Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/man/man3/ExperimentFile.3 @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 .TH ExperimentFile 3 "" "" "Staden Package" |
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2 |
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3 .SH NAME |
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4 |
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5 .LP |
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6 .BR exp_read_info , |
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7 .BR exp_fread_info , |
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8 .BR exp_create_info , |
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9 .BR exp_destroy_info , |
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10 .BR exp_create_range , |
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11 .BR exp_extract_range , |
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12 .BR exp_get_feature_index , |
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13 .BR exp_get_int , |
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14 .BR exp_get_rng , |
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15 .BR exp_get_str , |
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16 .BR exp_put_int , |
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17 .BR exp_put_rng , |
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18 .BR exp_put_str , |
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19 .BR exp_print_line , |
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20 .BR exp_print_seq , |
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21 .BR exp_print_file , |
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22 .BR opos2str , |
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23 .BR str2opos , |
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24 .BR conf2str , |
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25 .BR str2conf |
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26 \- Manipulations of the Experiment File format |
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27 |
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28 .IX "exp_read_info()" "" "exp_read_info()" |
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29 .IX "exp_fread_info()" "" "exp_fread_info()" |
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30 .IX "exp_create_info()" "" "exp_create_info()" |
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31 .IX "exp_destroy_info()" "" "exp_destroy_info()" |
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32 .IX "exp_create_range()" "" "exp_create_range()" |
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33 .IX "exp_extract_range()" "" "exp_extract_range()" |
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34 .IX "exp_get_feature_index()" "" "exp_get_feature_index()" |
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35 .IX "exp_get_int()" "" "exp_get_int()" |
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36 .IX "exp_get_rng()" "" "exp_get_rng()" |
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37 .IX "exp_get_str()" "" "exp_get_str()" |
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38 .IX "exp_put_int()" "" "exp_put_int()" |
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39 .IX "exp_put_rng()" "" "exp_put_rng()" |
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40 .IX "exp_put_str()" "" "exp_put_str()" |
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41 .IX "exp_print_line()" "" "exp_print_line()" |
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42 .IX "exp_print_seq()" "" "exp_print_seq()" |
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43 .IX "exp_print_file()" "" "exp_print_file()" |
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44 .IX "opos2str()" "" "opos2str()" |
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45 .IX "str2opos()" "" "str2opos()" |
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46 .IX "conf2str()" "" "conf2str()" |
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47 .IX "str2conf()" "" "str2conf()" |
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48 |
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49 .SH SYNOPSIS |
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50 .LP |
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51 .nf |
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52 .ft B |
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53 #include <expFileIO.h> |
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54 |
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55 .nf |
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56 .ft B |
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57 Exp_info *exp_read_info( |
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58 char *file); |
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59 .ft |
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60 .fi |
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61 .LP |
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62 .nf |
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63 .ft B |
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64 Exp_info *exp_fread_info( |
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65 FILE *fp); |
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66 .ft |
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67 .fi |
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68 .LP |
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69 .nf |
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70 .ft B |
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71 Exp_info *exp_create_info(); |
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72 .ft |
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73 .fi |
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74 .LP |
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75 .nf |
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76 .ft B |
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77 void exp_destroy_info( |
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78 Exp_info *e); |
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79 .ft |
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80 .fi |
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81 .LP |
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82 .nf |
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83 .ft B |
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84 char *exp_create_range( |
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85 char *str, |
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86 int start, |
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87 int end); |
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88 .ft |
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89 .fi |
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90 .LP |
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91 .nf |
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92 .ft B |
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93 int exp_extract_range( |
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94 char *str, |
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95 int *start, |
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96 int *end); |
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97 .ft |
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98 .fi |
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99 .LP |
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100 .nf |
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101 .ft B |
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102 int exp_get_feature_index( |
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103 char *e); |
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104 .ft |
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105 .fi |
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106 .LP |
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107 .nf |
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108 .ft B |
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109 int exp_get_int( |
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110 Exp_info *e, |
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111 int id, |
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112 int *val); |
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113 .ft |
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114 .fi |
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115 .LP |
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116 .nf |
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117 .ft B |
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118 int exp_get_rng( |
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119 Exp_info *e, |
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120 int id, |
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121 int *from, |
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122 int *to); |
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123 .ft |
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124 .fi |
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125 .LP |
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126 .nf |
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127 .ft B |
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128 int exp_get_str( |
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129 Exp_info *e, |
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130 int id, |
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131 char *s, |
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132 f_implicit s_l); |
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133 .ft |
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134 .fi |
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135 .LP |
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136 .nf |
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137 .ft B |
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138 int exp_put_int( |
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139 Exp_info *e, |
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140 int id, |
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141 int *val); |
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142 .ft |
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143 .fi |
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144 .LP |
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145 .nf |
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146 .ft B |
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147 int exp_put_rng( |
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148 Exp_info *e, |
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149 int id, |
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150 int *from, |
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151 int *to); |
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152 .ft |
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153 .fi |
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154 .LP |
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155 .nf |
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156 .ft B |
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157 int exp_put_str( |
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158 Exp_info *e, |
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159 int id, |
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160 char *s, |
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161 f_implicit s_l); |
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162 .ft |
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163 .fi |
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164 .LP |
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165 .nf |
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166 .ft B |
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167 int exp_print_line( |
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168 FILE *fp, |
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169 Exp_info *e, |
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170 int eflt, |
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171 int i); |
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172 .ft |
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173 .fi |
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174 .LP |
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175 .nf |
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176 .ft B |
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177 int exp_print_seq( |
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178 FILE *fp, |
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179 Exp_info *e, |
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180 int eflt, |
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181 int i); |
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182 .ft |
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183 .fi |
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184 .LP |
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185 .nf |
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186 .ft B |
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187 void exp_print_file( |
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188 FILE *fp, |
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189 Exp_info *e); |
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190 .ft |
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191 .fi |
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192 .LP |
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193 .nf |
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194 .ft B |
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195 char *opos2str( |
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196 int2 *opos, |
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197 int len, |
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198 char *buf); |
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199 .ft |
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200 .fi |
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201 .LP |
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202 .nf |
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203 .ft B |
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204 int str2opos( |
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205 int2 *opos, |
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206 char *buf); |
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207 .ft |
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208 .fi |
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209 .LP |
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210 .nf |
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211 .ft B |
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212 char *conf2str( |
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213 int1 *conf, |
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214 int len, |
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215 char *buf); |
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216 .ft |
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217 .fi |
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218 .LP |
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219 .nf |
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220 .ft B |
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221 int str2conf( |
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222 int1 *conf, |
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223 char *buf); |
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224 .ft |
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225 .fi |
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226 |
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227 .SH DESCRIPTION |
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228 .LP |
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229 These functions manipulate Experiment Files. They include functions for |
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230 reading, writing, and editing the files. The principle structure used by the |
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231 routines is the \fBExp_info\fR structure. This is as follows. |
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232 .EX 5 |
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233 .ft B |
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234 #define MAXIMUM_EFLT_LENGTH 4 |
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235 #define MAXIMUM_EFLTS 48 |
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236 #define EXP_FILE_LINE_LENGTH 128 |
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237 |
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238 typedef Array Exp_entries; |
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239 |
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240 typedef struct { |
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241 Array entries[MAXIMUM_EFLTS]; /* array of array of entries */ |
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242 int Nentries[MAXIMUM_EFLTS]; /* array of number of entries */ |
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243 FILE *fp; |
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244 } Exp_info; |
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245 |
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246 #define NULL_Exp_info ( (Exp_info *) NULL ) |
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247 .ft |
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248 .EE |
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249 .LP |
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250 For the purposes of simple and efficient coding, each line on an experiment |
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251 file must be smaller than the defined EXP_FILE_LINE_LENGTH, which is 128 |
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252 characters. |
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253 .LP |
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254 Many functions take an experiment file line type identifier as an argument. |
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255 These functions are listed in the prototypes as taking \fBint id\fR. Here |
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256 \fBid\fR should be specified using one of the macros defining in the header |
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257 file. They take the form of \fBEFLT_\fRXX where XX is the line type. For |
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258 instance, the \fBID\fR line type identifier should be written as |
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259 \fBEFLT_ID\fR. |
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260 .LP |
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261 The C functions available follow. Some FORTRAN interfaces are also available, |
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262 but these are not documented. See the include file for their prototypes. |
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263 .LP |
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264 .B exp_read_info |
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265 and |
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266 .B exp_fread_info |
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267 read an experiment file into an allocated \fBExp_info\fR structure. If |
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268 successful, the structure pointer is return. Otherwise the null pointer is |
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269 returned. |
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270 .LP |
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271 .B exp_create_info |
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272 allocates and initialises a new, blank, \fBExp_info\fR structure. If |
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273 successful, the structure pointer is return. Otherwise the null pointer is |
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274 returned. |
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275 .LP |
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276 .B exp_destroy_info |
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277 deallocates an \fBExp_info\fR structure. |
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278 .LP |
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279 .B exp_create_range |
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280 creates a string using the experiment file range format of "start..stop". This |
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281 format is used by the AQ, ON, TG and TC line types. The buffer specified |
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282 should be large enough to hold the string. The function returns the \fBstr\fR |
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283 pointer supplied as an argument. |
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284 .LP |
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285 .B exp_extract_range |
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286 extracts the start and end values from the string representation of a range; |
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287 "start..stop". The values are stored in the integer pointers sent as |
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288 arguments. If successful, the function returns 0. Otherwise -1 is returned. |
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289 .LP |
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290 .B exp_get_feature_index |
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291 converts from a string representation of an experiment file line type to the |
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292 integer value. For example, \fBexp_get_feature_index("SQ")\fR returns the |
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293 integer 22, which is the same as the \fBEFLT_SQ\fR definition. |
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294 .LP |
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295 .B exp_get_int |
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296 obtains the integer value held in a specific line type. The value is stored in |
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297 the integer pointer \fBval\fR. If successful, the function returns 0. |
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298 Otherwise 1 is returned. |
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299 .LP |
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300 .B exp_get_rng |
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301 obtains the range values held in a specific line type. The values are stored in |
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302 the integer pointers \fBfrom\fR and \fBto\fR. If successful, the function |
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303 returns 0. Otherwise 1 is returned. |
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304 .LP |
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305 .B exp_get_str |
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306 obtains the string value held in a specific line type. The value is stored in |
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307 the string \fBs\fR. At most \fBs_l\fR characters are copied. If successful, |
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308 the function returns 0. Otherwise 1 is returned. |
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309 .LP |
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310 .B exp_put_int |
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311 writes the integer pointed to by \fBval\fR to the specified line type. If |
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312 successful, the function returns 0. Otherwise 1 is returned. |
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313 .LP |
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314 .B exp_put_rng |
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315 writes the range pointed to by \fBfrom\fR and \fBto\fR to the specified line |
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316 type. If successful, the function returns 0. Otherwise 1 is returned. |
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317 .LP |
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318 .B exp_put_str |
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319 writes the string \fBs\fR of length \fBs_l\fR to the specified line type. If |
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320 successful, the function returns 0. Otherwise 1 is returned. |
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321 .LP |
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322 .B exp_print_line |
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323 outputs all entries of the specified type to the specified file pointer. |
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324 .LP |
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325 .B exp_print_seq |
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326 .LP |
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327 .B exp_print_file |
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328 outputs all entries of all line types to the specified file pointer. |
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329 .LP |
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330 .B opos2str |
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331 converts an array of original positions held in \fBopos\fR with \fBlen\fR |
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332 elements to a string suitable for use in the ON line type. The \fBbuf\fR |
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333 should be large enough to hold the string, which in the worst case will be |
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334 4 * sequence length. Returns \fBbuf\fR. |
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335 .LP |
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336 .B str2opos |
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337 converts the experiment file original position string held in \fBbuf\fR to an |
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338 array of original positions to be stored in \fBopos\fR. \fBopos\fR must be |
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339 large enough to hold the data, hence it should be of the same length as the |
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340 sequence. Returns the number of elements written to the \fBopos\fR array. |
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341 .LP |
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342 .B conf2str |
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343 converts an array of confidence values helf in \fBconf\dR with \fBlen\fR |
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344 elements to a string suitable for use in the AV line type. The \fBbuf\fR |
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345 should be large enough to hold the string, which in the worst case will be |
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346 4 * sequence length. Returns \fBbuf\fR. |
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347 .LP |
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348 .B str2conf |
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349 convers the experiment file confidence values string held in \fBbuf\fR to an |
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350 array of confidence values to be stored in \fBconf\fR. \fBconf\fR must be |
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351 large enough to hold the data, hence it should be of the same length as the |
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352 sequence. Returns the number of elements written to the \fBconf\fR array. |
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353 |
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354 .SH SEE ALSO |
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355 .LP |
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356 .BR ExperimentFile (4) |