forked from biogo/biogo
/
merge.go
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/
merge.go
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// Copyright ©2011-2013 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 filter
import (
"github.com/biogo/biogo/alphabet"
"github.com/biogo/biogo/index/kmerindex"
"github.com/biogo/biogo/seq/linear"
"sort"
)
const (
diagonalPadding = 2
)
// A Merger aggregates and clips an ordered set of trapezoids.
type Merger struct {
target, query *linear.Seq
filterParams *Params
maxIGap int
leftPadding, bottomPadding int
binWidth int
selfComparison bool
freeTraps, trapList *trapezoid
trapOrder, tail *trapezoid
eoTerm *trapezoid
trapCount int
valueToCode alphabet.Index
}
// Create a new Merger using the provided kmerindex, query sequence, filter parameters and maximum inter-segment gap length.
// If selfCompare is true only the upper diagonal of the comparison matrix is examined.
func NewMerger(ki *kmerindex.Index, query *linear.Seq, filterParams *Params, maxIGap int, selfCompare bool) *Merger {
tubeWidth := filterParams.TubeOffset + filterParams.MaxError
binWidth := tubeWidth - 1
leftPadding := diagonalPadding + binWidth
eoTerm := &trapezoid{Trapezoid: Trapezoid{
Left: query.Len() + 1 + leftPadding,
Right: query.Len() + 1,
Bottom: -1,
Top: query.Len() + 1,
}}
return &Merger{
target: ki.Seq(),
filterParams: filterParams,
maxIGap: maxIGap,
query: query,
selfComparison: selfCompare,
bottomPadding: ki.K() + 2,
leftPadding: leftPadding,
binWidth: binWidth,
eoTerm: eoTerm,
trapOrder: eoTerm,
valueToCode: ki.Seq().Alpha.LetterIndex(),
}
}
// Merge a filter hit into the collection.
func (m *Merger) MergeFilterHit(h *Hit) {
Left := -h.Diagonal
if m.selfComparison && Left <= m.filterParams.MaxError {
return
}
Top := h.To
Bottom := h.From
var temp, free *trapezoid
for base := m.trapOrder; ; base = temp {
temp = base.next
switch {
case Bottom-m.bottomPadding > base.Top:
if free == nil {
m.trapOrder = temp
} else {
free.join(temp)
}
m.trapList = base.join(m.trapList)
m.trapCount++
case Left-diagonalPadding > base.Right:
free = base
case Left+m.leftPadding >= base.Left:
if Left+m.binWidth > base.Right {
base.Right = Left + m.binWidth
}
if Left < base.Left {
base.Left = Left
}
if Top > base.Top {
base.Top = Top
}
if free != nil && free.Right+diagonalPadding >= base.Left {
free.Right = base.Right
if free.Bottom > base.Bottom {
free.Bottom = base.Bottom
}
if free.Top < base.Top {
free.Top = base.Top
}
free.join(temp)
m.freeTraps = base.join(m.freeTraps)
} else if temp != nil && temp.Left-diagonalPadding <= base.Right {
base.Right = temp.Right
if base.Bottom > temp.Bottom {
base.Bottom = temp.Bottom
}
if base.Top < temp.Top {
base.Top = temp.Top
}
base.join(temp.next)
m.freeTraps = temp.join(m.freeTraps)
temp = base.next
}
return
default:
if m.freeTraps == nil {
m.freeTraps = &trapezoid{}
}
if free == nil {
m.trapOrder = m.freeTraps
} else {
free.join(m.freeTraps)
}
free, m.freeTraps = m.freeTraps.decapitate()
free.join(base)
free.Top = Top
free.Bottom = Bottom
free.Left = Left
free.Right = Left + m.binWidth
return
}
}
}
func (m *Merger) clipVertical() {
for base := m.trapList; base != nil; base = base.next {
lagPosition := base.Bottom - m.maxIGap + 1
if lagPosition < 0 {
lagPosition = 0
}
lastPosition := base.Top + m.maxIGap
if lastPosition > m.query.Len() {
lastPosition = m.query.Len()
}
var pos int
for pos = lagPosition; pos < lastPosition; pos++ {
if m.valueToCode[m.query.Seq[pos]] >= 0 {
if pos-lagPosition >= m.maxIGap {
if lagPosition-base.Bottom > 0 {
if m.freeTraps == nil {
m.freeTraps = &trapezoid{}
}
m.freeTraps = m.freeTraps.prependFrontTo(base)
base.Top = lagPosition
base = base.next
base.Bottom = pos
m.trapCount++
} else {
base.Bottom = pos
}
}
lagPosition = pos + 1
}
}
if pos-lagPosition >= m.maxIGap {
base.Top = lagPosition
}
}
}
func (m *Merger) clipTrapezoids() {
for base := m.trapList; base != nil; base = base.next {
if base.Top-base.Bottom < m.bottomPadding-2 {
continue
}
aBottom := base.Bottom - base.Right
aTop := base.Top - base.Left
lagPosition := aBottom - m.maxIGap + 1
if lagPosition < 0 {
lagPosition = 0
}
lastPosition := aTop + m.maxIGap
if lastPosition > m.target.Len() {
lastPosition = m.target.Len()
}
lagClip := aBottom
var pos int
for pos = lagPosition; pos < lastPosition; pos++ {
if m.valueToCode[m.target.Seq[pos]] >= 0 {
if pos-lagPosition >= m.maxIGap {
if lagPosition > lagClip {
if m.freeTraps == nil {
m.freeTraps = &trapezoid{}
}
m.freeTraps = m.freeTraps.prependFrontTo(base)
base.clip(lagPosition, lagClip)
base = base.next
m.trapCount++
}
lagClip = pos
}
lagPosition = pos + 1
}
}
if pos-lagPosition < m.maxIGap {
lagPosition = aTop
}
base.clip(lagPosition, lagClip)
m.tail = base
}
}
// Finalise the merged collection and return a sorted slice of Trapezoids.
func (m *Merger) FinaliseMerge() Trapezoids {
var next *trapezoid
for base := m.trapOrder; base != m.eoTerm; base = next {
next = base.next
m.trapList = base.join(m.trapList)
m.trapCount++
}
m.clipVertical()
m.clipTrapezoids()
if m.tail != nil {
m.freeTraps = m.tail.join(m.freeTraps)
}
traps := make(Trapezoids, m.trapCount)
for i, z := 0, m.trapList; i < m.trapCount; i++ {
traps[i] = z.Trapezoid
z, z.next = z.next, nil
}
sort.Sort(traps)
return traps
}