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
87
88
89
90
91
92
93
94
95
96
97
98
|
/***
GFFSet is a container class for a set of GFF
records. This is to hide issues to do with
retrieving from a file, efficient memory use
etc. The initial implementation here is
designed for simplicity; by hiding the details
we can improve it later as needed without
a big impact on the calling code.
***/
#include "piler2.h"
#define GFFRecord GFFRecord2
GFFSet::GFFSet()
{
m_Recs = 0;
m_RecordCount = 0;
m_RecordBufferSize = 0;
m_GLIX = 0;
m_IIX = 0;
}
GFFSet::~GFFSet()
{
Free();
}
void GFFSet::Free()
{
for (int i = 0; i < m_RecordCount; ++i)
FreeGFFStrings(m_Recs[i]);
freemem(m_Recs);
delete m_GLIX;
delete m_IIX;
m_Recs = 0;
m_RecordCount = 0;
m_RecordBufferSize = 0;
m_GLIX = 0;
m_IIX = 0;
}
void GFFSet::FromFile(FILE *f)
{
Free();
GFFRecord Rec;
while (GetNextGFFRecord(f, Rec))
{
SaveGFFStrings(Rec);
Add(Rec);
}
}
// Caller's respsonsibility to allocate memory
// for string fields, Add() doesn't make copies.
// SaveGFFStrings() makes copies if needed.
void GFFSet::Add(const GFFRecord &Rec)
{
if (m_RecordCount > m_RecordBufferSize)
Quit("GFFSet::Add, m_RecordCount > m_BufferSize");
if (m_RecordCount == m_RecordBufferSize)
{
m_RecordBufferSize += BUFFER_SIZE_INC;
reall(m_Recs, GFFRecord, m_RecordBufferSize);
}
m_Recs[m_RecordCount++] = Rec;
}
const GFFRecord &GFFSet::Get(int RecordIndex) const
{
if (RecordIndex < 0 || RecordIndex >= m_RecordCount)
Quit("GFFRecord::Get(%d) out of range %d", RecordIndex, m_RecordCount);
return m_Recs[RecordIndex];
}
void GFFSet::MakeGLIX()
{
m_GLIX = new GLIX;
m_GLIX->Init();
m_GLIX->FromGFFSet(*this);
}
void GFFSet::MakeIIX()
{
const int GlobalLength = m_GLIX->GetGlobalLength();
m_IIX = new IIX;
m_IIX->Init(GlobalLength);
m_IIX->SetGLIX(m_GLIX);
for (int RecordIndex = 0; RecordIndex < m_RecordCount; ++RecordIndex)
{
const GFFRecord &Rec = Get(RecordIndex);
m_IIX->AddLocal(Rec.SeqName, Rec.Start - 1, Rec.End - 1, RecordIndex);
}
}
|
