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
82
83
84
85
86
|
#include "piler2.h"
char *ReadAFA(FILE *f, int *ptrSeqLength, int *ptrSeqCount)
{
rewind(f);
int FileSize = GetFileSize(f);
int BufferSize = FileSize;
char *Buffer = all(char, BufferSize);
char prev_c = '\n';
bool InLabel = false;
int Pos = 0;
int SeqStart = 0;
int SeqCount = 0;
int SeqLength;
for (;;)
{
int c = fgetc(f);
if (EOF == c)
{
if (feof(f))
break;
Quit("Stream error");
}
if (InLabel)
{
if (c == '\r')
continue;
if ('\n' == c)
InLabel = false;
}
else
{
if ('>' == c && '\n' == prev_c)
{
int ThisSeqLength = Pos - SeqStart;
if (0 == SeqCount)
;
else if (1 == SeqCount)
SeqLength = ThisSeqLength;
else if (SeqCount > 1)
{
if (SeqLength != ThisSeqLength)
Quit("ReadAFA: %u seqs, sequence lengths differ (a) %d %d",
SeqCount, SeqLength, ThisSeqLength);
}
++SeqCount;
SeqStart = Pos;
InLabel = true;
}
else if (!isspace(c))
{
if (Pos >= BufferSize)
Quit("ReadAFA: buffer too small");
Buffer[Pos++] = (c);
}
}
prev_c = c;
}
int ThisSeqLength = Pos - SeqStart;
if (1 == SeqCount)
SeqLength = ThisSeqLength;
else
{
if (SeqLength != ThisSeqLength)
Quit("ReadAFA: %u seqs, sequence lengths differ (b) %d %d",
SeqCount, SeqLength, ThisSeqLength);
}
*ptrSeqCount = SeqCount;
*ptrSeqLength = SeqLength;
if (Pos != SeqCount*SeqLength)
Quit("ReadAFA: Internal error");
return Buffer;
}
char *ReadAFA(const char FileName[], int *ptrSeqLength, int *ptrSeqCount)
{
FILE *f = OpenStdioFile(FileName);
char *Seqs = ReadAFA(f, ptrSeqLength, ptrSeqCount);
fclose(f);
return Seqs;
}
|
