1 | // ********************* INCLUDE |
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2 | #include <stdio.h> |
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3 | #include <stdlib.h> |
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4 | #include <string.h> |
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5 | #include <unistd.h> |
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6 | |
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7 | #include "ali_misc.hxx" |
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8 | #include "ali_pt.hxx" |
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9 | |
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10 | /* |
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11 | * Initialize the communication with the pt server |
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12 | */ |
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13 | int ALI_PT::init_communication(void) |
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14 | { |
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15 | const char *user = GB_getenvUSER(); |
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16 | |
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17 | /*** create and init local com structure ***/ |
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18 | if( aisc_create(link, PT_MAIN, com, MAIN_LOCS, PT_LOCS, &locs, LOCS_USER, user, NULL)){ |
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19 | return 1; |
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20 | } |
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21 | return 0; |
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22 | } |
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23 | |
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24 | char *ALI_PT::get_family_member(char *specifiedfamily,unsigned long number) |
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25 | { |
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26 | char *ptr = specifiedfamily; |
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27 | char *end; |
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28 | char *buffer, *dest; |
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29 | |
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30 | while (number > 0 && *ptr != '\0' && *ptr != ';') { |
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31 | while (*ptr != '\0' && *ptr != ';' && *ptr != ',') |
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32 | ptr++; |
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33 | if (*ptr == ',') |
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34 | ptr++; |
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35 | number--; |
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36 | } |
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37 | |
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38 | if (*ptr != '\0' && *ptr != ';') { |
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39 | end = ptr; |
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40 | while (*end != '\0' && *end != ',' && *end != ';') |
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41 | end++; |
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42 | |
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43 | buffer = dest = (char *) CALLOC((unsigned int) |
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44 | (end - ptr) + 1, sizeof(char)); |
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45 | if (buffer == 0) |
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46 | ali_fatal_error("Out of memory"); |
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47 | |
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48 | while (ptr != end) |
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49 | *dest++ = *ptr++; |
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50 | *dest = '\0'; |
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51 | |
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52 | return buffer; |
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53 | } |
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54 | return 0; |
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55 | } |
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56 | |
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57 | char *ALI_PT::get_extension_member(char *specifiedfamily, unsigned long number) |
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58 | { |
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59 | char *ptr = specifiedfamily; |
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60 | char *end; |
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61 | char *buffer, *dest; |
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62 | |
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63 | while (*ptr != '\0' && *ptr != ';') |
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64 | ptr++; |
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65 | if (*ptr == ';') |
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66 | ptr++; |
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67 | |
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68 | while (number > 0 && *ptr != '\0') { |
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69 | while (*ptr != '\0' && *ptr != ',') |
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70 | ptr++; |
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71 | if (*ptr == ',') |
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72 | ptr++; |
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73 | number--; |
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74 | } |
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75 | |
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76 | if (*ptr != '\0') { |
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77 | end = ptr; |
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78 | while (*end != '\0' && *end != ',') |
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79 | end++; |
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80 | |
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81 | buffer = dest = (char *) CALLOC((unsigned int) (end - ptr) + 1,sizeof(char)); |
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82 | if (buffer == 0) |
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83 | ali_fatal_error("Out of memory"); |
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84 | |
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85 | while (ptr != end) |
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86 | *dest++ = *ptr++; |
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87 | *dest = '\0'; |
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88 | |
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89 | return buffer; |
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90 | } |
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91 | |
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92 | return 0; |
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93 | } |
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94 | |
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95 | |
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96 | int ALI_PT::open(char *servername,GBDATA *gb_main) |
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97 | { |
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98 | if (arb_look_and_start_server(AISC_MAGIC_NUMBER,servername,gb_main)){ |
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99 | ali_message ("Cannot contact Probe bank server"); |
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100 | return -1; |
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101 | } |
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102 | |
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103 | const char *socketid = GBS_read_arb_tcp(servername); |
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104 | |
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105 | if (!socketid) { |
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106 | ali_message(GB_await_error()); |
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107 | return -1; |
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108 | } |
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109 | |
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110 | link = (aisc_com *)aisc_open(socketid,&com,AISC_MAGIC_NUMBER); |
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111 | |
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112 | if (!link) { |
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113 | ali_message ("Cannot contact Probe bank server "); |
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114 | return -1; |
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115 | } |
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116 | |
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117 | if (init_communication()) { |
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118 | ali_message ("Cannot contact Probe bank server (2)"); |
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119 | return -1; |
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120 | } |
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121 | |
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122 | return 0; |
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123 | } |
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124 | |
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125 | void ALI_PT::close(void) |
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126 | { |
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127 | if (link) aisc_close(link); |
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128 | link = 0; |
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129 | } |
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130 | |
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131 | /***************************************************************************** |
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132 | * |
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133 | * Public funktions |
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134 | * |
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135 | *****************************************************************************/ |
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136 | |
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137 | ALI_PT::ALI_PT(ALI_PT_CONTEXT *context) |
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138 | { |
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139 | link = 0; |
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140 | |
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141 | fam_list_max = context->fam_list_max; |
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142 | ext_list_max = context->ext_list_max; |
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143 | percent_min = context->percent_min; |
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144 | matches_min = context->matches_min; |
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145 | |
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146 | family_list = 0; |
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147 | extension_list = 0; |
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148 | |
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149 | if (context->use_specified_family != 0) { |
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150 | mode = SpecifiedMode; |
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151 | specified_family = strdup(context->use_specified_family); |
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152 | } |
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153 | else { |
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154 | mode = ServerMode; |
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155 | specified_family = 0; |
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156 | |
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157 | ali_message("Connecting to PT server"); |
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158 | if (open(context->servername,context->gb_main) != 0) { |
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159 | ali_fatal_error("Can't connect to PT server"); |
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160 | } |
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161 | ali_message("Connection established"); |
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162 | } |
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163 | } |
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164 | |
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165 | ALI_PT::~ALI_PT(void) |
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166 | { |
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167 | close(); |
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168 | |
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169 | if (family_list != 0 && !family_list->is_empty()) { |
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170 | delete family_list->first(); |
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171 | while (family_list->is_next()) |
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172 | delete family_list->next(); |
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173 | delete family_list; |
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174 | } |
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175 | if (extension_list != 0 && !extension_list->is_empty()) { |
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176 | delete extension_list->first(); |
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177 | while (extension_list->is_next()) |
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178 | delete extension_list->next(); |
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179 | delete extension_list; |
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180 | } |
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181 | } |
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182 | |
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183 | |
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184 | int ALI_PT::find_family(ALI_SEQUENCE *sequence, int find_type) |
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185 | { |
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186 | unsigned long number; |
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187 | int matches, max_matches; |
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188 | char *seq_name; |
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189 | T_PT_FAMILYLIST f_list; |
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190 | ali_pt_member *pt_member; |
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191 | char *species; |
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192 | |
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193 | bytestring bs; |
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194 | bs.data = sequence->string(); |
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195 | bs.size = strlen(bs.data)+1; |
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196 | |
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197 | family_list = new ALI_TLIST<ali_pt_member *>; |
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198 | extension_list = new ALI_TLIST<ali_pt_member *>; |
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199 | if (family_list == 0 || extension_list == 0) |
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200 | ali_fatal_error("Out of memory"); |
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201 | |
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202 | if (mode == ServerMode) { |
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203 | /* |
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204 | * Start find_family() at the PT_SERVER |
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205 | * |
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206 | * Here we have to make a loop, until the match count of the |
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207 | * first member is big enought |
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208 | * |
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209 | */ |
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210 | |
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211 | if (aisc_put(link, PT_LOCS, locs, |
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212 | LOCS_FF_FIND_TYPE, find_type, |
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213 | LOCS_FF_FIND_FAMILY, &bs, |
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214 | NULL)) |
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215 | { |
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216 | ali_message ("Communication Error (2)"); |
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217 | return -1; |
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218 | } |
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219 | |
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220 | /* |
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221 | * Read family list |
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222 | */ |
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223 | aisc_get(link, PT_LOCS, locs, LOCS_FF_FAMILY_LIST, &f_list, NULL); |
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224 | if (f_list == 0) |
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225 | ali_error("Family not found in PT Server"); |
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226 | |
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227 | aisc_get(link, PT_FAMILYLIST, f_list, |
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228 | FAMILYLIST_NAME,&seq_name, |
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229 | FAMILYLIST_MATCHES,&matches, |
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230 | FAMILYLIST_NEXT, &f_list, NULL); |
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231 | |
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232 | while (strcmp(seq_name,sequence->name()) == 0) { |
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233 | free(seq_name); |
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234 | if (f_list == 0) |
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235 | ali_error("Family too small in PT Server"); |
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236 | aisc_get(link, PT_FAMILYLIST, f_list, |
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237 | FAMILYLIST_NAME,&seq_name, |
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238 | FAMILYLIST_MATCHES,&matches, |
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239 | FAMILYLIST_NEXT, &f_list, NULL); |
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240 | } |
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241 | /* found the first element */ |
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242 | |
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243 | /* make the family list */ |
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244 | max_matches = matches; |
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245 | number = 0; |
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246 | do { |
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247 | pt_member = new ali_pt_member(seq_name,matches); |
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248 | family_list->append_end(pt_member); |
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249 | number++; |
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250 | do { |
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251 | if (f_list == 0) |
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252 | ali_error("Family too small in PT Server"); |
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253 | aisc_get(link, PT_FAMILYLIST, f_list, |
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254 | FAMILYLIST_NAME,&seq_name, |
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255 | FAMILYLIST_MATCHES,&matches, |
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256 | FAMILYLIST_NEXT, &f_list, NULL); |
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257 | if (strcmp(seq_name,sequence->name()) == 0) |
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258 | free(seq_name); |
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259 | } while (strcmp(seq_name,sequence->name()) == 0); |
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260 | } while (number < fam_list_max && |
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261 | (float) matches / (float) max_matches > percent_min); |
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262 | |
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263 | /* make the extension list */ |
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264 | number = 0; |
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265 | while (number < ext_list_max) { |
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266 | pt_member = new ali_pt_member(seq_name,matches); |
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267 | extension_list->append_end(pt_member); |
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268 | number++; |
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269 | do { |
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270 | if (f_list == 0) |
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271 | ali_error("Family too small in PT Server"); |
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272 | aisc_get(link, PT_FAMILYLIST, f_list, |
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273 | FAMILYLIST_NAME,&seq_name, |
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274 | FAMILYLIST_MATCHES,&matches, |
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275 | FAMILYLIST_NEXT, &f_list, NULL); |
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276 | if (strcmp(seq_name,sequence->name()) == 0) |
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277 | free(seq_name); |
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278 | } while (strcmp(seq_name,sequence->name()) == 0); |
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279 | } |
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280 | } |
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281 | else { |
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282 | number = 0; |
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283 | while ((species = get_family_member(specified_family, number)) != 0) { |
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284 | pt_member = new ali_pt_member(species,matches_min); |
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285 | if (pt_member == 0) |
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286 | ali_fatal_error("Out of memory"); |
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287 | family_list->append_end(pt_member); |
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288 | number++; |
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289 | } |
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290 | |
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291 | if (number == 0) |
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292 | ali_fatal_error("Specified family too small"); |
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293 | |
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294 | number = 0; |
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295 | while ((species = get_extension_member(specified_family, number)) != 0) { |
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296 | pt_member = new ali_pt_member(species, |
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297 | (int) (matches_min * percent_min) - 1); |
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298 | if (pt_member == 0) |
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299 | ali_fatal_error("Out of memory"); |
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300 | extension_list->append_end(pt_member); |
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301 | number++; |
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302 | } |
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303 | } |
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304 | |
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305 | free((char *) bs.data); |
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306 | return 0; |
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307 | } |
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308 | |
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309 | |
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310 | ALI_TLIST<ali_pt_member *> *ALI_PT::get_family_list(void) |
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311 | { |
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312 | ALI_TLIST<ali_pt_member *> *ret; |
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313 | |
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314 | ret = family_list; |
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315 | family_list = 0; |
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316 | |
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317 | return ret; |
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318 | } |
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319 | |
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320 | |
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321 | ALI_TLIST<ali_pt_member *> *ALI_PT::get_extension_list(void) |
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322 | { |
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323 | ALI_TLIST<ali_pt_member *> *ret; |
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324 | |
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325 | ret = extension_list; |
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326 | extension_list = 0; |
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327 | |
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328 | return ret; |
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329 | } |
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330 | |
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331 | |
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332 | |
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333 | /* |
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334 | int ALI_PT::first_family_(char **seq_name, int *matches) |
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335 | { |
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336 | if (mode == ServerMode) { |
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337 | aisc_get(link,PT_LOCS, locs,LOCS_FAMILY_LIST, &f_list, NULL); |
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338 | if (f_list == 0) |
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339 | return -1; |
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340 | |
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341 | aisc_get(link, PT_FAMILYLIST, f_list, |
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342 | FAMILYLIST_NAME,seq_name, |
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343 | FAMILYLIST_MATCHES,matches, |
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344 | FAMILYLIST_NEXT, &f_list, NULL); |
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345 | } |
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346 | else { |
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347 | *seq_name = strdup(family_list.first()); |
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348 | *matches = 1000; |
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349 | first_extension_call_flag = 1; |
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350 | } |
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351 | |
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352 | return 0; |
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353 | } |
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354 | |
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355 | int ALI_PT::next_family_(char **seq_name, int *matches) |
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356 | { |
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357 | if (mode == ServerMode) { |
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358 | |
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359 | if (f_list == 0) |
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360 | return -1; |
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361 | |
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362 | aisc_get(link, PT_FAMILYLIST, f_list, |
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363 | FAMILYLIST_NAME,seq_name, |
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364 | FAMILYLIST_MATCHES,matches, |
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365 | FAMILYLIST_NEXT, &f_list, NULL); |
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366 | } |
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367 | else { |
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368 | if (family_list.is_next()) { |
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369 | *seq_name = strdup(family_list.next()); |
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370 | *matches = 1000; |
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371 | first_extension_call_flag = 1; |
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372 | } |
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373 | else { |
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374 | if (extension_list.is_empty()) |
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375 | return -1; |
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376 | if (first_extension_call_flag == 1) { |
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377 | *seq_name = strdup(extension_list.first()); |
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378 | *matches = (int) (1000 * percent_for_family) - 1; |
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379 | first_extension_call_flag = 0; |
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380 | } |
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381 | else { |
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382 | if (extension_list.is_next()) { |
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383 | *seq_name = strdup(extension_list.next()); |
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384 | *matches = (int) (1000 * percent_for_family) - 1; |
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385 | } |
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386 | else { |
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387 | return -1; |
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388 | } |
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389 | } |
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390 | } |
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391 | } |
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392 | |
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393 | return 0; |
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394 | } |
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395 | |
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396 | |
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397 | */ |
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