minhash

Documentation

Overview

Package minhash contains implementations of KMV and KHF MinHash algorithms

Index

• type IntHeap
  • func (IntHeap IntHeap) Len() int
  • func (IntHeap IntHeap) Less(i, j int) bool
  • func (IntHeap *IntHeap) Pop() interface{}
  • func (IntHeap *IntHeap) Push(x interface{})
  • func (IntHeap IntHeap) Swap(i, j int)
• type KHFsketch
  • func NewKHFsketch(k, s uint) *KHFsketch
  • func (KHFsketch *KHFsketch) AddHash(hv uint64)
  • func (KHFsketch *KHFsketch) GetAlgo() string
  • func (KHFsketch *KHFsketch) GetMD5() string
  • func (KHFsketch *KHFsketch) GetSimilarity(mh2 MinHash) (float64, error)
  • func (KHFsketch *KHFsketch) GetSketch() []uint64
  • func (KHFsketch *KHFsketch) Merge(KHFsketch2 *KHFsketch)
  • func (KHFsketch *KHFsketch) SetMD5()
• type KMVsketch
  • func NewKMVsketch(k, s uint) *KMVsketch
  • func (KMVsketch *KMVsketch) AddHash(hv uint64)
  • func (KMVsketch *KMVsketch) GetAlgo() string
  • func (KMVsketch *KMVsketch) GetMD5() string
  • func (mh1 *KMVsketch) GetSimilarity(mh2 MinHash) (float64, error)
  • func (KMVsketch *KMVsketch) GetSketch() []uint64
  • func (KMVsketch *KMVsketch) SetMD5()
  • func (KMVsketch *KMVsketch) SetSketch()
• type MinHash

Types

type IntHeap

type IntHeap []uint64

IntHeap is a min-heap of uint64s (we're satisfying the heap interface: https://golang.org/pkg/container/heap/)

func (IntHeap) Len

func (IntHeap IntHeap) Len() int

func (IntHeap) Less

func (IntHeap IntHeap) Less(i, j int) bool

the less method is returning the larger value, so that it is at index position 0 in the heap

func (*IntHeap) Pop

func (IntHeap *IntHeap) Pop() interface{}

Pop is a method to remove an element from the heap

func (*IntHeap) Push

func (IntHeap *IntHeap) Push(x interface{})

Push is a method to add an element to the heap

func (IntHeap) Swap

func (IntHeap IntHeap) Swap(i, j int)

type KHFsketch

type KHFsketch struct {
	KmerSize   uint     `json:"ksize"`
	Md5sum     string   `json:"md5sum"`
	Sketch     []uint64 `json:"mins"`
	SketchSize uint     `json:"num"`
	// contains filtered or unexported fields
}

KHFsketch is the K-Hash Functions MinHash sketch of a set

func NewKHFsketch

func NewKHFsketch(k, s uint) *KHFsketch

NewKHFsketch is the constructor for a KHFsketch

func (*KHFsketch) AddHash

func (KHFsketch *KHFsketch) AddHash(hv uint64)

AddHash is a method to evaluate a hash value and add any minimums to the sketch

func (*KHFsketch) GetAlgo

func (KHFsketch *KHFsketch) GetAlgo() string

GetAlgo is a method to return the sketching algorithm used

func (*KHFsketch) GetMD5

func (KHFsketch *KHFsketch) GetMD5() string

GetMD5 is a method to return the MD5 currently calculated for the sketch

func (*KHFsketch) GetSimilarity

func (KHFsketch *KHFsketch) GetSimilarity(mh2 MinHash) (float64, error)

GetSimilarity is a function to estimate the Jaccard similarity between sketches

func (*KHFsketch) GetSketch

func (KHFsketch *KHFsketch) GetSketch() []uint64

GetSketch is a method to return the sketch held by a MinHash KHF sketch object

func (*KHFsketch) Merge

func (KHFsketch *KHFsketch) Merge(KHFsketch2 *KHFsketch)

Merge is a method to combine two MinHash objects TODO: this should check for consistency between MinHash objects

func (*KHFsketch) SetMD5

func (KHFsketch *KHFsketch) SetMD5()

SetMD5 is a method to calculate and store the MD5 for the sketch

type KMVsketch

type KMVsketch struct {
	KmerSize   uint     `json:"ksize"`
	Md5sum     string   `json:"md5sum"`
	Sketch     []uint64 `json:"mins"`
	SketchSize uint     `json:"num"`
	// contains filtered or unexported fields
}

KMVsketch is the bottom-k MinHash sketch of a set

func NewKMVsketch

func NewKMVsketch(k, s uint) *KMVsketch

NewKMVsketch is the constructor for a KMVsketch

func (*KMVsketch) AddHash

func (KMVsketch *KMVsketch) AddHash(hv uint64)

AddHash is a method to evaluate a hash value and add any minimums to the sketch

func (*KMVsketch) GetAlgo

func (KMVsketch *KMVsketch) GetAlgo() string

GetAlgo is a method to return the sketching algorithm used

func (*KMVsketch) GetMD5

func (KMVsketch *KMVsketch) GetMD5() string

GetMD5 is a method to return the MD5 currently calculated for the sketch

func (*KMVsketch) GetSimilarity

func (mh1 *KMVsketch) GetSimilarity(mh2 MinHash) (float64, error)

Similarity computes a similarity estimate for two KMV sketches

func (*KMVsketch) GetSketch

func (KMVsketch *KMVsketch) GetSketch() []uint64

GetSketch is a method to set and return the sketch held by a MinHash KMV sketch

func (*KMVsketch) SetMD5

func (KMVsketch *KMVsketch) SetMD5()

SetMD5 is a method to calculate and store the MD5 for the sketch

func (*KMVsketch) SetSketch

func (KMVsketch *KMVsketch) SetSketch()

SetSketch converts the current IntHeap into a []uint64 and sorts it low -> high

type MinHash

type MinHash interface {
	AddHash(uint64)
	GetSketch() []uint64
	GetSimilarity(mh2 MinHash) (float64, error)
}

MinHash is an interface to group the different flavours of MinHash implemented here