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1 #ifndef NC_LIST_CREATOR_HPP
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2 #define NC_LIST_CREATOR_HPP
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3
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4 #include "ncList.hpp"
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5 #include "table.hpp"
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6 #include "genomicInterval.hpp"
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7 #include <set>
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8 #include <map>
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9
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10 typedef set<string> Chromosomes;
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11 typedef map<string, NCList *> NCLists;
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12
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13 static const unsigned int H_CELL_SIZE = 2;
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14 static const unsigned int L_CELL_SIZE = 4;
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15 static const unsigned int T_CELL_SIZE = 5;
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16
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17 static const unsigned int START = 0;
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18 static const unsigned int END = 1;
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19 static const unsigned int LIST = 2;
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20 static const unsigned int PARENT = 3;
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21 static const unsigned int NEW = 4;
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22 static const unsigned int LENGTH = 1;
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23
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24
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25 class NCListCreator {
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26
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27 private:
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28 string inputFileName;
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29 Table *h, *l, *t;
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30
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31 string getFileName(string chromosome);
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32 void buildLists(string chromosome);
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33 void createTables(string chromosome);
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34 void initLists(string chromosome);
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35 void fillTables(string chromosome);
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36 void labelLists();
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37 void computeSubStart();
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38 void computeAbsPosition();
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39 void cleanFiles();
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40 void transfer(string chromosome);
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41 unsigned int nbLists, nbLines;
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42
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43
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44 public:
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45 Chromosomes chromosomes;
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46 NCLists ncLists;
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47
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48 NCListCreator (string inputFileName);
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49
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50 void splitFile ();
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51 void run ();
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52
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53 };
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54
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55 #endif
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56
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57
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