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// Copyright ©2011-2012 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 (
"github.com/biogo/biogo/feat"
"github.com/biogo/biogo/io/featio/gff"
"fmt"
"io"
)
// Writer is a type that writes PALS pair feature in GFFv2 format.
type Writer struct {
w *gff.Writer
t *gff.Feature
}
// NewWriter returns a new PALS writer that write PALS alignment features to the io.Writer w.
func NewWriter(w io.Writer, prec, width int, header bool) *Writer {
gw := gff.NewWriter(w, width, header)
gw.Precision = prec
return &Writer{
w: gw,
t: &gff.Feature{Source: "pals", Feature: "hit"},
}
}
// Write writes a single feature and return the number of bytes written and any error.
func (w *Writer) Write(pair *Pair) (n int, err error) {
t := w.t
t.SeqName = pair.B.Location().Name()
t.FeatStart = pair.B.Start()
t.FeatEnd = pair.B.End()
t.FeatScore = floatPtr(float64(pair.Score))
t.FeatStrand = pair.Strand
t.FeatFrame = gff.NoFrame
t.FeatAttributes = append(t.FeatAttributes[:0],
gff.Attribute{
Tag: "Target",
Value: fmt.Sprintf("%s %d %d", pair.A.Location().Name(), feat.ZeroToOne(pair.A.Start()), pair.A.End()),
},
gff.Attribute{
Tag: "maxe",
Value: fmt.Sprintf("%.2g", pair.Error),
},
)
return w.w.Write(t)
}
func floatPtr(f float64) *float64 { return &f }
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