+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package hgvs
import (
"fmt"
+ "strings"
"time"
"github.com/sergi/go-diff/diffmatchpatch"
Position int
Ref string
New string
+ Left string // base preceding an indel, if Ref or New is empty
}
func (v *Variant) String() string {
}
}
+// PadLeft returns a Variant that is equivalent to v but (if possible)
+// uses the stashed preceding base (the Left field) to avoid having a
+// non-empty Ref or New part, even for an insertion or deletion.
+//
+// For example, if v is {Position: 45, Ref: "", New: "A"}, PadLeft
+// might return {Position: 44, Ref: "T", New: "TA"}.
+func (v *Variant) PadLeft() Variant {
+ if len(v.Ref) == 0 || len(v.New) == 0 {
+ return Variant{
+ Position: v.Position - len(v.Left),
+ Ref: v.Left + v.Ref,
+ New: v.Left + v.New,
+ }
+ } else {
+ return *v
+ }
+}
+
func Diff(a, b string, timeout time.Duration) ([]Variant, bool) {
dmp := diffmatchpatch.New()
var deadline time.Time
diffs = cleanup(dmp.DiffCleanupEfficiency(diffs))
pos := 1
var variants []Variant
- for i := 0; i < len(diffs); i++ {
- switch diffs[i].Type {
- case diffmatchpatch.DiffEqual:
+ for i := 0; i < len(diffs); {
+ left := "" // last char before an insertion or deletion
+ for ; i < len(diffs) && diffs[i].Type == diffmatchpatch.DiffEqual; i++ {
pos += len(diffs[i].Text)
- case diffmatchpatch.DiffDelete:
- if i+1 < len(diffs) && diffs[i+1].Type == diffmatchpatch.DiffInsert {
- // deletion followed by insertion
- variants = append(variants, Variant{Position: pos, Ref: diffs[i].Text, New: diffs[i+1].Text})
- pos += len(diffs[i].Text)
- i++
- } else {
- variants = append(variants, Variant{Position: pos, Ref: diffs[i].Text})
- pos += len(diffs[i].Text)
+ if tlen := len(diffs[i].Text); tlen > 0 {
+ left = diffs[i].Text[tlen-1:]
}
- case diffmatchpatch.DiffInsert:
- if i+1 < len(diffs) && diffs[i+1].Type == diffmatchpatch.DiffDelete {
- // insertion followed by deletion
- variants = append(variants, Variant{Position: pos, Ref: diffs[i+1].Text, New: diffs[i].Text})
- pos += len(diffs[i+1].Text)
- i++
+ }
+ if i >= len(diffs) {
+ break
+ }
+ v := Variant{Position: pos, Left: left}
+ for ; i < len(diffs) && diffs[i].Type != diffmatchpatch.DiffEqual; i++ {
+ if diffs[i].Type == diffmatchpatch.DiffDelete {
+ v.Ref += diffs[i].Text
} else {
- variants = append(variants, Variant{Position: pos, New: diffs[i].Text})
+ v.New += diffs[i].Text
}
}
+ pos += len(v.Ref)
+ variants = append(variants, v)
+ left = ""
}
return variants, timedOut
}
func cleanup(in []diffmatchpatch.Diff) (out []diffmatchpatch.Diff) {
+ out = make([]diffmatchpatch.Diff, 0, len(in))
for i := 0; i < len(in); i++ {
d := in[i]
+ // Merge consecutive entries of same type (e.g.,
+ // "insert A; insert B")
for i < len(in)-1 && in[i].Type == in[i+1].Type {
d.Text += in[i+1].Text
i++
}
out = append(out, d)
}
+ in, out = out, make([]diffmatchpatch.Diff, 0, len(in))
+ for i := 0; i < len(in); i++ {
+ d := in[i]
+ // diffmatchpatch solves diff("AAX","XTX") with
+ // [delAA,=X,insTX] but we prefer to spell it
+ // [delAA,insXT,=X].
+ //
+ // So, when we see a [del,=,ins] sequence where the
+ // "=" part is a suffix of the "ins" part -- e.g.,
+ // [delAAA,=CGG,insTTTCGG] -- we rearrange it to the
+ // equivalent spelling [delAAA,insCGGTTT,=CGG].
+ if i < len(in)-2 &&
+ d.Type == diffmatchpatch.DiffDelete &&
+ in[i+1].Type == diffmatchpatch.DiffEqual &&
+ in[i+2].Type == diffmatchpatch.DiffInsert &&
+ strings.HasSuffix(in[i+2].Text, in[i+1].Text) {
+ eq, ins := in[i+1], in[i+2]
+ ins.Text = eq.Text + ins.Text[:len(ins.Text)-len(eq.Text)]
+ in[i+1] = ins
+ in[i+2] = eq
+ }
+ // diffmatchpatch solves diff("AXX","XXX") with
+ // [delA,=XX,insX] but we prefer to spell it
+ // [delA,insX,=XX].
+ //
+ // So, when we see a [del,=,ins] sequence that has the
+ // same effect after swapping the "=" and "ins" parts,
+ // we swap them.
+ if i < len(in)-2 &&
+ d.Type == diffmatchpatch.DiffDelete &&
+ in[i+1].Type == diffmatchpatch.DiffEqual &&
+ in[i+2].Type == diffmatchpatch.DiffInsert &&
+ in[i+1].Text+in[i+2].Text == in[i+2].Text+in[i+1].Text {
+ in[i+2], in[i+1] = in[i+1], in[i+2]
+ }
+ // when diffmatchpatch says [delAAA, insXAY] and
+ // len(X)==1, we prefer to treat the A>X as a snp.
+ if i < len(in)-1 &&
+ d.Type == diffmatchpatch.DiffDelete &&
+ in[i+1].Type == diffmatchpatch.DiffInsert &&
+ len(d.Text) >= 2 &&
+ len(in[i+1].Text) >= 2 &&
+ d.Text[1] == in[i+1].Text[1] {
+ eqend := 2
+ for ; eqend < len(d.Text) && eqend < len(in[i+1].Text) && d.Text[eqend] == in[i+1].Text[eqend]; eqend++ {
+ }
+ out = append(out,
+ diffmatchpatch.Diff{diffmatchpatch.DiffDelete, d.Text[:1]},
+ diffmatchpatch.Diff{diffmatchpatch.DiffInsert, in[i+1].Text[:1]},
+ diffmatchpatch.Diff{diffmatchpatch.DiffEqual, d.Text[1:eqend]})
+ in[i].Text, in[i+1].Text = in[i].Text[eqend:], in[i+1].Text[eqend:]
+ i--
+ continue
+ }
+ // when diffmatchpatch says [delAAA, insXaY] and
+ // len(Y)==1, we prefer to treat the A>Y as a snp.
+ if i < len(in)-1 &&
+ d.Type == diffmatchpatch.DiffDelete &&
+ in[i+1].Type == diffmatchpatch.DiffInsert &&
+ len(d.Text) >= 2 &&
+ len(in[i+1].Text) >= 2 &&
+ d.Text[len(d.Text)-2] == in[i+1].Text[len(in[i+1].Text)-2] {
+ // eqstart will be the number of equal chars
+ // before the terminal snp, plus 1 for the snp
+ // itself. Example, for [delAAAA, insTTAAG],
+ // eqstart will be 3.
+ eqstart := 2
+ for ; eqstart < len(d.Text) && eqstart < len(in[i+1].Text) && d.Text[len(d.Text)-eqstart] == in[i+1].Text[len(in[i+1].Text)-eqstart]; eqstart++ {
+ }
+ eqstart--
+ out = append(out,
+ diffmatchpatch.Diff{diffmatchpatch.DiffDelete, d.Text[:len(d.Text)-eqstart]},
+ diffmatchpatch.Diff{diffmatchpatch.DiffInsert, in[i+1].Text[:len(in[i+1].Text)-eqstart]},
+ diffmatchpatch.Diff{diffmatchpatch.DiffEqual, d.Text[len(d.Text)-eqstart : len(d.Text)-1]},
+ diffmatchpatch.Diff{diffmatchpatch.DiffDelete, d.Text[len(d.Text)-1:]},
+ diffmatchpatch.Diff{diffmatchpatch.DiffInsert, in[i+1].Text[len(in[i+1].Text)-1:]})
+ i++
+ continue
+ }
+ out = append(out, d)
+ }
return
}
+
+func Less(a, b Variant) bool {
+ if a.Position != b.Position {
+ return a.Position < b.Position
+ } else if a.New != b.New {
+ return a.New < b.New
+ } else {
+ return a.Ref < b.Ref
+ }
+}
projects / lightning.git / blobdiff