/
piler.go
229 lines (203 loc) · 5.82 KB
/
piler.go
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// Copyright ©2012 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 pals
import (
"fmt"
"log"
"github.com/biogo/biogo/feat"
"github.com/biogo/store/interval"
)
var duplicatePair = fmt.Errorf("pals: attempt to add duplicate feature pair to pile")
// Note Location must be comparable according to http://golang.org/ref/spec#Comparison_operators.
type pileInterval struct {
id uintptr
start, end int
pile *Pile
location feat.Feature
images []*Feature
overlap int
}
func (i *pileInterval) Overlap(b interval.IntRange) bool {
return i.end-i.overlap >= b.Start && i.start <= b.End-i.overlap
}
func (i *pileInterval) ID() uintptr { return i.id }
func (i *pileInterval) Range() interval.IntRange {
return interval.IntRange{Start: i.start + i.overlap, End: i.end - i.overlap}
}
// A Piler performs the aggregation of feature pairs according to the description in section 2.3
// of Edgar and Myers (2005) using an interval tree, giving O(nlogn) time but better space complexity
// and flexibility with feature overlap.
type Piler struct {
// Logger logs pile construction during
// Piles calls if non-nil.
Logger *log.Logger
// LogFreq specifies how frequently
// log lines are witten if not zero.
LogFreq int
intervals map[feat.Feature]*interval.IntTree
seen map[[2]sf]struct{}
overlap int
piled bool
// next provides the next ID
// for merged intervals. IDs
// are unique across all intervals.
next uintptr
}
type sf struct {
loc feat.Feature
s, e int
}
// NewPiler creates a Piler object ready for piling feature pairs.
func NewPiler(overlap int) *Piler {
return &Piler{
intervals: make(map[feat.Feature]*interval.IntTree),
seen: make(map[[2]sf]struct{}),
overlap: overlap,
}
}
// Add adds a feature pair to the piler incorporating the features into piles where appropriate.
func (p *Piler) Add(fp *Pair) error {
a := sf{loc: fp.A.Location(), s: fp.A.Start(), e: fp.A.End()}
b := sf{loc: fp.B.Location(), s: fp.B.Start(), e: fp.B.End()}
ab, ba := [2]sf{a, b}, [2]sf{b, a}
if _, ok := p.seen[ab]; ok {
return duplicatePair
}
if _, ok := p.seen[ba]; ok {
return duplicatePair
}
p.merge(&pileInterval{id: p.nextID(), start: fp.A.Start(), end: fp.A.End(), location: fp.A.Location(), images: []*Feature{fp.A}, overlap: p.overlap})
p.merge(&pileInterval{id: p.nextID(), start: fp.B.Start(), end: fp.B.End(), location: fp.B.Location(), images: []*Feature{fp.B}, overlap: p.overlap})
p.seen[ab] = struct{}{}
return nil
}
func (p *Piler) nextID() uintptr {
id := p.next
p.next++
return id
}
func min(a, b int) int {
if a < b {
return a
}
return b
}
func max(a, b int) int {
if a > b {
return a
}
return b
}
// merge merges an interval into the tree moving location meta data from the replaced intervals
// into the new interval.
func (p *Piler) merge(pi *pileInterval) {
var (
f = true
r []interval.IntInterface
qi = &pileInterval{start: pi.start, end: pi.end}
)
t, ok := p.intervals[pi.location]
if !ok {
t = &interval.IntTree{}
p.intervals[pi.location] = t
}
t.DoMatching(
func(e interval.IntInterface) (done bool) {
r = append(r, e)
iv := e.(*pileInterval)
pi.images = append(pi.images, iv.images...)
if f {
pi.start = min(iv.start, pi.start)
f = false
}
pi.end = max(iv.end, pi.end)
return
},
qi,
)
for _, d := range r {
t.Delete(d, false)
}
t.Insert(pi, false)
}
// A PairFilter is used to determine whether a Pair's images are included in a Pile.
type PairFilter func(*Pair) bool
// Piles returns a slice of piles determined by application of the filter function f to
// the feature pairs that have been added to the piler. Piles may be called more than once,
// but the piles returned in earlier invocations will be altered by subsequent calls.
func (p *Piler) Piles(f PairFilter) []*Pile {
var n int
if !p.piled {
for _, t := range p.intervals {
t.Do(func(e interval.IntInterface) (done bool) {
pa := e.(*pileInterval)
if pa.pile == nil {
pa.pile = &Pile{Loc: pa.location, From: pa.start, To: pa.end}
}
for _, im := range pa.images {
if checkSanity {
assertPileSanity(t, im, pa.pile)
}
im.Loc = pa.pile
}
return
})
n++
if p.Logger != nil && p.LogFreq != 0 && n%p.LogFreq == 0 {
p.Logger.Printf("piled %d intervals of %d", n, len(p.intervals))
}
}
p.piled = true
}
n = 0
var piles []*Pile
for _, t := range p.intervals {
t.Do(func(e interval.IntInterface) (done bool) {
pa := e.(*pileInterval)
pa.pile.Images = pa.pile.Images[:0]
for _, im := range pa.images {
if f != nil && !f(im.Pair) {
continue
}
if checkSanity {
assertPairSanity(im)
}
pa.pile.Images = append(pa.pile.Images, im)
}
piles = append(piles, pa.pile)
return
})
n++
if p.Logger != nil && p.LogFreq != 0 && n%p.LogFreq == 0 {
p.Logger.Printf("filtered %d intervals of %d", n, len(p.intervals))
}
}
return piles
}
const checkSanity = false
func assertPileSanity(t *interval.IntTree, im *Feature, pi *Pile) {
if im.Start() < pi.Start() || im.End() > pi.End() {
panic(fmt.Sprintf("image extends beyond pile: %#v", im))
}
if foundPiles := t.Get(&pileInterval{start: im.Start(), end: im.End()}); len(foundPiles) > 1 {
var containing int
for _, pile := range foundPiles {
r := pile.Range()
if (r.Start <= im.Start() && r.End > im.End()) || (r.Start < im.Start() && r.End >= im.End()) {
containing++
}
}
if containing > 1 {
panic(fmt.Sprintf("found too many piles for %#v", im))
}
}
}
func assertPairSanity(im *Feature) {
if _, ok := im.Loc.(*Pile); !ok {
panic(fmt.Sprintf("image not allocated to pile %#v", im))
}
if _, ok := im.Mate().Loc.(*Pile); !ok {
panic(fmt.Sprintf("image mate not allocated to pile %#v", im.Mate()))
}
}