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1 /*****************************************************************************
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2 tabFile.h
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licensed under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #ifndef TABFILE_H
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13 #define TABFILE_H
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14
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15 #include "gzstream.h"
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16 #include <vector>
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17 #include <string>
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18 #include <iostream>
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19
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20 using namespace std;
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21
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22 // enum to flag the state of a given line in a TAB file.
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23 enum TabLineStatus
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24 {
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25 TAB_INVALID = -1,
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26 TAB_HEADER = 0,
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27 TAB_BLANK = 1,
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28 TAB_VALID = 2
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29 };
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30
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31 typedef vector<string> TAB_FIELDS;
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32
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33 //************************************************
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34 // TabFile Class methods and elements
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35 //************************************************
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36 class TabFile {
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37
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38 public:
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39
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40 // Constructor
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41 TabFile(const string &tabFile);
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42
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43 // Destructor
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44 ~TabFile(void);
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45
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46 // Open a TAB file for reading (creates an istream pointer)
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47 void Open(void);
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48
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49 // Close an opened TAB file.
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50 void Close(void);
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51
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52 // Get the next TAB entry in an opened TAB file.
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53 TabLineStatus GetNextTabLine (TAB_FIELDS &tab, int &lineNum);
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54
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55 private:
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56
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57 // data
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58 istream *_tabStream;
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59 string _tabFile;
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60
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61 // methods
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62 inline TabLineStatus parseTabLine (const vector<string> &lineVector, int &lineNum) {
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63 // bail out if we have a blank line
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64 if (lineVector.size() == 0)
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65 return TAB_BLANK;
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66 // real line with data
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67 if (lineVector[0][0] != '#') {
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68 return TAB_VALID;
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69 }
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70 // comment or header line
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71 else {
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72 lineNum--;
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73 return TAB_HEADER;
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74 }
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75 // default
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76 return TAB_INVALID;
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77 }
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78 };
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79
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80 #endif /* TABFILE_H */
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