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comparison SMART/Java/Python/Cpp/inputFileParser.hpp @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #ifndef INPUT_FILE_PARSER_HPP
2 #define INPUT_FILE_PARSER_HPP
3
4 #include <string>
5 #include <vector>
6 #include <map>
7 #include "genomicInterval.hpp"
8
9 typedef vector<Interval *> IntervalsType;
10 typedef map<string, IntervalsType *> SortedIntervalsTypes;
11 typedef map<string, unsigned int> CounterType;
12 typedef pair<Interval *, unsigned int> NumberIntervalType;
13
14 static bool operator<(const NumberIntervalType &i1, const NumberIntervalType &i2) {
15 if (i1.first < i2.first) return true;
16 return ((i1.first == i2.first) && (i1.second < i2.second));
17 }
18
19 class InputFileParser {
20
21 private:
22 SortedIntervalsTypes sortedIntervals;
23 CounterType counter;
24
25 void addToList(GenomicInterval &genomicInterval);
26 void writeTmpFile(string &chromosome);
27 void syncFiles();
28 string getTmpName(const string &chromosome, unsigned int i);
29 string getTmpName(const string &chromosome);
30 void merge();
31 void merge(const string &chromosome, ofstream &outputFile);
32
33 public:
34 string inputFileName;
35 string outputFileName;
36 string outputFilePrefix;
37
38 InputFileParser(string inputFileName, string outputFileName);
39
40 void parse();
41
42 };
43
44 #endif
45