prep

package

v1.0.0 Latest Latest Go to latest Published: Jan 20, 2026 License: MIT Imports: 25 Imported by: 0

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Valid go.mod file
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Repository

github.com/jsdoublel/camus

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Documentation ¶

Overview ¶

Package used for preprocessing necessary data for the CAMUS algorithm

Index ¶

Variables
func ConvertToNetwork(ntw *tree.Tree) (network *gr.Network, err error)
func NetworkIsBinary(ntw *tree.Tree) bool
func Preprocess(tre *tree.Tree, geneTrees []*tree.Tree, nprocs int, opts QuartetFilterOptions, ...) (*gr.TreeData, error)
func TreeIsBinary(tre *tree.Tree) bool
func WriteDPResultsToCSV(td *gr.TreeData, newicks []string, qsat []float64, w io.Writer) (err error)
func WriteResultsLineplot(qstat []float64, prefix string) error
func WriteRetScoresToCSV(scores []*map[string]float64, names []string) error
type Format
- func (f *Format) Set(s string) error
- func (f Format) String() string
type GeneTrees
- func ReadInputFiles(treeFile, genetreesFile string, format Format) (*tree.Tree, *GeneTrees, error)
type QMode
- func (mode *QMode) Set(n int) error
- func (mode QMode) String() string
type QuartetFilterOptions
- func SetQuartetFilterOptions(mode int, threshold float64) (QuartetFilterOptions, error)
- func (opts QuartetFilterOptions) QuartetFilterOff() bool
type Threshold

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	ErrInvalidFile     = errors.New("invalid file")
	ErrInvalidFormat   = errors.New("invalid format")
	ErrNoReticulations = errors.New("no reticulations")
	ErrWritingFile     = errors.New("error writing file")
)

View Source

var (
	ErrUnrooted     = errors.New("not rooted")
	ErrNonBinary    = errors.New("not binary")
	ErrMulTree      = errors.New("contains duplicate labels")
	ErrTypeOutRange = errors.New("out of type range")
)

View Source

var ParseFormat = map[string]Format{
	"newick": Newick,
	"nexus":  Nexus,
}

Functions ¶

func ConvertToNetwork ¶

func ConvertToNetwork(ntw *tree.Tree) (network *gr.Network, err error)

Read in extended newick file and make network

func NetworkIsBinary ¶

func NetworkIsBinary(ntw *tree.Tree) bool

func Preprocess ¶

func Preprocess(tre *tree.Tree, geneTrees []*tree.Tree, nprocs int, opts QuartetFilterOptions, minSupp float64) (*gr.TreeData, error)

Preprocess necessary data. Returns an error if the constraint tree is not valid (e.g., not rooted/binary) or if the gene trees are not valid (bad leaf labels).

func TreeIsBinary ¶

func TreeIsBinary(tre *tree.Tree) bool

func WriteDPResultsToCSV ¶ added in v0.8.0

func WriteDPResultsToCSV(td *gr.TreeData, newicks []string, qsat []float64, w io.Writer) (err error)

Write DP results csv file to writer.

There are three columns: "Number of Branches", "Quartet Satisfied Percent", "Extended Newick"

func WriteResultsLineplot ¶ added in v0.8.0

func WriteResultsLineplot(qstat []float64, prefix string) error

func WriteRetScoresToCSV ¶

func WriteRetScoresToCSV(scores []*map[string]float64, names []string) error

Write csv file containing reticulation branch scores to stdout

Types ¶

type Format ¶

type Format int

const (
	Newick Format = iota
	Nexus
)

func (*Format) Set ¶

func (f *Format) Set(s string) error

func (Format) String ¶

func (f Format) String() string

type GeneTrees ¶

type GeneTrees struct {
	Trees []*tree.Tree // gene trees
	Names []string     // gene names
}

func ReadInputFiles ¶

func ReadInputFiles(treeFile, genetreesFile string, format Format) (*tree.Tree, *GeneTrees, error)

Reads in and validates constraint tree and gene tree input files. Returns an error if the newick format is invalid, or the file is invalid for some other reason (e.g., more than one constraint tree)

type QMode ¶

type QMode int

const (
	NonRestrictive QMode = iota + 1
	Restrictive
)

func (*QMode) Set ¶

func (mode *QMode) Set(n int) error

func (QMode) String ¶

func (mode QMode) String() string

type QuartetFilterOptions ¶ added in v0.4.1

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

Options for quartet filter mode

func SetQuartetFilterOptions ¶ added in v0.4.1

func SetQuartetFilterOptions(mode int, threshold float64) (QuartetFilterOptions, error)

func (QuartetFilterOptions) QuartetFilterOff ¶ added in v0.4.1

func (opts QuartetFilterOptions) QuartetFilterOff() bool

type Threshold ¶ added in v0.4.1

type Threshold float64

func (Threshold) Keep ¶ added in v0.4.1

func (thresh Threshold) Keep(counts []uint32) bool

func (*Threshold) Set ¶ added in v0.4.1

func (thresh *Threshold) Set(n float64) error

func (Threshold) String ¶ added in v0.4.1

func (thresh Threshold) String() string

Source Files ¶

View all Source files

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