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// Copyright ©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/seq"
"github.com/biogo/graph"
"fmt"
)
// A Contig is a base feature type. Other features in the pals package point to this type in
// their location fields.
type Contig string
// Name returns the value of the receiver as a string.
func (c Contig) Name() string { return string(c) }
// Description returns the string "contig".
func (c Contig) Description() string { return "contig" }
// Start returns the value 0.
func (c Contig) Start() int { return 0 }
// End returns the value 0.
func (c Contig) End() int { return 0 }
// Len returns the value 0.
func (c Contig) Len() int { return 0 }
// Location returns a nil feat.Feature.
func (c Contig) Location() feat.Feature { return nil }
// String returns the value of the receiver as a string.
func (c Contig) String() string { return string(c) }
// A Feature is a description of a pals feature interval.
type Feature struct {
ID string
From int
To int
Loc feat.Feature
Pair *Pair
}
func (f *Feature) Name() string {
if f == nil {
return "<nil>"
}
return f.ID
}
// Description returns the string "pals feature".
func (f *Feature) Description() string { return "pals feature" }
func (f *Feature) Start() int { return f.From }
func (f *Feature) End() int { return f.To }
func (f *Feature) Len() int { return f.To - f.From }
func (f *Feature) Location() feat.Feature { return f.Loc }
func (f *Feature) String() string {
if f == nil {
return "<nil>"
}
return fmt.Sprintf("%s[%d,%d)", f.Loc.Name(), f.From, f.To)
}
// Mate returns the feature pair mate of the receiver.
func (f *Feature) Mate() *Feature {
switch f {
case f.Pair.A:
return f.Pair.B
case f.Pair.B:
return f.Pair.A
}
return nil
}
// A Pile is a collection of features covering a maximal (potentially contiguous, depending on
// the value of overlap used for creation of the Piler) region of copy count > 0.
//
// The graph.Node interface support of Pile is subject to change.
// TODO(kortschak): Replace biogo/graph use with gonum/graph.
type Pile struct {
From int
To int
Strand seq.Strand
Loc feat.Feature
Images []*Feature
graph.Node
}
func (p *Pile) Name() string {
if p == nil {
return "<nil>"
}
return fmt.Sprintf("%s[%d,%d)", p.Loc.Name(), p.From, p.To)
}
// Description returns the string "pile".
func (p *Pile) Description() string { return "pile" }
func (p *Pile) Start() int { return p.From }
func (p *Pile) End() int { return p.To }
func (p *Pile) Len() int { return p.To - p.From }
func (p *Pile) Location() feat.Feature { return p.Loc }
func (p *Pile) String() string {
if p == nil {
return "<nil>"
}
return fmt.Sprintf("{%s[%d,%d): %v}", p.Loc.Name(), p.From, p.To, p.Images)
}
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