1 | #ifndef theplu_yat_omic_gemomic_position |
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2 | #define theplu_yat_omic_gemomic_position |
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3 | |
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4 | /* |
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5 | $Id: GenomicPosition.h 2919 2012-12-19 06:54:23Z peter $ |
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6 | |
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7 | Copyright (C) 2010, 2012 Peter Johansson |
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8 | |
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9 | The yat library is free software; you can redistribute it and/or |
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10 | modify it under the terms of the GNU General Public License as |
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11 | published by the Free Software Foundation; either version 3 of the |
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12 | License, or (at your option) any later version. |
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13 | |
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14 | The yat library is distributed in the hope that it will be useful, |
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15 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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16 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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17 | General Public License for more details. |
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18 | |
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19 | You should have received a copy of the GNU General Public License |
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20 | along with this program. If not, see <http://www.gnu.org/licenses/>. |
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21 | */ |
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22 | |
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23 | #include <boost/operators.hpp> |
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24 | |
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25 | #include <string> |
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26 | |
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27 | namespace theplu { |
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28 | namespace yat { |
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29 | namespace omic { |
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30 | |
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31 | /** |
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32 | Class used to hold genomic location, i.e., chromosome and |
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33 | position. |
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34 | |
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35 | The class inherits from boost::operators, which means besides the |
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36 | operators directly implemented (operator== and operator<) also |
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37 | operator<=, operator>, operator>=, and operator!= are supported. |
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38 | |
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39 | \since New in yat 0.7 |
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40 | */ |
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41 | class GenomicPosition : boost::operators<GenomicPosition> |
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42 | { |
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43 | public: |
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44 | /** |
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45 | Creates a GenomicPosition with undefined values. |
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46 | */ |
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47 | GenomicPosition(void); |
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48 | |
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49 | /** |
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50 | \brief Constructor |
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51 | \param chr chromosome |
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52 | \param pos non-negative number describing location on chromosome |
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53 | */ |
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54 | GenomicPosition(unsigned short chr , unsigned long pos); |
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55 | |
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56 | /** |
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57 | \brief Constructor |
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58 | \param chr chromosome |
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59 | \param pos non-negative number describing location on chromosome |
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60 | |
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61 | chr2int is used to translate \a chr into an \c unsigned \c |
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62 | short, and utility::convert is used to translate \a pos into an |
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63 | \c unsigned \c long. |
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64 | |
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65 | \see chr2int |
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66 | */ |
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67 | GenomicPosition(const std::string& chr, const std::string& pos); |
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68 | |
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69 | /** |
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70 | \return reference to chr |
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71 | */ |
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72 | unsigned short& chromosome(void); |
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73 | |
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74 | /** |
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75 | \return const reference to chr |
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76 | */ |
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77 | const unsigned short& chromosome(void) const; |
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78 | |
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79 | /** |
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80 | \return reference to position |
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81 | */ |
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82 | unsigned long int& position(void); |
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83 | |
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84 | /** |
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85 | \return const reference to position |
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86 | */ |
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87 | const unsigned long int& position(void) const; |
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88 | |
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89 | private: |
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90 | unsigned short chr_; |
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91 | unsigned long pos_; |
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92 | }; |
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93 | |
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94 | /** |
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95 | \relates GenomicPosition |
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96 | |
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97 | \return \c true if chromosome of \a lhs is less than chromosome |
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98 | of \a rhs or if chromosome of \a lhs equals chromosome of \a rhs |
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99 | and position of \a lhs is less than position of \a rhs. |
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100 | |
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101 | \since New in yat 0.7 |
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102 | */ |
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103 | bool operator<(const GenomicPosition& lhs, const GenomicPosition& rhs); |
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104 | |
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105 | /** |
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106 | \relates GenomicPosition |
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107 | |
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108 | \return \c true if chromosomes and positions are the same. |
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109 | |
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110 | \since New in yat 0.7 |
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111 | */ |
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112 | bool operator==(const GenomicPosition& lhs, const GenomicPosition& rhs); |
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113 | |
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114 | /** |
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115 | \brief transform a string to unsigned short chromosome number |
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116 | |
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117 | If \a str starts with 'chr' that prefix is stripped away before |
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118 | translating the string to chromosome number. Function translates |
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119 | "X" to 23, "Y" to 24, and "M" or "MT" to 25. For other inputs |
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120 | utility::convert is used to transform the input to an unsigned |
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121 | short. |
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122 | |
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123 | \return chromosome number |
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124 | |
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125 | \since New in yat 0.7 |
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126 | */ |
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127 | unsigned short chr2int(const std::string& str); |
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128 | |
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129 | }}} |
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130 | #endif |
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