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1 #ifndef GENOMIC_INTERVAL_HPP
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2 #define GENOMIC_INTERVAL_HPP
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3
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4 #include "interval.hpp"
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5 #include <stdio.h>
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6 #include <stdlib.h>
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7 #include <string>
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8 #include <sstream>
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9
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10 class GenomicInterval: public Interval {
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11
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12 public:
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13 string chromosome;
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14
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15 GenomicInterval(string chromosome = "", unsigned int start = 0, unsigned int end = 0): Interval(start, end), chromosome(chromosome) { }
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16
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17 bool onSameChromosome(const GenomicInterval &i) const {
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18 return (chromosome == i.chromosome);
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19 }
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20
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21 // friend bool operator==(const GenomicInterval &i1, const GenomicInterval &i2) {
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22 // return ((i1.onSameChromosome(i2)) && (Interval::i1 == Interval::i2));
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23 // }
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24
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25 // friend bool operator<(const GenomicInterval &i1, const GenomicInterval &i2) {
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26 // return ((i1.onSameChromosome(i2)) && (Interval::i1 < Interval::i2));
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27 // }
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28
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29 friend ofstream& operator<<(ofstream &stream, const GenomicInterval &i) {
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30 stream << i.chromosome << '\t' << i.start << '\t' << i.end << '\n';
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31 return stream;
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32 }
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33
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34 void parseFromLine(string &line) {
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35 string strStart, strEnd;
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36 istringstream iss(line);
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37 getline(iss, chromosome, '\t');
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38 getline(iss, strStart, '\t');
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39 getline(iss, strEnd, '\t');
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40 start = atoi(strStart.c_str());
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41 end = atoi(strEnd.c_str());
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42 //cout << "read " << chromosome << ":" << start << ".." << end << endl;
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43 }
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44
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45 };
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46
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47 #endif
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