Inst        string
	Loc         string
	Name        string
	Type        string
	Mnfr        string
	WellsX      int
	WellsY      int
	Nwells      int
	Bounds      BBox
	Welltype    *LHWell
	Wellcoords  map[string]*LHWell
	WellXOffset float64 // distance (mm) between well centres in X direction
	WellYOffset float64 // distance (mm) between well centres in Y direction
	WellXStart  float64 // offset (mm) to first well in X direction
	WellYStart  float64 // offset (mm) to first well in Y direction
	WellZStart  float64 // offset (mm) to bottom of well in Z direction
}

serializable, stripped-down version of the LHPlate

func (SLHPlate) FillPlate 

func (slhp SLHPlate) FillPlate(plate *Plate)

type SequenceDatabase 

type SequenceDatabase struct {
	Name      string
	Filename  string
	Type      string
	Sequences []BioSequence
}

type SequentialTipLoadingBehaviour 

type SequentialTipLoadingBehaviour int
const (
	//NoSequentialTipLoading tips are loaded all at once, an error is raised if not possible
	NoSequentialTipLoading SequentialTipLoadingBehaviour = iota
	//ForwardSequentialTipLoading chunks of contiguous tips are loaded sequentially in the order encountered
	ForwardSequentialTipLoading
	//ReverseSequentialTipLoading chunks of contiguous tips are loaded sequentially in reverse order
	ReverseSequentialTipLoading
)

func (SequentialTipLoadingBehaviour) String 

func (s SequentialTipLoadingBehaviour) String() string

type SerializableHead 

type SerializableHead struct {
	Name         string
	Manufacturer string
	ID           string
	AdaptorIndex int
	Params       *LHChannelParameter
	TipLoading   TipLoadingBehaviour
}

func NewSerializableHead 

func NewSerializableHead(head *LHHead, adaptors map[*LHAdaptor]int) *SerializableHead

func (*SerializableHead) Fill 

func (sh *SerializableHead) Fill(head *LHHead, adaptors []*LHAdaptor)

type SerializableHeadAssembly 

type SerializableHeadAssembly struct {
	Positions      []*sHeadAssemblyPosition
	MotionLimits   *BBox
	VelocityLimits *VelocityRange
}

SerializableHeadAssembly an easily serialisable representation of LHHEadAssembly referring to heads by index in some array

func NewSerializableHeadAssembly 

func NewSerializableHeadAssembly(ha *LHHeadAssembly, heads map[*LHHead]int) *SerializableHeadAssembly

NewSerializableHeadAssembly convert to an easily serialisable representation of a head assembly heads is a map of heads to list index

func (*SerializableHeadAssembly) Fill 

func (sha *SerializableHeadAssembly) Fill(ha *LHHeadAssembly, heads []*LHHead)

type Shape 

type Shape struct {
	Type       *shapeType
	LengthUnit string
	H          float64
	W          float64
	D          float64
}

func NewShape 

func NewShape(shapetype *shapeType, lengthunit string, h, w, d float64) *Shape

func (*Shape) Depth 

func (sh *Shape) Depth() wunit.Length

func (*Shape) Dup 

func (sh *Shape) Dup() *Shape

func (*Shape) Equals 

func (sh *Shape) Equals(sh2 *Shape) bool

func (*Shape) Height 

func (sh *Shape) Height() wunit.Length

func (*Shape) MarshalJSON 

func (st *Shape) MarshalJSON() ([]byte, error)

func (*Shape) MaxCrossSectionalArea 

func (sh *Shape) MaxCrossSectionalArea() (wunit.Area, error)

func (*Shape) String 

func (sh *Shape) String() string

func (*Shape) UnmarshalJSON 

func (st *Shape) UnmarshalJSON(bs []byte) error

func (*Shape) Volume 

func (sh *Shape) Volume() (volume wunit.Volume, err error)

func (*Shape) Width 

func (sh *Shape) Width() wunit.Length

type SimpleAlignment 

type SimpleAlignment []AlignedBioSequence

func (SimpleAlignment) Column 

func (aln SimpleAlignment) Column(i int) string

type SortableRules 

type SortableRules []LHPolicyRule

func (SortableRules) Len 

func (s SortableRules) Len() int

func (SortableRules) Less 

func (s SortableRules) Less(i, j int) bool

func (SortableRules) Swap 

func (s SortableRules) Swap(i, j int)

type Suspension 

type Suspension struct {
}

type TOL 

type TOL struct {
	UID      string
	Name     string
	Taxid    string
	Parent   *TOL
	Depth    int
	Children []*TOL
}

we use the open tree of life to define taxonomic relationships

func Load_TOL 

func Load_TOL(filename string) (*TOL, *map[string]*TOL)

read the data from the opentree file

func (TOL) Find_string 

func (t TOL) Find_string(name string) *TOL

find a node by name

func (TOL) Get_taxonomy 

func (t TOL) Get_taxonomy(arr []string) []string

extract the lineage of one particular node

func (TOL) IsAncestorOf 

func (t TOL) IsAncestorOf(t2 *TOL) string

returns the string name of the LCA if t is the ancestor of t2

type Targetted 

type Targetted interface {
	//GetTargetOffset Gets the well target location for the numbered channel of the named adaptor
	GetTargetOffset(string, int) Coordinates3D
	//GetTargets return all the defined targets for the named adaptor
	GetTargets(string) []Coordinates3D
}

type Ticker 

type Ticker struct {
	TickEvery int
	TickBy    int
	Val       int
	// contains filtered or unexported fields
}

func (*Ticker) Dup 

func (t *Ticker) Dup() *Ticker

func (*Ticker) Tick 

func (t *Ticker) Tick() int

type TipEstimate 

type TipEstimate struct {
	TipType   string // identifier describing which tips are to be used
	NTips     int    // count of tips used total
	NTipBoxes int    // count of tip boxes to be used
}

A Tip Estimate provides information on how many tips and tip boxes of a given type are expected to be used

func (TipEstimate) String 

func (self TipEstimate) String() string

type TipLoadingBehaviour 

type TipLoadingBehaviour struct {
	//OverrideLoadTipsCommand true it the liquid handler will override which tips are loaded
	OverrideLoadTipsCommand bool
	//AutoRefillTipboxes are tipboxes automaticall refilled
	AutoRefillTipboxes bool
	//LoadingOrder are tips loaded ColumnWise or RowWise
	LoadingOrder MajorOrder
	//VerticalLoadingDirection the direction along which columns are loaded
	VerticalLoadingDirection VerticalDirection
	//HorizontalLoadingDirection the direction along which rows are loaded
	HorizontalLoadingDirection HorizontalDirection
	//ChunkingBehaviour how to load tips when the requested number aren't available contiguously
	ChunkingBehaviour SequentialTipLoadingBehaviour
}

TipLoadingBehaviour describe the way in which tips are loaded

func (TipLoadingBehaviour) String 

func (s TipLoadingBehaviour) String() string

String get a string description for debuggin

type TypeIIs 

type TypeIIs struct {
	RestrictionEnzyme
}

func ToTypeIIs 

func ToTypeIIs(typeIIenzyme RestrictionEnzyme) (typeIIsenz TypeIIs, err error)

type Typed 

type Typed interface {
	GetType() string
}

type VelocityRange 

type VelocityRange struct {
	Min, Max *wunit.Velocity3D
}

VelocityRange the minimum and maximum velocities for the head assembly. nil implies no limit

func (*VelocityRange) Dup 

func (self *VelocityRange) Dup() *VelocityRange

Dup return a copy of the range

type VerticalDirection 

type VerticalDirection int
const (
	BottomToTop VerticalDirection = -1
	TopToBottom VerticalDirection = 1
)

func (VerticalDirection) String 

func (s VerticalDirection) String() string

type Warning 

type Warning string

Warning is a representation of a non fatal error in Antha which implements the golang error interface.

func NewWarning 

func NewWarning(arguments ...interface{}) Warning

NewWarning generate a new Warning using the default formats for its arguments. Spaces are added between operands when neither is a string.

func NewWarningf 

func NewWarningf(format string, arguments ...interface{}) Warning

NewWarningf generates a new Warning from a formatted string.

func (Warning) Error 

func (w Warning) Error() string

Error returns a string error message.

type WellBottomType 

type WellBottomType int
const (
	FlatWellBottom WellBottomType = iota
	UWellBottom
	VWellBottom
)

func (WellBottomType) String 

func (bt WellBottomType) String() string

type WellCoordArrayCol 

type WellCoordArrayCol []WellCoords

func (WellCoordArrayCol) Len 

func (wca WellCoordArrayCol) Len() int

func (WellCoordArrayCol) Less 

func (wca WellCoordArrayCol) Less(i, j int) bool

func (WellCoordArrayCol) Swap 

func (wca WellCoordArrayCol) Swap(i, j int)

type WellCoordArrayRow 

type WellCoordArrayRow []WellCoords

func (WellCoordArrayRow) Len 

func (wca WellCoordArrayRow) Len() int

func (WellCoordArrayRow) Less 

func (wca WellCoordArrayRow) Less(i, j int) bool

func (WellCoordArrayRow) Swap 

func (wca WellCoordArrayRow) Swap(i, j int)

type WellCoordSlice 

type WellCoordSlice []WellCoords

func (WellCoordSlice) Trim 

func (self WellCoordSlice) Trim() WellCoordSlice

Trim remove nil well coords from begining and end of the slice

type WellCoords 

type WellCoords struct {
	X int
	Y int
}

convenience structure for handling well coordinates

func MakeWellCoords 

func MakeWellCoords(wc string) WellCoords

func MakeWellCoords1A 

func MakeWellCoords1A(a1 string) WellCoords

make well coordinates in the "1A" convention

func MakeWellCoordsA1 

func MakeWellCoordsA1(a1 string) WellCoords

make well coordinates in the "A1" convention

func MakeWellCoordsArray 

func MakeWellCoordsArray(sa []string) []WellCoords

func MakeWellCoordsXY 

func MakeWellCoordsXY(xy string) WellCoords

func MakeWellCoordsXYsep 

func MakeWellCoordsXYsep(x, y string) WellCoords

make well coordinates in a manner compatble with "X1,Y1" etc.

func WCArrayFromStrings 

func WCArrayFromStrings(arr []string) []WellCoords

func WCArrayFromWells 

func WCArrayFromWells(wells []*LHWell) []WellCoords

func ZeroWellCoords 

func ZeroWellCoords() WellCoords

func (WellCoords) ColLessThan 

func (wc WellCoords) ColLessThan(wc2 WellCoords) bool

func (WellCoords) ColNumString 

func (wc WellCoords) ColNumString() string

func (WellCoords) Equals 

func (wc WellCoords) Equals(w2 WellCoords) bool

func (WellCoords) Format1A 

func (wc WellCoords) Format1A() string

func (WellCoords) FormatA1 

func (wc WellCoords) FormatA1() string

func (WellCoords) FormatXY 

func (wc WellCoords) FormatXY() string

return well coordinates in "X1Y1" format

func (WellCoords) IsZero 

func (wc WellCoords) IsZero() bool

func (WellCoords) RowLessThan 

func (wc WellCoords) RowLessThan(wc2 WellCoords) bool

func (WellCoords) RowLettString 

func (wc WellCoords) RowLettString() string

func (WellCoords) WellNumber 

func (wc WellCoords) WellNumber(platetype *Plate, byRow bool) int

WellNumber returns the index of the well coordinates on a platetype based on looking up the number of wells in the X, Y directions of the platetype. Setting byRow to true will count along each sequential row rather down each sequential column. e.g. if byRow == true: A1 = 0, A2 = 1, A12 = 11 if byRow == false: A1 = 0, B1 = 1, E1 = 4

type WellReference 

type WellReference int

WellReference used for specifying position within a well particularly for signify the intended locations for tip movements. Offsets are taken relative to these 

const (
	UnknownReference WellReference = iota - 1 // -1
	BottomReference                           //0
	TopReference                              //1
	LiquidReference                           //2
)

func NewWellReference 

func NewWellReference(s string) (WellReference, error)

NewWellReference construct a WellReference from its descriptive name. returns UnkonwnReference and an error if the reference is not recognised

func (WellReference) AsInt 

func (self WellReference) AsInt() int

func (WellReference) String 

func (self WellReference) String() string

String returns a descriptive name for the reference which is interpreted by the front end

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