func (self *Multi) Stitch(f feat.FeatureSet) (err error) {
tr := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
i, err = interval.New(emptyString, feature.Start, feature.End, 0, nil)
if err != nil {
return
} else {
tr.Insert(i)
}
}
span, err := interval.New(emptyString, self.Start(), self.End(), 0, nil)
if err != nil {
panic("Sequence.End() < Sequence.Start()")
}
fs, _ := tr.Flatten(span, 0, 0)
ff := feat.FeatureSet{}
for _, seg := range fs {
ff = append(ff, &feat.Feature{
Start: util.Max(seg.Start(), self.Start()),
End: util.Min(seg.End(), self.End()),
})
}
return self.Compose(ff)
}
// Stitch provides a function that may be used by polymer types to implement Stitcher.
// It makes use of reflection and so may be slower than type-specific implementations.
// This is the reference implementation and should be used to compare type-specific
// implementation against in testing.
func Stitch(pol interface{}, offset int, f feat.FeatureSet) (s interface{}, err error) {
t := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
i, err = interval.New(emptyString, feature.Start, feature.End, 0, nil)
if err != nil {
return
} else {
t.Insert(i)
}
}
pv := reflect.ValueOf(pol)
pLen := pv.Len()
end := pLen + offset
span, err := interval.New(emptyString, offset, end, 0, nil)
if err != nil {
panic("Sequence.End() < Sequence.Start()")
}
fs, _ := t.Flatten(span, 0, 0)
l := 0
for _, seg := range fs {
l += util.Min(seg.End(), end) - util.Max(seg.Start(), offset)
}
tv := reflect.MakeSlice(pv.Type(), 0, l)
for _, seg := range fs {
tv = reflect.AppendSlice(tv, pv.Slice(util.Max(seg.Start()-offset, 0), util.Min(seg.End()-offset, pLen)))
}
return tv.Interface(), nil
}
// Join sequentially order disjunct segments of the sequence, returning any error.
func (self *Seq) Stitch(f feat.FeatureSet) (err error) {
tr := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
i, err = interval.New(emptyString, feature.Start, feature.End, 0, nil)
if err != nil {
return
} else {
tr.Insert(i)
}
}
span, err := interval.New(emptyString, self.offset, self.End(), 0, nil)
if err != nil {
panic("packed: Sequence.End() < Sequence.Start()")
}
fs, _ := tr.Flatten(span, 0, 0)
l := 0
for _, seg := range fs {
l += util.Min(seg.End(), self.End()) - util.Max(seg.Start(), self.Start())
}
t := &Seq{}
*t = *self
t.S = &Packing{Letters: make([]alphabet.Pack, 0, (l+3)/4)}
var tseg seq.Sequence
for _, seg := range fs {
tseg, err = self.Subseq(util.Max(seg.Start(), self.Start()), util.Min(seg.End(), self.End()))
if err != nil {
return
}
s := tseg.(*Seq).S
s.Align(seq.Start)
t.S.Align(seq.End)
t.S.Letters = append(t.S.Letters, s.Letters...)
t.S.RightPad = s.RightPad
}
*self = *t
return
}
func (self *Quality) Stitch(f feat.FeatureSet) (q *Quality, err error) {
t := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
i, err = interval.New(emptyString, feature.Start, feature.End, 0, nil)
if err != nil {
return
} else {
t.Insert(i)
}
}
span, err := interval.New(emptyString, self.Start(), self.End(), 0, nil)
if err != nil {
panic("Seq.End() < Seq.Start()")
}
fs, _ := t.Flatten(span, 0, 0)
if self.Inplace {
q = self
q.Qual = self.stitch(fs)
q.Offset = 0
q.Circular = false
} else {
q = &Quality{
ID: self.ID,
Qual: self.stitch(fs),
Offset: 0,
Strand: self.Strand,
Circular: false,
}
}
return
}
func (self *Seq) Stitch(f feat.FeatureSet) (s *Seq, err error) {
if !self.Inplace && self.Quality != nil && self.Quality.Inplace {
return nil, bio.NewError("Inplace operation on Quality with non-Inplace operation on parent Seq.", 0, self)
}
t := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
i, err = interval.New(emptyString, feature.Start, feature.End, 0, nil)
if err != nil {
return
} else {
t.Insert(i)
}
}
span, err := interval.New(emptyString, self.Start(), self.End(), 0, nil)
if err != nil {
panic("Seq.End() < Seq.Start()")
}
fs, _ := t.Flatten(span, 0, 0)
if self.Inplace {
self.Seq = self.stitch(fs)
self.Offset = 0
self.Circular = false
if self.Quality != nil {
var q *Quality
if !self.Quality.Inplace {
q = &Quality{ID: self.Quality.ID}
}
q.Qual = self.Quality.stitch(fs)
q.Offset = 0
q.Circular = false
self.Quality = q
}
s = self
} else {
var q *Quality
if self.Quality != nil {
q = &Quality{
ID: self.Quality.ID,
Qual: self.Quality.stitch(fs),
Offset: 0,
Circular: false,
}
}
s = &Seq{
ID: self.ID,
Seq: self.stitch(fs),
Offset: 0,
Strand: self.Strand,
Circular: false,
Moltype: self.Moltype,
Quality: q,
}
}
return
}
func (self Alignment) Stitch(f feat.FeatureSet) (a Alignment, err error) {
for _, s := range self {
if !s.Inplace && s.Quality != nil && s.Quality.Inplace {
return nil, bio.NewError("Inplace operation on Quality with non-Inplace operation on parent Seq.", 0, s)
}
}
t := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
i, err = interval.New("", feature.Start, feature.End, 0, nil)
if err != nil {
return
} else {
t.Insert(i)
}
}
start := self.Start()
a = make(Alignment, len(self))
span, err := interval.New("", start, self.End(), 0, nil)
if err != nil {
panic("Seq.End() < Seq.Start()")
}
fs, _ := t.Flatten(span, 0, 0)
var offset int
for i, s := range self {
if s.Inplace {
s.Seq = s.stitch(fs)
if s.Offset -= fs[0].Start(); offset < 0 {
s.Offset = 0
}
s.Circular = false
if s.Quality != nil {
var q *Quality
if s.Quality.Inplace {
q = s.Quality
} else {
q = &Quality{ID: s.Quality.ID}
}
q.Qual = s.Quality.stitch(fs)
if q.Offset = s.Quality.Offset - fs[0].Start(); q.Offset < 0 {
q.Offset = 0
}
q.Circular = false
s.Quality = q
}
a[i] = s
} else {
var q *Quality
if s.Quality != nil {
if offset = s.Quality.Offset - fs[0].Start(); offset < 0 {
offset = 0
}
q = &Quality{
ID: s.Quality.ID,
Qual: s.Quality.stitch(fs),
Offset: offset,
Circular: false,
}
}
if offset = s.Offset - fs[0].Start(); offset < 0 {
offset = 0
}
a[i] = &Seq{
ID: s.ID,
Seq: s.stitch(fs),
Offset: offset,
Strand: s.Strand,
Circular: false,
Moltype: s.Moltype,
Quality: q,
}
}
}
return
}
