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// Copyright ©2015 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Package cache provides basic block cache types for the bgzf package.
package cache
import (
"sync"
"github.com/biogo/hts/bgzf"
)
var (
_ Cache = (*LRU)(nil)
_ Cache = (*FIFO)(nil)
_ Cache = (*Random)(nil)
)
// Free attempts to drop as many blocks from c as needed allow
// n successful Put calls on c. It returns a boolean indicating
// whether n slots were made available.
func Free(n int, c Cache) bool {
empty := c.Cap() - c.Len()
if n <= empty {
return true
}
c.Drop(n - empty)
return c.Cap()-c.Len() >= n
}
// Cache is an extension of bgzf.Cache that allows inspection
// and manipulation of the cache.
type Cache interface {
bgzf.Cache
// Len returns the number of elements held by
// the cache.
Len() int
// Cap returns the maximum number of elements
// that can be held by the cache.
Cap() int
// Resize changes the capacity of the cache to n,
// dropping excess blocks if n is less than the
// number of cached blocks.
Resize(n int)
// Drop evicts n elements from the cache according
// to the cache eviction policy.
Drop(n int)
}
func insertAfter(pos, n *node) {
n.prev = pos
pos.next, n.next, pos.next.prev = n, pos.next, n
}
func remove(n *node, table map[int64]*node) {
delete(table, n.b.Base())
n.prev.next = n.next
n.next.prev = n.prev
n.next = nil
n.prev = nil
}
// NewLRU returns an LRU cache with n slots. If n is less than 1
// a nil cache is returned.
func NewLRU(n int) Cache {
if n < 1 {
return nil
}
c := LRU{
table: make(map[int64]*node, n),
cap: n,
}
c.root.next = &c.root
c.root.prev = &c.root
return &c
}
// LRU satisfies the Cache interface with least recently used eviction
// behavior where Unused Blocks are preferentially evicted.
type LRU struct {
mu sync.RWMutex
root node
table map[int64]*node
cap int
}
type node struct {
b bgzf.Block
next, prev *node
}
// Len returns the number of elements held by the cache.
func (c *LRU) Len() int {
c.mu.RLock()
defer c.mu.RUnlock()
return len(c.table)
}
// Cap returns the maximum number of elements that can be held by the cache.
func (c *LRU) Cap() int {
c.mu.RLock()
defer c.mu.RUnlock()
return c.cap
}
// Resize changes the capacity of the cache to n, dropping excess blocks
// if n is less than the number of cached blocks.
func (c *LRU) Resize(n int) {
c.mu.Lock()
if n < len(c.table) {
c.drop(len(c.table) - n)
}
c.cap = n
c.mu.Unlock()
}
// Drop evicts n elements from the cache according to the cache eviction policy.
func (c *LRU) Drop(n int) {
c.mu.Lock()
c.drop(n)
c.mu.Unlock()
}
func (c *LRU) drop(n int) {
for ; n > 0 && c.Len() > 0; n-- {
remove(c.root.prev, c.table)
}
}
// Get returns the Block in the Cache with the specified base or a nil Block
// if it does not exist.
func (c *LRU) Get(base int64) bgzf.Block {
c.mu.Lock()
defer c.mu.Unlock()
n, ok := c.table[base]
if !ok {
return nil
}
remove(n, c.table)
return n.b
}
// Peek returns a boolean indicating whether a Block exists in the Cache for
// the given base offset and the expected offset for the subsequent Block in
// the BGZF stream.
func (c *LRU) Peek(base int64) (exist bool, next int64) {
c.mu.RLock()
defer c.mu.RUnlock()
n, exist := c.table[base]
if !exist {
return false, -1
}
next = n.b.NextBase()
return exist, next
}
// Put inserts a Block into the Cache, returning the Block that was evicted or
// nil if no eviction was necessary and the Block was retained. Unused Blocks
// are not retained but are returned if the Cache is full.
func (c *LRU) Put(b bgzf.Block) (evicted bgzf.Block, retained bool) {
c.mu.Lock()
defer c.mu.Unlock()
var d bgzf.Block
if _, ok := c.table[b.Base()]; ok {
return b, false
}
used := b.Used()
if len(c.table) == c.cap {
if !used {
return b, false
}
d = c.root.prev.b
remove(c.root.prev, c.table)
}
n := &node{b: b}
c.table[b.Base()] = n
if used {
insertAfter(&c.root, n)
} else {
insertAfter(c.root.prev, n)
}
return d, true
}
// NewFIFO returns a FIFO cache with n slots. If n is less than 1
// a nil cache is returned.
func NewFIFO(n int) Cache {
if n < 1 {
return nil
}
c := FIFO{
table: make(map[int64]*node, n),
cap: n,
}
c.root.next = &c.root
c.root.prev = &c.root
return &c
}
// FIFO satisfies the Cache interface with first in first out eviction
// behavior where Unused Blocks are preferentially evicted.
type FIFO struct {
mu sync.RWMutex
root node
table map[int64]*node
cap int
}
// Len returns the number of elements held by the cache.
func (c *FIFO) Len() int {
c.mu.RLock()
defer c.mu.RUnlock()
return len(c.table)
}
// Cap returns the maximum number of elements that can be held by the cache.
func (c *FIFO) Cap() int {
c.mu.RLock()
defer c.mu.RUnlock()
return c.cap
}
// Resize changes the capacity of the cache to n, dropping excess blocks
// if n is less than the number of cached blocks.
func (c *FIFO) Resize(n int) {
c.mu.Lock()
if n < len(c.table) {
c.drop(len(c.table) - n)
}
c.cap = n
c.mu.Unlock()
}
// Drop evicts n elements from the cache according to the cache eviction policy.
func (c *FIFO) Drop(n int) {
c.mu.Lock()
c.drop(n)
c.mu.Unlock()
}
func (c *FIFO) drop(n int) {
for ; n > 0 && c.Len() > 0; n-- {
remove(c.root.prev, c.table)
}
}
// Get returns the Block in the Cache with the specified base or a nil Block
// if it does not exist.
func (c *FIFO) Get(base int64) bgzf.Block {
c.mu.Lock()
defer c.mu.Unlock()
n, ok := c.table[base]
if !ok {
return nil
}
if !n.b.Used() {
remove(n, c.table)
}
return n.b
}
// Peek returns a boolean indicating whether a Block exists in the Cache for
// the given base offset and the expected offset for the subsequent Block in
// the BGZF stream.
func (c *FIFO) Peek(base int64) (exist bool, next int64) {
c.mu.RLock()
defer c.mu.RUnlock()
n, exist := c.table[base]
if !exist {
return false, -1
}
next = n.b.NextBase()
return exist, next
}
// Put inserts a Block into the Cache, returning the Block that was evicted or
// nil if no eviction was necessary and the Block was retained. Unused Blocks
// are not retained but are returned if the Cache is full.
func (c *FIFO) Put(b bgzf.Block) (evicted bgzf.Block, retained bool) {
c.mu.Lock()
defer c.mu.Unlock()
var d bgzf.Block
if _, ok := c.table[b.Base()]; ok {
return b, false
}
used := b.Used()
if len(c.table) == c.cap {
if !used {
return b, false
}
d = c.root.prev.b
remove(c.root.prev, c.table)
}
n := &node{b: b}
c.table[b.Base()] = n
if used {
insertAfter(&c.root, n)
} else {
insertAfter(c.root.prev, n)
}
return d, true
}
// NewRandom returns a random eviction cache with n slots. If n is less than 1
// a nil cache is returned.
func NewRandom(n int) Cache {
if n < 1 {
return nil
}
return &Random{
table: make(map[int64]bgzf.Block, n),
cap: n,
}
}
// Random satisfies the Cache interface with random eviction behavior
// where Unused Blocks are preferentially evicted.
type Random struct {
mu sync.RWMutex
table map[int64]bgzf.Block
cap int
}
// Len returns the number of elements held by the cache.
func (c *Random) Len() int {
c.mu.RLock()
defer c.mu.RUnlock()
return len(c.table)
}
// Cap returns the maximum number of elements that can be held by the cache.
func (c *Random) Cap() int {
c.mu.RLock()
defer c.mu.RUnlock()
return c.cap
}
// Resize changes the capacity of the cache to n, dropping excess blocks
// if n is less than the number of cached blocks.
func (c *Random) Resize(n int) {
c.mu.Lock()
if n < len(c.table) {
c.drop(len(c.table) - n)
}
c.cap = n
c.mu.Unlock()
}
// Drop evicts n elements from the cache according to the cache eviction policy.
func (c *Random) Drop(n int) {
c.mu.Lock()
c.drop(n)
c.mu.Unlock()
}
func (c *Random) drop(n int) {
if n < 1 {
return
}
for k, b := range c.table {
if b.Used() {
continue
}
delete(c.table, k)
if n--; n == 0 {
return
}
}
for k := range c.table {
delete(c.table, k)
if n--; n == 0 {
break
}
}
}
// Get returns the Block in the Cache with the specified base or a nil Block
// if it does not exist.
func (c *Random) Get(base int64) bgzf.Block {
c.mu.Lock()
defer c.mu.Unlock()
b, ok := c.table[base]
if !ok {
return nil
}
delete(c.table, base)
return b
}
// Peek returns a boolean indicating whether a Block exists in the Cache for
// the given base offset and the expected offset for the subsequent Block in
// the BGZF stream.
func (c *Random) Peek(base int64) (exist bool, next int64) {
c.mu.RLock()
defer c.mu.RUnlock()
n, exist := c.table[base]
if !exist {
return false, -1
}
next = n.NextBase()
return exist, next
}
// Put inserts a Block into the Cache, returning the Block that was evicted or
// nil if no eviction was necessary and the Block was retained. Unused Blocks
// are not retained but are returned if the Cache is full.
func (c *Random) Put(b bgzf.Block) (evicted bgzf.Block, retained bool) {
c.mu.Lock()
defer c.mu.Unlock()
var d bgzf.Block
if _, ok := c.table[b.Base()]; ok {
return b, false
}
if len(c.table) == c.cap {
if !b.Used() {
return b, false
}
for k, v := range c.table {
if v.Used() {
continue
}
delete(c.table, k)
d = v
goto done
}
for k, v := range c.table {
delete(c.table, k)
d = v
break
}
done:
}
c.table[b.Base()] = b
return d, true
}
// StatsRecorder allows a bgzf.Cache to capture cache statistics.
type StatsRecorder struct {
bgzf.Cache
mu sync.RWMutex
stats Stats
}
// Stats represents statistics of a bgzf.Cache.
type Stats struct {
Gets int // number of Get operations
Misses int // number of cache misses
Puts int // number of Put operations
Retains int // number of times a Put has resulted in Block retention
Evictions int // number of times a Put has resulted in a Block eviction
}
// Stats returns the current statistics for the cache.
func (s *StatsRecorder) Stats() Stats {
s.mu.RLock()
defer s.mu.RUnlock()
return s.stats
}
// Reset zeros the statistics kept by the StatsRecorder.
func (s *StatsRecorder) Reset() {
s.mu.Lock()
s.stats = Stats{}
s.mu.Unlock()
}
// Get returns the Block in the underlying Cache with the specified base or a nil
// Block if it does not exist. It updates the gets and misses statistics.
func (s *StatsRecorder) Get(base int64) bgzf.Block {
s.mu.Lock()
s.stats.Gets++
blk := s.Cache.Get(base)
if blk == nil {
s.stats.Misses++
}
s.mu.Unlock()
return blk
}
// Put inserts a Block into the underlying Cache, returning the Block and eviction
// status according to the underlying cache behavior. It updates the puts, retains and
// evictions statistics.
func (s *StatsRecorder) Put(b bgzf.Block) (evicted bgzf.Block, retained bool) {
s.mu.Lock()
s.stats.Puts++
blk, retained := s.Cache.Put(b)
if retained {
s.stats.Retains++
if blk != nil {
s.stats.Evictions++
}
}
s.mu.Unlock()
return blk, retained
}
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