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suffixtree.go 4.43 KB
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package suffixtree
import (
"bytes"
"fmt"
"math"
"strings"
)
const infinity = math.MaxInt32
// Pos denotes position in data slice.
type Pos int32
type Token interface {
Val() int
}
// STree is a struct representing a suffix tree.
type STree struct {
data []Token
root *state
auxState *state // auxiliary state
// active point
s *state
start, end Pos
}
// New creates new suffix tree.
func New() *STree {
t := new(STree)
t.data = make([]Token, 0, 50)
t.root = newState(t)
t.auxState = newState(t)
t.root.linkState = t.auxState
t.s = t.root
return t
}
// Update refreshes the suffix tree to by new data.
func (t *STree) Update(data ...Token) {
t.data = append(t.data, data...)
for _ = range data {
t.update()
t.s, t.start = t.canonize(t.s, t.start, t.end)
t.end++
}
}
// update transforms suffix tree T(n) to T(n+1).
func (t *STree) update() {
oldr := t.root
// (s, (start, end)) is the canonical reference pair for the active point
s := t.s
start, end := t.start, t.end
var r *state
for {
var endPoint bool
r, endPoint = t.testAndSplit(s, start, end-1)
if endPoint {
break
}
r.fork(end)
if oldr != t.root {
oldr.linkState = r
}
oldr = r
s, start = t.canonize(s.linkState, start, end-1)
}
if oldr != t.root {
oldr.linkState = r
}
// update active point
t.s = s
t.start = start
}
// testAndSplit tests whether a state with canonical ref. pair
// (s, (start, end)) is the end point, that is, a state that have
// a c-transition. If not, then state (exs, (start, end)) is made
// explicit (if not already so).
func (t *STree) testAndSplit(s *state, start, end Pos) (exs *state, endPoint bool) {
c := t.data[t.end]
if start <= end {
tr := s.findTran(t.data[start])
splitPoint := tr.start + end - start + 1
if t.data[splitPoint].Val() == c.Val() {
return s, true
}
// make the (s, (start, end)) state explicit
newSt := newState(s.tree)
newSt.addTran(splitPoint, tr.end, tr.state)
tr.end = splitPoint - 1
tr.state = newSt
return newSt, false
}
if s == t.auxState || s.findTran(c) != nil {
return s, true
}
return s, false
}
// canonize returns updated state and start position for ref. pair
// (s, (start, end)) of state r so the new ref. pair is canonical,
// that is, referenced from the closest explicit ancestor of r.
func (t *STree) canonize(s *state, start, end Pos) (*state, Pos) {
if s == t.auxState {
s, start = t.root, start+1
}
if start > end {
return s, start
}
var tr *tran
for {
if start <= end {
tr = s.findTran(t.data[start])
if tr == nil {
panic(fmt.Sprintf("there should be some transition for '%d' at %d",
t.data[start].Val(), start))
}
}
if tr.end-tr.start > end-start {
break
}
start += tr.end - tr.start + 1
s = tr.state
}
if s == nil {
panic("there should always be some suffix link resolution")
}
return s, start
}
func (t *STree) At(p Pos) Token {
if p < 0 || p >= Pos(len(t.data)) {
panic("position out of bounds")
}
return t.data[p]
}
func (t *STree) String() string {
buf := new(bytes.Buffer)
printState(buf, t.root, 0)
return buf.String()
}
func printState(buf *bytes.Buffer, s *state, ident int) {
for _, tr := range s.trans {
fmt.Fprint(buf, strings.Repeat(" ", ident))
fmt.Fprintf(buf, "* (%d, %d)\n", tr.start, tr.ActEnd())
printState(buf, tr.state, ident+1)
}
}
// state is an explicit state of the suffix tree.
type state struct {
tree *STree
trans []*tran
linkState *state
}
func newState(t *STree) *state {
return &state{
tree: t,
trans: make([]*tran, 0),
linkState: nil,
}
}
func (s *state) addTran(start, end Pos, r *state) {
s.trans = append(s.trans, newTran(start, end, r))
}
// fork creates a new branch from the state s.
func (s *state) fork(i Pos) *state {
r := newState(s.tree)
s.addTran(i, infinity, r)
return r
}
// findTran finds c-transition.
func (s *state) findTran(c Token) *tran {
for _, tran := range s.trans {
if s.tree.data[tran.start].Val() == c.Val() {
return tran
}
}
return nil
}
// tran represents a state's transition.
type tran struct {
start, end Pos
state *state
}
func newTran(start, end Pos, s *state) *tran {
return &tran{start, end, s}
}
func (t *tran) len() int {
return int(t.end - t.start + 1)
}
// ActEnd returns actual end position as consistent with
// the actual length of the data in the STree.
func (t *tran) ActEnd() Pos {
if t.end == infinity {
return Pos(len(t.state.tree.data)) - 1
}
return t.end
}
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