Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

https://github.com/kussell-lab/mcorr
23 January 2022, 09:11:33 UTC
  • Code
  • Branches (5)
  • Releases (0)
  • Visits
    • Branches
    • Releases
    • HEAD
    • refs/heads/2019natmethods
    • refs/heads/2021biorxiv
    • refs/heads/dev
    • refs/heads/master
    • refs/heads/x
    No releases to show
  • ffcddc8
  • /
  • collector.go
Raw File Download
Take a new snapshot of a software origin

If the archived software origin currently browsed is not synchronized with its upstream version (for instance when new commits have been issued), you can explicitly request Software Heritage to take a new snapshot of it.

Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.
swh spinner

Processing "take a new snapshot" request ...

Permalinks

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
  • revision
  • snapshot
origin badgecontent badge Iframe embedding
swh:1:cnt:4a80b8a94dd4894facc2b994b8e91edee786d9f8
origin badgedirectory badge Iframe embedding
swh:1:dir:ffcddc89ba2c0f13614ac49f75a9bda0bb0d8a58
origin badgerevision badge
swh:1:rev:4816f2a300d7bbae1084b1940959ea35973104e1
origin badgesnapshot badge
swh:1:snp:bc0e5aa6513599be660f007d7b46ba12cce5b7e5
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
  • revision
  • snapshot
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Tip revision: 4816f2a300d7bbae1084b1940959ea35973104e1 authored by Mingzhi Lin on 23 August 2017, 14:12:59 UTC
add nucl_cov_test
Tip revision: 4816f2a
collector.go
package mcorr

// Collector collect correlation results.
type Collector struct {
	m map[string][]*MeanVar
}

// NewCollector return a new Collector.
func NewCollector() *Collector {
	c := Collector{}
	c.m = make(map[string][]*MeanVar)
	return &c
}

// Add add an array of CorrResult.
func (c *Collector) Add(results CorrResults) {
	for _, res := range results.Results {
		for len(c.m[res.Type]) <= res.Lag {
			c.m[res.Type] = append(c.m[res.Type], NewMeanVar())
		}
		if res.N > 0 {
			c.m[res.Type][res.Lag].Add(res.Mean)
		}
	}
}

// Means return means of a particular type.
func (c *Collector) Means(corrType string) (values []float64) {
	for _, mv := range c.MeanVars(corrType) {
		values = append(values, mv.Mean())
	}
	return
}

// Vars return variances of a particular type.
func (c *Collector) Vars(corrType string) (values []float64) {
	for _, mv := range c.MeanVars(corrType) {
		values = append(values, mv.Variance())
	}
	return
}

// Ns return variances of a particular type.
func (c *Collector) Ns(corrType string) (nums []int) {
	for _, mv := range c.MeanVars(corrType) {
		nums = append(nums, mv.N)
	}
	return
}

// MeanVars return a list of meanvar.MeanVar.
func (c *Collector) MeanVars(corrType string) (values []*MeanVar) {
	return c.m[corrType]
}

// CorrTypes return all corr types.
func (c *Collector) CorrTypes() (corrTypes []string) {
	for key := range c.m {
		corrTypes = append(corrTypes, key)
	}
	return
}

// Results get results
func (c *Collector) Results() (results []CorrResult) {
	corrTypes := c.CorrTypes()
	// calculate ks first
	ks := c.Means("P2")[0]
	results = append(results,
		CorrResult{
			Lag:      0,
			N:        c.Ns("P2")[0],
			Type:     "Ks",
			Mean:     c.Means("P2")[0],
			Variance: c.Vars("P2")[0],
		})
	if ks == 0 {
		return
	}

	for _, ctype := range corrTypes {
		means := c.Means(ctype)
		vars := c.Vars(ctype)
		ns := c.Ns(ctype)
		for i := 0; i < len(means); i++ {
			if !(ctype == "P2" && i == 0) && ns[i] > 0 {
				res := CorrResult{}
				res.Lag = i
				res.N = ns[i]
				res.Type = ctype
				res.Mean = means[i] / ks
				res.Variance = vars[i] / (ks * ks)
				results = append(results, res)
			}
		}
	}

	return
}

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

back to top