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
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
|
#include <pbdata/metagenome/TitleTable.hpp>
TitleTable::TitleTable()
{
table = NULL;
tableLength = 0;
}
TitleTable::~TitleTable() { Free(); }
void TitleTable::Copy(char **src, int nSrc)
{
Free(); //Free before copy
table = ProtectedNew<char *>(nSrc);
tableLength = nSrc;
int i;
for (i = 0; i < nSrc; i++) {
int lenStrI = strlen(src[i]);
table[i] = ProtectedNew<char>(lenStrI + 1);
memcpy(table[i], src[i], lenStrI);
table[i][lenStrI] = '\0';
}
}
void TitleTable::Write(std::string &name)
{
std::ofstream out;
CrucialOpen(name, out, std::ios::out);
Write(out);
}
void TitleTable::Write(std::ofstream &out)
{
int i;
for (i = 0; i < tableLength; i++) {
out << table[i] << std::endl;
}
}
void TitleTable::Read(std::string &inFileName)
{
std::ifstream in;
CrucialOpen(inFileName, in, std::ios::in);
Read(in);
}
void TitleTable::CopyFromVector(std::vector<std::string> &titles)
{
Free(); //Free before copy.
tableLength = titles.size();
table = ProtectedNew<char *>(tableLength);
int i;
for (i = 0; i < tableLength; i++) {
table[i] = ProtectedNew<char>(titles[i].size() + 1);
memcpy(table[i], titles[i].c_str(), titles[i].size());
table[i][titles[i].size()] = '\0';
}
}
void TitleTable::Read(std::ifstream &in)
{
std::vector<std::string> titles;
while (in) {
char title[1024];
in.getline(title, 1024);
if (not std::string(title).empty()) titles.push_back(title);
}
if (titles.size() > 0) {
CopyFromVector(titles);
} else {
tableLength = 0;
table = NULL;
}
}
void TitleTable::Free()
{
int i;
for (i = 0; i < tableLength; i++) {
if (table[i]) {
delete[] table[i];
table[i] = NULL;
}
}
if (table) {
delete[] table;
};
table = NULL;
tableLength = 0;
}
bool TitleTable::Lookup(std::string title, int &index)
{
int i;
for (i = 0; i < tableLength; i++) {
if (table[i] == title) {
index = i;
return true;
}
}
return false;
}
void TitleTable::ResetTableToIntegers(char **table, int *tableLengths, int nTable)
{
int i;
for (i = 0; i < nTable; i++) {
delete[] table[i];
std::stringstream namestrm;
namestrm << i;
std::string name;
name = namestrm.str();
table[i] = ProtectedNew<char>(name.size() + 1);
memcpy(table[i], name.c_str(), name.size());
table[i][name.size()] = '\0';
tableLengths[i] = (int)name.size() + 1;
}
}
|
