1 | // =============================================================== // |
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2 | // // |
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3 | // File : ali_sequence.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // =============================================================== // |
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10 | |
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11 | #include "ali_sequence.hxx" |
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12 | |
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13 | // --------------------- |
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14 | // ALI_SEQUENCE |
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15 | |
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16 | int ALI_SEQUENCE::check() |
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17 | { |
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18 | unsigned char *seq_buf; |
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19 | unsigned long i; |
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20 | |
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21 | seq_buf = seq; |
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22 | for (i = 0; i < seq_len; i++, seq_buf++) |
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23 | if (*seq_buf > 6) |
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24 | ali_fatal_error("STOP"); |
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25 | |
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26 | return 1; |
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27 | } |
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28 | |
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29 | char *ALI_SEQUENCE::string() |
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30 | { |
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31 | char *str, *str_buf; |
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32 | unsigned char *seq_buf; |
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33 | unsigned long i; |
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34 | |
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35 | str = (char *) CALLOC((unsigned int) seq_len + 1, sizeof(char)); |
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36 | |
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37 | str_buf = str; |
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38 | seq_buf = seq; |
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39 | for (i = 0; i < seq_len; i++) { |
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40 | *(str_buf++) = *(seq_buf++); |
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41 | } |
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42 | *str_buf = '\0'; |
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43 | ali_sequence_to_string((unsigned char*) str, seq_len); |
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44 | |
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45 | return str; |
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46 | } |
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47 | |
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48 | // -------------------------- |
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49 | // ALI_NORM_SEQUENCE |
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50 | |
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51 | ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(char *Name, char *String) |
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52 | { |
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53 | unsigned long counter; |
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54 | unsigned char *s; |
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55 | int dot_flag; |
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56 | char *str; |
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57 | |
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58 | // Count only _BASES_ |
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59 | for (counter = 0, str = String; *str != '\0'; str++) |
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60 | if (ali_is_base(*str)) |
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61 | counter++; |
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62 | seq_len = counter; |
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63 | |
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64 | seq = (unsigned char*) CALLOC((unsigned int) seq_len, sizeof(unsigned char)); |
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65 | dots = (unsigned char **) CALLOC((unsigned int) (seq_len/8)+1, sizeof(unsigned char)); |
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66 | seq_name = strdup(Name); |
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67 | |
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68 | if (seq == 0 || dots == 0 || seq_name == 0) { |
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69 | ali_fatal_error("Out of memory"); |
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70 | } |
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71 | |
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72 | dot_flag = 0; |
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73 | (*dots)[0] |= (unsigned char) (1<<7); |
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74 | for (counter = 0, str = String, s = seq; *str != '\0'; str++) { |
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75 | if (ali_is_base(*str)) { |
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76 | *s++ = ali_base_to_number(*str); |
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77 | dot_flag = 0; |
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78 | counter++; |
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79 | } |
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80 | else { |
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81 | if (dot_flag == 0 && ali_is_dot(*str)) { |
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82 | (*dots)[(counter/8)] |= (unsigned char) (1<<(7-(counter%8))); |
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83 | dot_flag = 1; |
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84 | } |
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85 | } |
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86 | } |
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87 | } |
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88 | |
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89 | ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(ALI_SEQUENCE *SEQ) |
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90 | { |
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91 | unsigned long counter, pos; |
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92 | unsigned char *s; |
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93 | int dot_flag; |
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94 | unsigned char *str; |
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95 | |
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96 | for (counter = pos = 0, str = SEQ->sequence(); |
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97 | pos < SEQ->length(); pos++, str++) |
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98 | if (ali_is_base(*str)) |
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99 | counter++; |
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100 | seq_len = counter; |
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101 | |
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102 | seq = (unsigned char*) CALLOC((unsigned int) seq_len, sizeof(unsigned char)); |
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103 | dots = (unsigned char **) CALLOC((unsigned int) (seq_len/8)+1, sizeof(unsigned char)); |
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104 | seq_name = strdup(SEQ->name()); |
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105 | |
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106 | if (seq == 0 || dots == 0 || seq_name == 0) { |
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107 | ali_fatal_error("Out of memory"); |
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108 | } |
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109 | |
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110 | dot_flag = 0; |
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111 | (*dots)[0] |= (unsigned char) (1<<7); |
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112 | for (counter = pos = 0, str = SEQ->sequence(), s = seq; |
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113 | pos < SEQ->length(); str++, pos++) { |
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114 | if (ali_is_base(*str)) { |
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115 | *s++ = *str; |
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116 | dot_flag = 0; |
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117 | counter++; |
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118 | } |
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119 | else { |
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120 | if (dot_flag == 0 && ali_is_dot(*str)) { |
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121 | (*dots)[(counter/8)] |= (unsigned char) (1<<(7-(counter%8))); |
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122 | dot_flag = 1; |
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123 | } |
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124 | } |
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125 | } |
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126 | } |
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127 | |
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128 | char *ALI_NORM_SEQUENCE::string() |
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129 | { |
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130 | char *str, *str_buf; |
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131 | unsigned char *seq_buf; |
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132 | unsigned long i; |
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133 | |
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134 | str = (char *) CALLOC((unsigned int) seq_len + 1, sizeof(char)); |
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135 | if (str == 0) |
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136 | ali_fatal_error("Out of memory"); |
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137 | |
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138 | for (i = seq_len, str_buf = str, seq_buf = seq; i-- > 0;) |
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139 | *str_buf++ = *seq_buf++; |
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140 | *str_buf = '\0'; |
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141 | |
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142 | ali_sequence_to_string((unsigned char*) str, seq_len); |
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143 | |
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144 | return str; |
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145 | } |
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146 | |
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