1 | #ifndef BI_HELIX_HXX |
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2 | #define BI_HELIX_HXX |
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3 | |
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4 | #ifndef ARB_ASSERT_H |
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5 | #include <arb_assert.h> |
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6 | #endif |
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7 | #define bi_assert(bed) arb_assert(bed) |
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8 | |
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9 | #ifndef _CPP_CSTDLIB |
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10 | #include <cstdlib> |
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11 | #endif |
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12 | #ifndef _CPP_CSTDIO |
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13 | #include <cstdio> |
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14 | #endif |
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15 | #ifndef _CPP_CSTRING |
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16 | #include <cstring> |
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17 | #endif |
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18 | |
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19 | #ifndef ARBDB_H |
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20 | #include <arbdb.h> |
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21 | #endif |
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22 | |
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23 | typedef enum { |
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24 | HELIX_NONE, // used in entries |
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25 | HELIX_STRONG_PAIR, |
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26 | HELIX_PAIR, // used in entries |
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27 | HELIX_WEAK_PAIR, |
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28 | HELIX_NO_PAIR, // used in entries |
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29 | HELIX_USER0, |
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30 | HELIX_USER1, |
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31 | HELIX_USER2, |
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32 | HELIX_USER3, |
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33 | HELIX_DEFAULT, |
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34 | HELIX_NON_STANDARD0, // used in entries |
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35 | HELIX_NON_STANDARD1, // used in entries |
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36 | HELIX_NON_STANDARD2, // used in entries |
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37 | HELIX_NON_STANDARD3, // used in entries |
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38 | HELIX_NON_STANDARD4, // used in entries |
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39 | HELIX_NON_STANDARD5, // used in entries |
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40 | HELIX_NON_STANDARD6, // used in entries |
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41 | HELIX_NON_STANDARD7, // used in entries |
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42 | HELIX_NON_STANDARD8, // used in entries |
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43 | HELIX_NON_STANDARD9, // used in entries |
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44 | HELIX_NO_MATCH, |
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45 | HELIX_MAX |
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46 | } BI_PAIR_TYPE; |
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47 | |
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48 | struct BI_helix_entry { |
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49 | long pair_pos; |
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50 | BI_PAIR_TYPE pair_type; |
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51 | char *helix_nr; |
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52 | |
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53 | long next_pair_pos; /* next position with pair_type != HELIX_NONE |
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54 | * contains |
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55 | * 0 if uninitialized, |
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56 | * -1 behind last position */ |
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57 | bool allocated; |
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58 | }; |
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59 | |
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60 | class BI_helix { |
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61 | BI_helix_entry *entries; |
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62 | size_t Size; |
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63 | |
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64 | void _init(void); |
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65 | |
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66 | static char *helix_error; // error occurring during init is stored here |
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67 | |
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68 | const char *init(GBDATA *gb_main, const char *alignment_name, const char *helix_nr_name, const char *helix_name); |
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69 | |
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70 | protected: |
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71 | |
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72 | char *pairs[HELIX_MAX]; |
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73 | char *char_bind[HELIX_MAX]; |
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74 | |
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75 | bool is_pairtype(char left, char right, BI_PAIR_TYPE pair_type); |
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76 | |
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77 | public: |
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78 | |
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79 | static char *get_error() { return helix_error; } |
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80 | static void clear_error() { freeset(helix_error, NULL); } |
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81 | static void set_error(const char *err) { freedup(helix_error, err); } |
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82 | |
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83 | BI_helix(void); |
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84 | ~BI_helix(void); |
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85 | |
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86 | const char *init(GBDATA *gb_main); |
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87 | const char *init(GBDATA *gb_main, const char *alignment_name); |
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88 | const char *init(GBDATA *gb_helix_nr,GBDATA *gb_helix,size_t size); |
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89 | const char *initFromData(const char *helix_nr, const char *helix, size_t size); |
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90 | |
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91 | int check_pair(char left, char right, BI_PAIR_TYPE pair_type); // return 1 if bases form a pair |
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92 | |
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93 | size_t size() const { return Size; } |
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94 | bool has_entries() const { return entries; } |
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95 | const BI_helix_entry& entry(size_t pos) const { |
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96 | bi_assert(pos<Size); |
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97 | bi_assert(entries); |
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98 | return entries[pos]; |
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99 | } |
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100 | |
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101 | size_t opposite_position(size_t pos) const { |
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102 | const BI_helix_entry& Entry = entry(pos); |
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103 | bi_assert(Entry.pair_type != HELIX_NONE); // not a pair -> no opposite position |
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104 | return Entry.pair_pos; |
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105 | } |
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106 | BI_PAIR_TYPE pairtype(size_t pos) const { return pos<Size ? entry(pos).pair_type : HELIX_NONE; } |
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107 | const char *helixNr(size_t pos) const { return pairtype(pos) == HELIX_NONE ? 0 : entry(pos).helix_nr; } |
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108 | // Note: results of helixNr may be compared by == (instead of strcmp()) |
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109 | |
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110 | long first_pair_position() const; // first pair position (or -1) |
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111 | long next_pair_position(size_t pos) const; // next pair position behind 'pos' (or -1) |
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112 | |
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113 | long first_position(const char *helixNr) const; // returns -1 for non-existing helixNr's |
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114 | long last_position(const char *helixNr) const; // returns -1 for non-existing helixNr's |
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115 | }; |
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116 | |
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117 | |
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118 | |
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119 | |
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120 | class BI_ecoli_ref { |
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121 | size_t absLen; |
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122 | size_t relLen; |
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123 | |
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124 | size_t *abs2rel; |
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125 | size_t *rel2abs; |
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126 | |
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127 | void bi_exit(); |
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128 | |
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129 | public: |
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130 | BI_ecoli_ref(); |
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131 | ~BI_ecoli_ref(); |
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132 | |
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133 | const char *init(GBDATA *gb_main); |
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134 | const char *init(GBDATA *gb_main,char *alignment_name, char *ref_name); |
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135 | const char *init(const char *seq, size_t size); |
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136 | |
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137 | bool gotData() const { return abs2rel != 0; } |
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138 | |
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139 | size_t abs_2_rel(size_t abs) const { |
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140 | bi_assert(gotData()); |
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141 | if (abs >= absLen) abs = absLen-1; |
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142 | return abs2rel[abs]; |
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143 | } |
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144 | |
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145 | size_t rel_2_abs(size_t rel) const { |
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146 | bi_assert(gotData()); |
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147 | if (rel >= relLen) rel = relLen-1; |
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148 | return rel2abs[rel]; |
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149 | } |
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150 | |
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151 | size_t base_count() const { return relLen; } |
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152 | }; |
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153 | |
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154 | |
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155 | #endif |
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