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
|
#ifndef NORMALIZER_H
#define NORMALIZER_H
#include <string>
#include <iostream>
class PublicNexusReader;
void writeAsNexus(PublicNexusReader & nexusReader, std::ostream & os);
class TranslatingConventions {
public:
TranslatingConventions()
:idPrefix(),
globalIncrementingIDs(false),
currentOTUIndex(0),
currentOTUsIndex(0),
currentCharsIndex(0),
currentCharIndex(0),
currentStateIndex(0),
currentStateSetIndex(0),
currentTreesIndex(0),
currentTreeIndex(0),
currentNodeIndex(0),
currentEdgeIndex(0),
treatNodeLabelsAsStrings(false),
emitTreesAndTaxaOnly(false) {
}
std::string idPrefix;
bool globalIncrementingIDs;
unsigned currentOTUIndex;
unsigned currentOTUsIndex;
unsigned currentCharsIndex;
unsigned currentCharIndex;
unsigned currentRowIndex;
unsigned currentStateIndex;
unsigned currentStateSetIndex;
unsigned currentTreesIndex;
unsigned currentTreeIndex;
unsigned currentNodeIndex;
unsigned currentEdgeIndex;
bool treatNodeLabelsAsStrings;
bool emitTreesAndTaxaOnly;
};
#endif
|
