1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
package assemble;
import dna.AminoAcid;
import structures.ByteBuilder;
public class Edge {
public Edge(int origin_, int destination_, int length_, int orientation_, int depth_, byte[] bases_){
origin=origin_;
destination=destination_;
length=length_;
orientation=orientation_;
depth=depth_;
bases=bases_;
}
@Override
public String toString(){
return appendTo(new ByteBuilder()).toString();
}
public ByteBuilder appendTo(ByteBuilder bb){
bb.append('(');
bb.append(destination).append('-')/*.append(direction).append('-')*/.append(orientation);
bb.append('-').append(length).append('-').append(depth).append('-').append(bases);
bb.append(')');
return bb;
}
public void toDot(ByteBuilder bb){
bb.append(origin);
bb.append(" -> ");
bb.append(destination);
bb.append(" [label=\"").append(((orientation&1)==0) ? "LEFT" : "RIGHT").append("\\nlen=").append(length);
bb.append("\\norient=").append(orientation).append("\"]").append('\n');
}
public boolean destRight() {
return (orientation&2)==2;
}
public boolean sourceRight() {
return (orientation&1)==1;
}
void flipSource(){
if(Tadpole.verbose){System.err.print("Flipping edge source "+this+" -> ");}
if(bases!=null){AminoAcid.reverseComplementBasesInPlace(bases);}
orientation^=1;
if(Tadpole.verbose){System.err.println(this);}
}
void flipDest(){
if(Tadpole.verbose){System.err.print("Flipping edge dest "+this+" -> ");}
orientation^=2;
if(Tadpole.verbose){System.err.println(this);}
}
void merge(Edge e){
assert(e.origin==origin);
assert(e.destination==destination);
assert(e.orientation==orientation);
if(e.depth>depth){
length=e.length;
bases=e.bases;
orientation=e.orientation;
depth+=e.depth;
}else{
depth+=e.depth;
}
}
byte[] bases;
int origin;
int destination;
int length;
int orientation; //left source to left dest; 1 right source to left dest; 2 left source to right dest; 3 right source to right dest
// int orientation; //0 left kmer, 1 left rkmer, 2 right kmer, 3 right rkmer (of dest)
// final int direction; //0 forward, 1 backward //They are all forward edges now
int depth;
}
|
