antha: github.com/antha-lang/antha/antha/anthalib/wtype Index | Files | Directories

package wtype

import "github.com/antha-lang/antha/antha/anthalib/wtype"

Package wtype contains core Antha types

Index

Package Files

LiquidType.go absorbance.go annotatedsequence.go aparam.go bioinformatics.go biology.go biotree.go centrifuge.go componentvector.go configitem.go constants.go electroshock.go entity.go environment.go executetypes.go file.go functions.go geometry.go globals.go haswelladdress.go instructionparameter.go lhcomponent.go lherror.go lhinstruction.go lhplate.go lhpolicy.go lhtip.go lhtipbox.go lhtipwaste.go lhtypes.go lhwell.go locations.go matchComponent.go named.go platedestmap.go plateiterator.go platelocation.go rational.go readem.go sbslabware.go serialize.go shape.go suspension.go ticker.go uuid.go volumecorrection.go warning.go wellcoords.go wtype.go

Constants

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"
)
const (
    FALSE     = 0
    BLUNT     = 1
    OVERHANG  = 2
    UNDERHANG = -1
)
const (
    NEITHER = 0
    TOP     = 1
    BOTTOM  = 2
)
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
)
const (
    LHIEND = iota
    LHIMIX
    LHIWAI
    LHIPRM
)
const (
    BYROW    = true
    BYCOLUMN = false
)
const (
    LHP_AND int = iota
    LHP_OR
)
const (
    LHVChannel = iota // vertical orientation
    LHHChannel        // horizontal orientation
)
const (
    LHWBFLAT = iota
    LHWBU
    LHWBV
)
const (
    FORCE bool = true // Optional parameter to use in AddDNASequence method to override error check preventing addition of a duplicate sequence.
)
const MIXDELIMITER = "+"

the standard delimiter to be used when concatenating mixed components into a new component name

const SEQSKEY = "DNASequences"

Variables

var (
    Globals = LHGlobals{
        MIN_REASONABLE_VOLUME_UL: 0.01,
        VOL_RESOLUTION_DIGITS:    2,
    }
)
var InsNames = []string{"END", "MIX", "WAIT", "PROMPT"}

func A1ArrayFromWellCoords Uses

func A1ArrayFromWellCoords(arr []WellCoords) []string

func AutoExportPlateCSV Uses

func AutoExportPlateCSV(outputfilename string, plate *LHPlate) error

func BottomType Uses

func BottomType(well *LHWell) (desc string)

func ChannelWells Uses

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

func ChannelsUsed Uses

func ChannelsUsed(wf []string) []bool

func Comp Uses

func Comp(s string) string

func CompareStringWellCoordsCol Uses

func CompareStringWellCoordsCol(sw1, sw2 string) int

func CompareStringWellCoordsRow Uses

func CompareStringWellCoordsRow(sw1, sw2 string) int

func CompareWellCoordsCol Uses

func CompareWellCoordsCol(w1, w2 WellCoords) int

func CompareWellCoordsRow Uses

func CompareWellCoordsRow(w1, w2 WellCoords) int

func CopyComponentArray Uses

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

func EPSILON_64 Uses

func EPSILON_64() float64

func ErrorDesc Uses

func ErrorDesc(code int) string

func ErrorName Uses

func ErrorName(code int) string

func ExportPlateCSV Uses

func ExportPlateCSV(outputpilename string, plate *LHPlate, platename string, wells []string, liquids []*LHComponent, Volumes []wunit.Volume) error

func FirstIndexInStrArray Uses

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

func GetUUID Uses

func GetUUID() string

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

func IndexOfString Uses

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

func IndexOfStringArray Uses

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

func Initialize_Wells Uses

func Initialize_Wells(plate *LHPlate)

func InsType Uses

func InsType(i int) string

func LHError Uses

func LHError(code int, detail string) error

func LHErrorCodeFromErr Uses

func LHErrorCodeFromErr(err error) int

func LHErrorIsInternal Uses

func LHErrorIsInternal(err error) bool

func MakeWellCoordsArray Uses

func MakeWellCoordsArray(sa []string) []WellCoords

func Makeseq Uses

func Makeseq(dir string, seq BioSequence) string

creates a fasta file containing the sequence

func MatchString Uses

func MatchString(s1, s2 string) bool

func NewMultiIteratorRule Uses

func NewMultiIteratorRule(multi int) func(PlateIterator) []WellCoords

func NewUUID Uses

func NewUUID() string

func Normalize Uses

func Normalize(tx []string) []string

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

func Prefix Uses

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

func Rev Uses

func Rev(s string) string

func RevComp Uses

func RevComp(s string) string

Reverse Complement

func SameLocation Uses

func SameLocation(l, m Location, level int) bool

defines when two locations are the same level = 0 means only the exact same place level = 1 means they share a parent etc

func Suffix Uses

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

func TipsPerWell Uses

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

func TipsWellsAligned Uses

func TipsWellsAligned(prm LHChannelParameter, plt LHPlate, wellsfrom []string) bool

are tips going to align to wells?

func WCArrayFromStrings Uses

func WCArrayFromStrings(arr []string) []WellCoords

type AParam Uses

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

a typed parameter, with description

func (AParam) TypeName Uses

func (alhpi AParam) TypeName() string

type AParamSet Uses

type AParamSet map[string]AParam

func GetLHPolicyOptions Uses

func GetLHPolicyOptions() AParamSet

func GetPolicyConsequents Uses

func GetPolicyConsequents() AParamSet

func MakeInstructionParameters Uses

func MakeInstructionParameters() AParamSet

func MakePolicyItems Uses

func MakePolicyItems() AParamSet

func (AParamSet) CodeForIt Uses

func (alhpis AParamSet) CodeForIt() string

func (AParamSet) OrderedList Uses

func (alhpis AParamSet) OrderedList() []string

func (AParamSet) TypeList Uses

func (alhpis AParamSet) TypeList() string

type Absorbance Uses

type Absorbance struct {
    Reading    float64
    Wavelength float64
    Pathlength wunit.Length
    Status     []string
    Reader     string
}

func (*Absorbance) BlankCorrect Uses

func (sample *Absorbance) BlankCorrect(blank Absorbance)

func (*Absorbance) PathlengthCorrect Uses

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

type AlignedBioSequence Uses

type AlignedBioSequence struct {
    Query   string
    Subject string
    Score   float64
}

type AlignedSequence Uses

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 Uses

func NewAlignedSequence() AlignedSequence

constructor for an AlignedSequence object, makes an empty structure

type BLASTSearchParameters Uses

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

func DefaultBLASTSearchParameters Uses

func DefaultBLASTSearchParameters() BLASTSearchParameters

type BasicPlateIterator Uses

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

func (*BasicPlateIterator) Curr Uses

func (it *BasicPlateIterator) Curr() WellCoords

func (*BasicPlateIterator) Next Uses

func (it *BasicPlateIterator) Next() WellCoords

func (*BasicPlateIterator) Rewind Uses

func (it *BasicPlateIterator) Rewind() WellCoords

func (*BasicPlateIterator) SetCurTo Uses

func (it *BasicPlateIterator) SetCurTo(wc WellCoords)

func (*BasicPlateIterator) SetStartTo Uses

func (it *BasicPlateIterator) SetStartTo(wc WellCoords)

func (*BasicPlateIterator) Valid Uses

func (it *BasicPlateIterator) Valid() bool

type BioSequence Uses

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

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

type BlastHit Uses

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

struct for holding a particular hit

func NewBlastHit Uses

func NewBlastHit() BlastHit

constructor, makes an empty BlastHit structure

type BlastResults Uses

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 Uses

func NewBlastResults() BlastResults

constructor, makes an empty BlastResults structure

type BlockID Uses

type BlockID struct {
    Value string
}

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

func NewBlockID Uses

func NewBlockID(id string) BlockID

func (BlockID) String Uses

func (a BlockID) String() string

type CentrifugeParameters Uses

type CentrifugeParameters map[string]interface{}

type ComponentMatch Uses

type ComponentMatch struct {
    Matches []Match
}

type ComponentVector Uses

type ComponentVector []*LHComponent

func (ComponentVector) Dup Uses

func (cv ComponentVector) Dup() ComponentVector

func (ComponentVector) GetNames Uses

func (cv ComponentVector) GetNames() []string

func (ComponentVector) GetPlateIds Uses

func (cv ComponentVector) GetPlateIds() []string

func (ComponentVector) GetVols Uses

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

func (ComponentVector) GetWellCoords Uses

func (cv ComponentVector) GetWellCoords() []string

func (ComponentVector) String Uses

func (cv ComponentVector) String() string

type ConcreteLocation Uses

type ConcreteLocation struct {
    ID   string
    Inst string
    Name string
    Psns []*ConcreteLocation
    Cntr *ConcreteLocation
    Shap *Shape
}

func (*ConcreteLocation) Container Uses

func (cl *ConcreteLocation) Container() Location

func (*ConcreteLocation) Location_ID Uses

func (cl *ConcreteLocation) Location_ID() string

func (*ConcreteLocation) Location_Name Uses

func (cl *ConcreteLocation) Location_Name() string

func (*ConcreteLocation) Positions Uses

func (cl *ConcreteLocation) Positions() []Location

func (*ConcreteLocation) Shape Uses

func (cl *ConcreteLocation) Shape() *Shape

type ConfigItem Uses

type ConfigItem map[string]interface{}

type Container Uses

type Container interface{} //deferred to the shape

type Coordinates Uses

type Coordinates struct {
    X   float64
    Y   float64
    Z   float64
}

func (Coordinates) Dim Uses

func (a Coordinates) Dim(x int) float64

Value for dimension

type DNA Uses

type DNA struct {
    Seq DNASequence
}

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

type DNASeqSet Uses

type DNASeqSet []*DNASequence

func (DNASeqSet) AsBioSequences Uses

func (dss DNASeqSet) AsBioSequences() []BioSequence

type DNASequence Uses

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 AddFeatures Uses

func AddFeatures(annotated DNASequence, features []Feature) (updated DNASequence)

func Annotate Uses

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

func ConcatenateFeatures Uses

func ConcatenateFeatures(name string, featuresinorder []Feature) (annotated DNASequence)

func MakeDNASequence Uses

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

func MakeLinearDNASequence Uses

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

func MakePlasmidDNASequence Uses

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

func MakeSingleStrandedDNASequence Uses

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

func Phosphorylate Uses

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

func (*DNASequence) Append Uses

func (dna *DNASequence) Append(s string)

func (*DNASequence) Blast Uses

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

func (DNASequence) Dup Uses

func (seq DNASequence) Dup() DNASequence

func (DNASequence) FeatureEnd Uses

func (annotated DNASequence) FeatureEnd(featurename string) (featureEnd int)

func (DNASequence) FeatureNames Uses

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

func (DNASequence) FeatureStart Uses

func (annotated DNASequence) FeatureStart(featurename string) (featureStart int)

func (DNASequence) GetFeatureByName Uses

func (annotated DNASequence) GetFeatureByName(featurename string) (returnedfeature *Feature)

func (*DNASequence) MolecularWeight Uses

func (seq *DNASequence) MolecularWeight() float64

func (*DNASequence) Name Uses

func (dna *DNASequence) Name() string

func (*DNASequence) Prepend Uses

func (dna *DNASequence) Prepend(s string)

func (*DNASequence) ReName Uses

func (dna *DNASequence) ReName(newname string)

func (*DNASequence) Sequence Uses

func (dna *DNASequence) Sequence() string

type ElectroshockParameters Uses

type ElectroshockParameters map[string]interface{}

type Entity Uses

type Entity interface {
    IsEntity() bool
}

type Environment Uses

type Environment struct {
    Temperature         wunit.Temperature
    Pressure            wunit.Pressure
    Humidity            float64
    MeanAirFlowVelocity wunit.Velocity
}

type Enzyme Uses

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

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

type Feature Uses

type Feature struct {
    Name          string `json:"name"`
    Class         string `json:"class	"` //int // 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"`
}

func (*Feature) Coordinates Uses

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 Uses

func (f Feature) DNASequence() DNASequence

type File Uses

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

Representation of a file.

func (File) MarshalJSON Uses

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

func (*File) ReadAll Uses

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

ReadAll returns contents of file.

func (*File) UnmarshalBlob Uses

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

func (*File) UnmarshalJSON Uses

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

func (*File) WriteAll Uses

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

WriteAll replaces contents of file with data.

type FromFactory Uses

type FromFactory struct {
    String string
}

func (*FromFactory) MarshalJSON Uses

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

func (*FromFactory) UnmarshalJSON Uses

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

type Geometry Uses

type Geometry interface {
    Height() wunit.Length
    Width() wunit.Length
    Depth() wunit.Length
}

interface to 3D geometry

type Haswelladdress Uses

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

type LHAdaptor Uses

type LHAdaptor struct {
    Name          string
    ID            string
    Manufacturer  string
    Params        *LHChannelParameter
    Ntipsloaded   int
    Tiptypeloaded *LHTip
}

adaptor TODO -- should be an array of loaded tips

func NewLHAdaptor Uses

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

func (*LHAdaptor) Dup Uses

func (lha *LHAdaptor) Dup() *LHAdaptor

func (*LHAdaptor) GetParams Uses

func (lha *LHAdaptor) GetParams() *LHChannelParameter

func (*LHAdaptor) LoadTips Uses

func (lha *LHAdaptor) LoadTips(n int, tiptype *LHTip) bool

func (*LHAdaptor) UnloadTips Uses

func (lha *LHAdaptor) UnloadTips() bool

type LHCategoryCondition Uses

type LHCategoryCondition struct {
    Category string
}

func (LHCategoryCondition) IsEqualTo Uses

func (lhcc LHCategoryCondition) IsEqualTo(other LHCondition) bool

func (LHCategoryCondition) Match Uses

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

func (LHCategoryCondition) Type Uses

func (lhcc LHCategoryCondition) Type() string

type LHChannelParameter Uses

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 int
    Head        int
}

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

func NewLHChannelParameter Uses

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

func (LHChannelParameter) CanMove Uses

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

func (*LHChannelParameter) Dup Uses

func (lhcp *LHChannelParameter) Dup() *LHChannelParameter

func (LHChannelParameter) GetConstraint Uses

func (lhcp LHChannelParameter) GetConstraint(n int) LHMultiChannelConstraint

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

func (LHChannelParameter) MarshalJSON Uses

func (lhcp LHChannelParameter) MarshalJSON() ([]byte, error)

func (*LHChannelParameter) MergeWithTip Uses

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

func (LHChannelParameter) String Uses

func (lhcp LHChannelParameter) String() string

func (LHChannelParameter) VolumeLimitString Uses

func (lhcp LHChannelParameter) VolumeLimitString() string

type LHComponent Uses

type LHComponent struct {
    ID                 string
    BlockID            BlockID
    DaughterID         string
    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
    Extra              map[string]interface{}
    Loc                string // refactor to PlateLocation
    Destination        string
}

structure describing a liquid component and its desired properties

func NewLHComponent Uses

func NewLHComponent() *LHComponent

func (*LHComponent) AddDNASequence Uses

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

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 (*LHComponent) AddDaughterComponent Uses

func (cmp *LHComponent) AddDaughterComponent(cmp2 *LHComponent)

func (*LHComponent) AddParentComponent Uses

func (cmp *LHComponent) AddParentComponent(cmp2 *LHComponent)

func (*LHComponent) AddPolicy Uses

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

func (*LHComponent) AddVolumeRule Uses

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

func (*LHComponent) CNID Uses

func (lhc *LHComponent) CNID() string

func (*LHComponent) Concentration Uses

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

new

func (*LHComponent) Cp Uses

func (lhc *LHComponent) Cp() *LHComponent

func (*LHComponent) DNASequences Uses

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

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

func (*LHComponent) DeclareInstance Uses

func (lhc *LHComponent) DeclareInstance()

func (*LHComponent) DeclareNotInstance Uses

func (lhc *LHComponent) DeclareNotInstance()

func (*LHComponent) Dup Uses

func (lhc *LHComponent) Dup() *LHComponent

func (*LHComponent) FindDNASequence Uses

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

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 (*LHComponent) Generation Uses

func (lhc *LHComponent) Generation() int

func (*LHComponent) GetConc Uses

func (lhc *LHComponent) GetConc() float64

func (*LHComponent) GetCunit Uses

func (lhc *LHComponent) GetCunit() string

func (*LHComponent) GetExtra Uses

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

func (*LHComponent) GetPolicies Uses

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

func (*LHComponent) GetSmax Uses

func (lhc *LHComponent) GetSmax() float64

func (*LHComponent) GetType Uses

func (lhc *LHComponent) GetType() string

func (*LHComponent) GetVisc Uses

func (lhc *LHComponent) GetVisc() float64

func (*LHComponent) GetVunit Uses

func (lhc *LHComponent) GetVunit() string

func (*LHComponent) HasAnyParent Uses

func (cmp *LHComponent) HasAnyParent() bool

func (*LHComponent) HasConcentration Uses

func (lhc *LHComponent) HasConcentration() bool

func (*LHComponent) HasDaughter Uses

func (lhc *LHComponent) HasDaughter(s string) bool

func (*LHComponent) HasParent Uses

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

func (*LHComponent) IsInstance Uses

func (lhc *LHComponent) IsInstance() bool

func (*LHComponent) IsSameKindAs Uses

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

func (*LHComponent) IsSample Uses

func (cmp *LHComponent) IsSample() bool

func (*LHComponent) IsValuable Uses

func (lhc *LHComponent) IsValuable() bool

func (*LHComponent) IsZero Uses

func (lhc *LHComponent) IsZero() bool

func (*LHComponent) Kind Uses

func (lhc *LHComponent) Kind() string

func (*LHComponent) Mix Uses

func (cmp *LHComponent) Mix(cmp2 *LHComponent)

add cmp2 to cmp

func (*LHComponent) MixPreserveTvol Uses

func (cmp *LHComponent) MixPreserveTvol(cmp2 *LHComponent)

func (*LHComponent) Name Uses

func (lhc *LHComponent) Name() string

func (*LHComponent) ParentTree Uses

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

func (*LHComponent) ParentTreeString Uses

func (cmp *LHComponent) ParentTreeString() string

graphviz format

func (*LHComponent) PlateLocation Uses

func (lhc *LHComponent) PlateLocation() PlateLocation

func (*LHComponent) Remove Uses

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

func (*LHComponent) RemoveDNASequence Uses

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

Removes 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 (*LHComponent) RemoveDNASequenceAtPosition Uses

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

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

func (*LHComponent) RemoveDNASequences Uses

func (lhc *LHComponent) RemoveDNASequences() error

Remove all DNASequences from the component.

func (*LHComponent) ReplaceDaughterID Uses

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

func (*LHComponent) Sample Uses

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

func (*LHComponent) SetConcentration Uses

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

Sets concentration to an LHComponent; assumes conc is valid; overwrites existing concentration

func (*LHComponent) SetGeneration Uses

func (lhc *LHComponent) SetGeneration(i int)

func (*LHComponent) SetPolicies Uses

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

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

func (*LHComponent) SetSample Uses

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

func (*LHComponent) SetValue Uses

func (lhc *LHComponent) SetValue(b bool)

func (*LHComponent) SetVolume Uses

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

func (*LHComponent) String Uses

func (cmp *LHComponent) String() string

func (*LHComponent) TypeName Uses

func (lhc *LHComponent) TypeName() string

func (*LHComponent) UpdateDNASequence Uses

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

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 (*LHComponent) Volume Uses

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

type LHCondition Uses

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

type LHDevice Uses

type LHDevice struct {
    ID   string
    Name string
    Mnfr string
}

func NewLHDevice Uses

func NewLHDevice(name, mfr string) *LHDevice

func (*LHDevice) Dup Uses

func (lhd *LHDevice) Dup() *LHDevice

type LHGlobals Uses

type LHGlobals struct {
    MIN_REASONABLE_VOLUME_UL float64
    VOL_RESOLUTION_DIGITS    int
}

type LHHead Uses

type LHHead struct {
    Name         string
    Manufacturer string
    ID           string
    Adaptor      *LHAdaptor
    Params       *LHChannelParameter
}

head

func NewLHHead Uses

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

func (*LHHead) Dup Uses

func (head *LHHead) Dup() *LHHead

func (*LHHead) GetParams Uses

func (lhh *LHHead) GetParams() *LHChannelParameter

type LHInstruction Uses

type LHInstruction struct {
    ID            string
    ProductID     string
    BlockID       BlockID
    SName         string
    Order         int
    Components    []*LHComponent
    ContainerType string
    Welladdress   string

    Platetype        string
    Vol              float64
    Type             int
    Conc             float64
    Tvol             float64
    Majorlayoutgroup int
    Result           *LHComponent

    PlateName   string
    OutPlate    *LHPlate
    Message     string
    PassThrough map[string]*LHComponent // 1:1 pass through, only applies to prompts
    // contains filtered or unexported fields
}

high-level instruction to a liquid handler

func NewLHMixInstruction Uses

func NewLHMixInstruction() *LHInstruction

func NewLHPromptInstruction Uses

func NewLHPromptInstruction() *LHInstruction

func (*LHInstruction) AddComponent Uses

func (inst *LHInstruction) AddComponent(cmp *LHComponent)

func (*LHInstruction) AddProduct Uses

func (inst *LHInstruction) AddProduct(cmp *LHComponent)

func (*LHInstruction) ComponentsMoving Uses

func (ins *LHInstruction) ComponentsMoving() string

func (*LHInstruction) Generation Uses

func (ins *LHInstruction) Generation() int

func (*LHInstruction) HasAnyParent Uses

func (ins *LHInstruction) HasAnyParent() bool

func (*LHInstruction) HasParent Uses

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

func (*LHInstruction) IsMixInPlace Uses

func (ins *LHInstruction) IsMixInPlace() bool

func (*LHInstruction) ParentString Uses

func (ins *LHInstruction) ParentString() string

func (*LHInstruction) PlateID Uses

func (ins *LHInstruction) PlateID() string

func (*LHInstruction) SetGeneration Uses

func (ins *LHInstruction) SetGeneration(i int)

func (*LHInstruction) SetPlateID Uses

func (ins *LHInstruction) SetPlateID(pid string)

func (*LHInstruction) Wellcoords Uses

func (ins *LHInstruction) Wellcoords() WellCoords

type LHMultiChannelConstraint Uses

type LHMultiChannelConstraint struct {
    X   int
    Y   int
    M   int
}

what constraints apply to adjacent channels

func (LHMultiChannelConstraint) Equals Uses

func (lhmcc LHMultiChannelConstraint) Equals(lhmcc2 LHMultiChannelConstraint) bool

func (LHMultiChannelConstraint) Satisfied Uses

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

func (LHMultiChannelConstraint) SatisfiedV Uses

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

type LHNumericCondition Uses

type LHNumericCondition struct {
    Upper float64
    Lower float64
}

func (LHNumericCondition) IsEqualTo Uses

func (lhnc LHNumericCondition) IsEqualTo(other LHCondition) bool

func (LHNumericCondition) Match Uses

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

func (LHNumericCondition) Type Uses

func (lhnc LHNumericCondition) Type() string

type LHPlate Uses

type LHPlate 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
    Height      float64            // plate height (unit below)
    Hunit       string             // unit of plate height
    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
}

structure describing a microplate

func NewLHPlate Uses

func NewLHPlate(platetype, mfr string, nrows, ncols int, height float64, hunit string, welltype *LHWell, wellXOffset, wellYOffset, wellXStart, wellYStart, wellZStart float64) *LHPlate

func New_Plate Uses

func New_Plate(platetype *LHPlate) *LHPlate

func (*LHPlate) AddComponent Uses

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

func (*LHPlate) AllNonEmptyWells Uses

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

func (*LHPlate) AllWellPositions Uses

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

func (*LHPlate) BetterGetComponent Uses

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

this gets ONE component... possibly from several wells

func (*LHPlate) DeclareAutoallocated Uses

func (p *LHPlate) DeclareAutoallocated()

func (*LHPlate) DeclareSpecial Uses

func (p *LHPlate) DeclareSpecial()

func (*LHPlate) DeclareTemporary Uses

func (p *LHPlate) DeclareTemporary()

func (*LHPlate) Dup Uses

func (lhp *LHPlate) Dup() *LHPlate

func (*LHPlate) DupKeepIDs Uses

func (lhp *LHPlate) DupKeepIDs() *LHPlate

func (*LHPlate) Empty Uses

func (lhp *LHPlate) Empty() bool

func (*LHPlate) Evaporate Uses

func (p *LHPlate) Evaporate(time time.Duration, env Environment) []VolumeCorrection

func (*LHPlate) FindAndUpdateID Uses

func (p *LHPlate) FindAndUpdateID(before string, after *LHComponent) bool

func (*LHPlate) FindComponentsMulti Uses

func (lhp *LHPlate) FindComponentsMulti(cmps ComponentVector, ori, multi int, independent bool) (plateIDs, wellCoords [][]string, vols [][]wunit.Volume, err error)

func (*LHPlate) GetA1WellCoordsFromOrdering Uses

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

func (*LHPlate) GetComponent Uses

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

func (*LHPlate) GetContentVector Uses

func (lhp *LHPlate) GetContentVector(wv []WellCoords) ComponentVector

func (*LHPlate) GetName Uses

func (lhp *LHPlate) GetName() string

func (*LHPlate) GetOrderingFromA1WellCoords Uses

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

func (*LHPlate) GetOrderingFromWellCoords Uses

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

func (*LHPlate) GetWellCoordsFromOrdering Uses

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

func (*LHPlate) IsAutoallocated Uses

func (p *LHPlate) IsAutoallocated() bool

func (*LHPlate) IsConstrainedOn Uses

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

func (*LHPlate) IsSpecial Uses

func (p *LHPlate) IsSpecial() bool

func (*LHPlate) IsTemporary Uses

func (p *LHPlate) IsTemporary() bool

func (*LHPlate) IsUserAllocated Uses

func (p *LHPlate) IsUserAllocated() bool

func (*LHPlate) MarkNonEmptyWellsUserAllocated Uses

func (p *LHPlate) MarkNonEmptyWellsUserAllocated()

func (*LHPlate) MergeWith Uses

func (p *LHPlate) MergeWith(p2 *LHPlate)

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

func (LHPlate) Name Uses

func (lhp LHPlate) Name() string

func (*LHPlate) NextEmptyWell Uses

func (lhp *LHPlate) NextEmptyWell(it PlateIterator) WellCoords

func (*LHPlate) NumCols Uses

func (p *LHPlate) NumCols() int

func (*LHPlate) NumRows Uses

func (p *LHPlate) NumRows() int

func (LHPlate) OutputLayout Uses

func (plate LHPlate) OutputLayout()

func (*LHPlate) PlateHeight Uses

func (p *LHPlate) PlateHeight() float64

func (*LHPlate) ProtectAllWells Uses

func (p *LHPlate) ProtectAllWells()

func (*LHPlate) RemoveComponent Uses

func (p *LHPlate) RemoveComponent(well string, vol wunit.Volume) *LHComponent

func (*LHPlate) ResetID Uses

func (p *LHPlate) ResetID(newID string)

func (*LHPlate) SetConstrained Uses

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

func (LHPlate) String Uses

func (lhp LHPlate) String() string

func (*LHPlate) UnProtectAllWells Uses

func (p *LHPlate) UnProtectAllWells()

func (*LHPlate) WellAt Uses

func (lhp *LHPlate) WellAt(wc WellCoords) *LHWell

func (*LHPlate) WellAtString Uses

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

func (*LHPlate) WellMap Uses

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

func (*LHPlate) Welldimensions Uses

func (plate *LHPlate) Welldimensions() *LHWellType

func (*LHPlate) Wells Uses

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

func (*LHPlate) WellsX Uses

func (lhp *LHPlate) WellsX() int

func (*LHPlate) WellsY Uses

func (lhp *LHPlate) WellsY() int

type LHPolicy Uses

type LHPolicy map[string]interface{}

this structure defines parameters

func DupLHPolicy Uses

func DupLHPolicy(in LHPolicy) LHPolicy

func NewLHPolicy Uses

func NewLHPolicy() LHPolicy

func (LHPolicy) IsEqualTo Uses

func (lhp LHPolicy) IsEqualTo(lh2 LHPolicy) bool

func (LHPolicy) MergeWith Uses

func (lhp LHPolicy) MergeWith(other LHPolicy) LHPolicy

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

func (*LHPolicy) Set Uses

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

func (*LHPolicy) UnmarshalJSON Uses

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

type LHPolicyRule Uses

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 Uses

func NewLHPolicyRule(name string) LHPolicyRule

func (*LHPolicyRule) AddCategoryConditionOn Uses

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

func (*LHPolicyRule) AddNumericConditionOn Uses

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

func (LHPolicyRule) HasCondition Uses

func (lhpr LHPolicyRule) HasCondition(cond LHVariableCondition) bool

func (LHPolicyRule) IsEqualTo Uses

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 Uses

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

func CloneLHPolicyRuleSet Uses

func CloneLHPolicyRuleSet(parent *LHPolicyRuleSet) *LHPolicyRuleSet

func NewLHPolicyRuleSet Uses

func NewLHPolicyRuleSet() *LHPolicyRuleSet

func (*LHPolicyRuleSet) AddRule Uses

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

func (LHPolicyRuleSet) GetEquivalentRuleTo Uses

func (lhpr LHPolicyRuleSet) GetEquivalentRuleTo(rule LHPolicyRule) string

func (*LHPolicyRuleSet) IsEqualTo Uses

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

func (*LHPolicyRuleSet) MergeWith Uses

func (lhpr *LHPolicyRuleSet) MergeWith(other *LHPolicyRuleSet)

func (*LHPolicyRuleSet) SetOption Uses

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

type LHPosition Uses

type LHPosition struct {
    ID    string
    Name  string
    Num   int
    Extra []LHDevice
    Maxh  float64
}

describes a position on the liquid handling deck and its current state

func NewLHPosition Uses

func NewLHPosition(position_number int, name string, maxh float64) *LHPosition

func (*LHPosition) Container Uses

func (lhp *LHPosition) Container() Location

func (*LHPosition) Location_ID Uses

func (lhp *LHPosition) Location_ID() string

func (*LHPosition) Location_Name Uses

func (lhp *LHPosition) Location_Name() string

func (*LHPosition) Positions Uses

func (lhp *LHPosition) Positions() []Location

func (*LHPosition) Shape Uses

func (lhp *LHPosition) Shape() *Shape

type LHSolution Uses

type LHSolution struct {
    ID               string
    BlockID          BlockID
    Inst             string
    SName            string
    Order            int
    Components       []*LHComponent
    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 Uses

func NewLHSolution() *LHSolution

func New_Solution Uses

func New_Solution() *LHSolution

func (*LHSolution) GetAssignment Uses

func (lhs *LHSolution) GetAssignment() string

func (LHSolution) GetComponentVolume Uses

func (sol LHSolution) GetComponentVolume(key string) float64

func (LHSolution) String Uses

func (sol LHSolution) String() string

type LHTip Uses

type LHTip struct {
    ID     string
    Type   string
    Mnfr   string
    Dirty  bool
    MaxVol wunit.Volume
    MinVol wunit.Volume
}

TODO add extra properties, i.e. filter

func CopyTip Uses

func CopyTip(tt LHTip) *LHTip

func NewLHTip Uses

func NewLHTip(mfr, ttype string, minvol, maxvol float64, volunit string) *LHTip

func (*LHTip) Dup Uses

func (tip *LHTip) Dup() *LHTip

func (*LHTip) GetParams Uses

func (tip *LHTip) GetParams() *LHChannelParameter

func (*LHTip) IsNil Uses

func (tip *LHTip) IsNil() bool

type LHTipbox Uses

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
    TipXOffset float64
    TipYOffset float64
    TipXStart  float64
    TipYStart  float64
    TipZStart  float64
}

func NewLHTipbox Uses

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

func (*LHTipbox) Dup Uses

func (tb *LHTipbox) Dup() *LHTipbox

lazy sunuva

func (*LHTipbox) GetName Uses

func (tb *LHTipbox) GetName() string

func (*LHTipbox) GetTips Uses

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

func (*LHTipbox) N_clean_tips Uses

func (tb *LHTipbox) N_clean_tips() int

func (*LHTipbox) NumCols Uses

func (tipbox *LHTipbox) NumCols() int

func (*LHTipbox) NumRows Uses

func (tipbox *LHTipbox) NumRows() int

func (*LHTipbox) PlateHeight Uses

func (tipbox *LHTipbox) PlateHeight() float64

func (*LHTipbox) Refill Uses

func (tb *LHTipbox) Refill()

func (*LHTipbox) Refresh Uses

func (tb *LHTipbox) Refresh()

func (LHTipbox) String Uses

func (tb LHTipbox) String() string

type LHTipwaste Uses

type LHTipwaste struct {
    ID         string
    Type       string
    Mnfr       string
    Capacity   int
    Contents   int
    Height     float64
    WellXStart float64
    WellYStart float64
    WellZStart float64
    AsWell     *LHWell
}

func NewLHTipwaste Uses

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

func (*LHTipwaste) Dispose Uses

func (lht *LHTipwaste) Dispose(n int) bool

func (*LHTipwaste) Dup Uses

func (tw *LHTipwaste) Dup() *LHTipwaste

func (*LHTipwaste) Empty Uses

func (lht *LHTipwaste) Empty()

func (*LHTipwaste) GetName Uses

func (tw *LHTipwaste) GetName() string

func (*LHTipwaste) NumCols Uses

func (lht *LHTipwaste) NumCols() int

func (*LHTipwaste) NumRows Uses

func (lht *LHTipwaste) NumRows() int

func (*LHTipwaste) PlateHeight Uses

func (lht *LHTipwaste) PlateHeight() float64

func (LHTipwaste) SpaceLeft Uses

func (tw LHTipwaste) SpaceLeft() int

func (LHTipwaste) String Uses

func (te LHTipwaste) String() string

type LHVariableCondition Uses

type LHVariableCondition struct {
    TestVariable string
    Condition    LHCondition
}

func NewLHVariableCondition Uses

func NewLHVariableCondition(testvariable string) LHVariableCondition

func (LHVariableCondition) IsEqualTo Uses

func (lhvc LHVariableCondition) IsEqualTo(other LHVariableCondition) bool

func (*LHVariableCondition) SetCategoric Uses

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

func (*LHVariableCondition) SetNumeric Uses

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

func (*LHVariableCondition) UnmarshalJSON Uses

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

type LHWell Uses

type LHWell struct {
    ID        string
    Inst      string
    Plateinst string
    Plateid   string
    Platetype string
    Crds      string
    MaxVol    float64
    Vunit     string
    WContents *LHComponent
    Rvol      float64
    WShape    *Shape
    Bottom    int
    Xdim      float64
    Ydim      float64
    Zdim      float64
    Bottomh   float64
    Dunit     string
    Extra     map[string]interface{}
    Plate     *LHPlate `gotopb:"-" json:"-"`
}

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

func Get_Next_Well Uses

func Get_Next_Well(plate *LHPlate, component *LHComponent, curwell *LHWell) (*LHWell, bool)

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

func NewLHWell Uses

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

make a new well structure

func (*LHWell) Add Uses

func (w *LHWell) Add(c *LHComponent)

func (*LHWell) AddDimensions Uses

func (w *LHWell) AddDimensions(lhwt *LHWellType)

func (*LHWell) AreaForVolume Uses

func (lhw *LHWell) AreaForVolume() wunit.Area

func (*LHWell) CDup Uses

func (lhw *LHWell) CDup() *LHWell

copy of type

func (*LHWell) CalculateMaxCrossSectionArea Uses

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

func (*LHWell) CalculateMaxVolume Uses

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

func (*LHWell) Clear Uses

func (w *LHWell) Clear()

func (*LHWell) ClearUserAllocated Uses

func (w *LHWell) ClearUserAllocated()

func (*LHWell) ContainerType Uses

func (w *LHWell) ContainerType() string

func (*LHWell) Contains Uses

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

func (*LHWell) Contents Uses

func (w *LHWell) Contents() *LHComponent

func (*LHWell) CurrVolume Uses

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

func (*LHWell) CurrentVolume Uses

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

func (*LHWell) Currvol Uses

func (w *LHWell) Currvol() float64

func (*LHWell) DeclareAutoallocated Uses

func (well *LHWell) DeclareAutoallocated()

func (*LHWell) DeclareNotAutoallocated Uses

func (well *LHWell) DeclareNotAutoallocated()

func (*LHWell) DeclareNotTemporary Uses

func (well *LHWell) DeclareNotTemporary()

func (*LHWell) DeclareTemporary Uses

func (well *LHWell) DeclareTemporary()

func (*LHWell) Dup Uses

func (lhw *LHWell) Dup() *LHWell

copy of instance

func (*LHWell) DupKeepIDs Uses

func (lhw *LHWell) DupKeepIDs() *LHWell

func (*LHWell) Empty Uses

func (w *LHWell) Empty() bool

func (*LHWell) Evaporate Uses

func (well *LHWell) Evaporate(time time.Duration, env Environment) VolumeCorrection

func (*LHWell) GetAfVFunc Uses

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

func (*LHWell) HeightForVolume Uses

func (lhw *LHWell) HeightForVolume() wunit.Length

func (*LHWell) IsAutoallocated Uses

func (well *LHWell) IsAutoallocated() bool

func (*LHWell) IsTemporary Uses

func (well *LHWell) IsTemporary() bool

func (*LHWell) IsUserAllocated Uses

func (w *LHWell) IsUserAllocated() bool

func (*LHWell) Location_ID Uses

func (lhw *LHWell) Location_ID() string

func (*LHWell) Location_Name Uses

func (lhw *LHWell) Location_Name() string

func (*LHWell) MaxVolume Uses

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

func (*LHWell) PlateLocation Uses

func (w *LHWell) PlateLocation() PlateLocation

func (*LHWell) Protect Uses

func (w *LHWell) Protect()

func (*LHWell) Protected Uses

func (w *LHWell) Protected() bool

func (*LHWell) Remove Uses

func (w *LHWell) Remove(v wunit.Volume) *LHComponent

func (*LHWell) ResetPlateID Uses

func (w *LHWell) ResetPlateID(newID string)

func (*LHWell) ResidualVolume Uses

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

func (*LHWell) SetAfVFunc Uses

func (lhw *LHWell) SetAfVFunc(f string)

func (*LHWell) SetUserAllocated Uses

func (w *LHWell) SetUserAllocated()

func (*LHWell) Shape Uses

func (lhw *LHWell) Shape() *Shape

func (LHWell) String Uses

func (w LHWell) String() string

func (*LHWell) UnProtect Uses

func (w *LHWell) UnProtect()

func (*LHWell) UpdateContentID Uses

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

func (*LHWell) WorkingVolume Uses

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

type LHWellType Uses

type LHWellType struct {
    Vol       float64
    Vunit     string
    Rvol      float64
    ShapeName string
    Bottom    int
    Xdim      float64
    Ydim      float64
    Zdim      float64
    Bottomh   float64
    Dunit     string
}

type LiquidType Uses

type LiquidType int
const (
    LTNIL LiquidType = iota
    LTWater
    LTDefault
    LTGlycerol
    LTEthanol
    LTDetergent
    LTCulture
    LTProtein
    LTDNA
    LTload
    LTDoNotMix
    LTloadwater
    LTNeedToMix
    LTPreMix
    LTPostMix
    LTVISCOUS
    LTPAINT
    LTDISPENSEABOVE
    LTPEG
    LTProtoplasts
    LTCulutureReuse
    LTDNAMIX
    LTPLATEOUT
    LTCOLONY
    LTCOLONYMIX
    LTDNACELLSMIX
    LTMultiWater
    LTCSrc
    LTNSrc
    LTMegaMix
    LTSolvent
)

func LiquidTypeFromString Uses

func LiquidTypeFromString(s PolicyName) (LiquidType, error)

func (LiquidType) String Uses

func (l LiquidType) String() PolicyName

type Location Uses

type Location interface {
    Location_ID() string
    Location_Name() string
    Positions() []Location
    Container() Location
    Shape() *Shape
}

a Location is somewhere something can be it can recursively contain other Locations

func NewLocation Uses

func NewLocation(name string, nPositions int, shape *Shape) Location

type Match Uses

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
}

type Movable Uses

type Movable interface{} //Entity

type MultiPlateIterator Uses

type MultiPlateIterator struct {
    BasicPlateIterator
    // contains filtered or unexported fields
}

func (*MultiPlateIterator) Curr Uses

func (mpi *MultiPlateIterator) Curr() []WellCoords

func (*MultiPlateIterator) Next Uses

func (mpi *MultiPlateIterator) Next() []WellCoords

func (*MultiPlateIterator) Rewind Uses

func (mpi *MultiPlateIterator) Rewind() []WellCoords

func (*MultiPlateIterator) Valid Uses

func (mpi *MultiPlateIterator) Valid() bool

type Named Uses

type Named interface {
    GetName() string
}

type Organism Uses

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 Overhang Uses

type Overhang struct {
    //Strand          int // i.e. 1 or 2 (top or bottom
    End             int    `json:"end"`  // i.e. 5 or 3 or 0
    Type            int    `json:"type"` //as contants above
    Length          int    `json:"length"`
    Sequence        string `json:"sequence"`
    Phosphorylation bool   `json:"phosphorylation"`
}

func MakeOverhang Uses

func MakeOverhang(sequence DNASequence, end int, toporbottom int, length int, phosphorylated bool) (overhang Overhang, err error)

func (Overhang) OverHangAt3PrimeEnd Uses

func (oh Overhang) OverHangAt3PrimeEnd() (sequence string)

func (Overhang) OverHangAt5PrimeEnd Uses

func (oh Overhang) OverHangAt5PrimeEnd() (sequence string)

type Plasmid Uses

type Plasmid struct {
}

defines a plasmid

type PlateIterator Uses

type PlateIterator interface {
    Rewind() WellCoords
    Next() WellCoords
    Curr() WellCoords
    Valid() bool
    SetStartTo(WellCoords)
    SetCurTo(WellCoords)
}

func NewColumnWiseIterator Uses

func NewColumnWiseIterator(p *LHPlate) PlateIterator

func NewOneTimeColumnWiseIterator Uses

func NewOneTimeColumnWiseIterator(p *LHPlate) PlateIterator

func NewOneTimeRowWiseIterator Uses

func NewOneTimeRowWiseIterator(p *LHPlate) PlateIterator

func NewRowWiseIterator Uses

func NewRowWiseIterator(p *LHPlate) PlateIterator

type PlateLocation Uses

type PlateLocation struct {
    ID     string
    Coords WellCoords
}

func PlateLocationFromString Uses

func PlateLocationFromString(s string) PlateLocation

func ZeroPlateLocation Uses

func ZeroPlateLocation() PlateLocation

func (PlateLocation) Equals Uses

func (pc PlateLocation) Equals(opc PlateLocation) bool

func (PlateLocation) IsZero Uses

func (pc PlateLocation) IsZero() bool

func (PlateLocation) ToString Uses

func (pc PlateLocation) ToString() string

type Platedestmap Uses

type Platedestmap [][][]*LHInstruction

func NewPlatedestmap Uses

func NewPlatedestmap() Platedestmap

func (Platedestmap) Print Uses

func (pdm Platedestmap) Print()

type PolicyName Uses

type PolicyName string

func LiquidTypeName Uses

func LiquidTypeName(lt LiquidType) PolicyName

func PolicyNameFromString Uses

func PolicyNameFromString(s string) PolicyName

func (PolicyName) String Uses

func (l PolicyName) String() string

type Population Uses

type Population struct {
}

a set of organisms, can be mixed or homogeneous

type Protein Uses

type Protein struct {
    Seq ProteinSequence
}

physical protein sample has a ProteinSequence

type ProteinSequence Uses

type ProteinSequence struct {
    Nm  string
    Seq string
}

ProteinSequence object is a type of Biosequence

func (*ProteinSequence) Append Uses

func (prot *ProteinSequence) Append(s string)

func (*ProteinSequence) Blast Uses

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

func (*ProteinSequence) Molecularweight Uses

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

Estimate molecular weight of protein product

func (*ProteinSequence) Name Uses

func (prot *ProteinSequence) Name() string

func (*ProteinSequence) Prepend Uses

func (prot *ProteinSequence) Prepend(s string)

func (*ProteinSequence) Sequence Uses

func (prot *ProteinSequence) Sequence() string

type RNA Uses

type RNA struct {
    Seq RNASequence
}

RNA sample: physical RNA, has an RNASequence object

type RNASequence Uses

type RNASequence struct {
    Nm  string
    Seq string
}

RNASequence object is a type of Biosequence

func (*RNASequence) Append Uses

func (rna *RNASequence) Append(s string)

func (*RNASequence) Blast Uses

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

func (*RNASequence) Name Uses

func (rna *RNASequence) Name() string

func (*RNASequence) Prepend Uses

func (rna *RNASequence) Prepend(s string)

func (*RNASequence) Sequence Uses

func (rna *RNASequence) Sequence() string

type Rational Uses

type Rational struct {
    N   int
    D   int
}

type ReadEMParameters Uses

type ReadEMParameters map[string]interface{}

type Reading Uses

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

type RestrictionEnzyme Uses

type RestrictionEnzyme struct {
    // other fields required but for now the main things are...
    RecognitionSequence               string
    EndLength                         int
    Name                              string
    Prototype                         string
    Topstrand3primedistancefromend    int
    Bottomstrand5primedistancefromend int
    MethylationSite                   string   //"attr, <4>"
    CommercialSource                  []string //string "attr, <5>"
    References                        []int
    Class                             string
}

type SBSLabware Uses

type SBSLabware interface {
    NumRows() int
    NumCols() int
    PlateHeight() float64
}

type SLHPlate Uses

type SLHPlate struct {
    ID             string
    Inst           string
    Loc            string
    Name           string
    Type           string
    Mnfr           string
    WellsX         int
    WellsY         int
    Nwells         int
    Height         float64
    Hunit          string
    Welltype       *LHWell
    Wellcoords     map[string]*LHWell
    Welldimensions *LHWellType
}

serializable, stripped-down version of the LHPlate

func (SLHPlate) FillPlate Uses

func (slhp SLHPlate) FillPlate(plate *LHPlate)

type SLHWell Uses

type SLHWell struct {
    ID        string
    Inst      string
    Plateinst string
    Plateid   string
    Coords    string
    Contents  *LHComponent
}

func (SLHWell) FillWell Uses

func (slw SLHWell) FillWell(lw *LHWell)

type SequenceDatabase Uses

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

type Shape Uses

type Shape struct {
    ShapeName  string
    LengthUnit string
    H          float64
    W          float64
    D          float64
}

func NewNilShape Uses

func NewNilShape() *Shape

func NewShape Uses

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

func (*Shape) Depth Uses

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

func (*Shape) Dup Uses

func (sh *Shape) Dup() *Shape

func (*Shape) Height Uses

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

func (*Shape) IsZero Uses

func (sh *Shape) IsZero() bool

func (*Shape) MaxCrossSectionalArea Uses

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

func (*Shape) Volume Uses

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

func (*Shape) Width Uses

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

type SortableRules Uses

type SortableRules []LHPolicyRule

func (SortableRules) Len Uses

func (s SortableRules) Len() int

func (SortableRules) Less Uses

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

func (SortableRules) Swap Uses

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

type Suspension Uses

type Suspension struct {
}

type TOL Uses

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 Uses

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

read the data from the opentree file

func (TOL) Find_string Uses

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

find a node by name

func (TOL) Get_taxonomy Uses

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

extract the lineage of one particular node

func (TOL) IsAncestorOf Uses

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

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

type Ticker Uses

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

func (*Ticker) Dup Uses

func (t *Ticker) Dup() *Ticker

func (*Ticker) Tick Uses

func (t *Ticker) Tick() int

type TickingColVectorIterator Uses

type TickingColVectorIterator struct {
    Plate  *LHPlate
    Multi  int
    Ticker *Ticker
    // contains filtered or unexported fields
}

still an issue with this generating out-of-bounds wells in single mode?!

func (*TickingColVectorIterator) Curr Uses

func (tcvi *TickingColVectorIterator) Curr() []WellCoords

func (*TickingColVectorIterator) Next Uses

func (tcvi *TickingColVectorIterator) Next() []WellCoords

func (*TickingColVectorIterator) Rewind Uses

func (tcvi *TickingColVectorIterator) Rewind() []WellCoords

func (*TickingColVectorIterator) SetCurTo Uses

func (tcvi *TickingColVectorIterator) SetCurTo(wc WellCoords)

func (*TickingColVectorIterator) SetStartTo Uses

func (tcvi *TickingColVectorIterator) SetStartTo(wc WellCoords)

func (*TickingColVectorIterator) Valid Uses

func (tcvi *TickingColVectorIterator) Valid() bool

type TypeIIs Uses

type TypeIIs struct {
    RestrictionEnzyme
    Name                              string
    Isoschizomers                     []string
    Topstrand3primedistancefromend    int
    Bottomstrand5primedistancefromend int
}

func ToTypeIIs Uses

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

type VectorPlateIterator Uses

type VectorPlateIterator interface {
    Rewind() []WellCoords
    Next() []WellCoords
    Curr() []WellCoords
    Valid() bool
    SetStartTo(WellCoords)
    SetCurTo(WellCoords)
}

func NewColVectorIterator Uses

func NewColVectorIterator(p *LHPlate, multi int) VectorPlateIterator

func NewRowVectorIterator Uses

func NewRowVectorIterator(p *LHPlate, multi int) VectorPlateIterator

func NewTickingColVectorIterator Uses

func NewTickingColVectorIterator(p *LHPlate, multi, tpw, wpt int) VectorPlateIterator

type VolumeCorrection Uses

type VolumeCorrection struct {
    Type     string
    Volume   wunit.Volume
    Location string // refactor point: location strings to types
}

type Warning Uses

type Warning string

Representation of a non fatal error in Antha which implements the golang error interface.

func NewWarning Uses

func NewWarning(s string) Warning

generate a new Warning

func (Warning) Error Uses

func (w Warning) Error() string

type WellCoordArrayCol Uses

type WellCoordArrayCol []WellCoords

func (WellCoordArrayCol) Len Uses

func (wca WellCoordArrayCol) Len() int

func (WellCoordArrayCol) Less Uses

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

func (WellCoordArrayCol) Swap Uses

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

type WellCoordArrayRow Uses

type WellCoordArrayRow []WellCoords

func (WellCoordArrayRow) Len Uses

func (wca WellCoordArrayRow) Len() int

func (WellCoordArrayRow) Less Uses

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

func (WellCoordArrayRow) Swap Uses

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

type WellCoords Uses

type WellCoords struct {
    X   int
    Y   int
}

convenience structure for handling well coordinates

func AlongOneRow Uses

func AlongOneRow(wc WellCoords, p *LHPlate) WellCoords

func DownOneColumn Uses

func DownOneColumn(wc WellCoords, p *LHPlate) WellCoords

func MakeWellCoords Uses

func MakeWellCoords(wc string) WellCoords

func MakeWellCoords1A Uses

func MakeWellCoords1A(a1 string) WellCoords

make well coordinates in the "1A" convention

func MakeWellCoordsA1 Uses

func MakeWellCoordsA1(a1 string) WellCoords

make well coordinates in the "A1" convention

func MakeWellCoordsXY Uses

func MakeWellCoordsXY(xy string) WellCoords

func MakeWellCoordsXYsep Uses

func MakeWellCoordsXYsep(x, y string) WellCoords

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

func NextInColumn Uses

func NextInColumn(wc WellCoords, p *LHPlate) WellCoords

func NextInColumnOnce Uses

func NextInColumnOnce(wc WellCoords, p *LHPlate) WellCoords

func NextInRow Uses

func NextInRow(wc WellCoords, p *LHPlate) WellCoords

func NextInRowOnce Uses

func NextInRowOnce(wc WellCoords, p *LHPlate) WellCoords

func ZeroWellCoords Uses

func ZeroWellCoords() WellCoords

func (WellCoords) ColLessThan Uses

func (wc WellCoords) ColLessThan(wc2 WellCoords) bool

func (WellCoords) ColNumString Uses

func (wc WellCoords) ColNumString() string

func (WellCoords) Equals Uses

func (wc WellCoords) Equals(w2 WellCoords) bool

func (WellCoords) Format1A Uses

func (wc WellCoords) Format1A() string

func (WellCoords) FormatA1 Uses

func (wc WellCoords) FormatA1() string

func (WellCoords) FormatXY Uses

func (wc WellCoords) FormatXY() string

return well coordinates in "X1Y1" format

func (WellCoords) IsZero Uses

func (wc WellCoords) IsZero() bool

func (WellCoords) RowLessThan Uses

func (wc WellCoords) RowLessThan(wc2 WellCoords) bool

func (WellCoords) RowLettString Uses

func (wc WellCoords) RowLettString() string

func (WellCoords) WellNumber Uses

func (wc WellCoords) WellNumber() int

Directories

PathSynopsis
liquidtypePackage for converting liquidtypes from design files

Package wtype imports 26 packages (graph) and is imported by 45 packages. Updated 2017-09-21. Refresh now. Tools for package owners.