1 | #include <stdio.h> |
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2 | #include <arbdb.h> |
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3 | #include <arbdbt.h> |
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4 | #include <aw_root.hxx> |
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5 | #include <aw_device.hxx> |
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6 | #include <aw_window.hxx> |
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7 | #include <aw_awars.hxx> |
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8 | #include <awt_sel_boxes.hxx> |
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9 | #include <servercntrl.h> |
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10 | #include <PT_com.h> |
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11 | #include <client.h> |
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12 | |
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13 | #include <sys/types.h> |
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14 | #include <sys/wait.h> |
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15 | |
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16 | #include <unistd.h> |
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17 | |
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18 | #include <stdlib.h> |
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19 | #include <string> |
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20 | #include <sstream> |
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21 | #include <iostream> |
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22 | #include <vector> |
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23 | |
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24 | #include <string.h> |
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25 | |
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26 | // need to use AWTC_faligner_cd defined here to get selected species |
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27 | #include <fast_aligner.hxx> |
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28 | #include "graph_aligner_gui.hxx" |
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29 | #include "ed4_defs.hxx" |
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30 | |
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31 | using std::cerr; |
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32 | using std::cout; |
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33 | using std::endl; |
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34 | |
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35 | #define GA_AWAR_ROOT "sina/" |
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36 | #define GA_AWAR_CMD GA_AWAR_ROOT "command" |
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37 | #define GA_AWAR_TGT GA_AWAR_ROOT "target" |
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38 | #define GA_AWAR_SAI GA_AWAR_ROOT "sai" |
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39 | #define GA_AWAR_ALIGNMENT GA_AWAR_ROOT "alignment" |
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40 | #define GA_AWAR_PROTECTION GA_AWAR_ROOT "protection" |
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41 | #define GA_AWAR_TURN_CHECK GA_AWAR_ROOT "turncheck" |
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42 | #define GA_AWAR_LOGLEVEL GA_AWAR_ROOT "loglevel" |
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43 | #define GA_AWAR_REALIGN GA_AWAR_ROOT "realign" |
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44 | #define GA_AWAR_PTLOAD GA_AWAR_ROOT "ptload" |
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45 | #define GA_AWAR_COPYMARKREF GA_AWAR_ROOT "copymarkref" |
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46 | #define GA_AWAR_GAP_PEN GA_AWAR_ROOT "gap_pen" |
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47 | #define GA_AWAR_GAP_EXT GA_AWAR_ROOT "gap_ext" |
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48 | #define GA_AWAR_ADVANCED GA_AWAR_ROOT "advanced" |
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49 | #define GA_AWAR_FS_MIN GA_AWAR_ROOT "fs_min" |
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50 | #define GA_AWAR_FS_MAX GA_AWAR_ROOT "fs_max" |
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51 | #define GA_AWAR_FS_MSC GA_AWAR_ROOT "fs_msc" |
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52 | #define GA_AWAR_MIN_FULL GA_AWAR_ROOT "min_full" |
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53 | #define GA_AWAR_FULL_MINLEN GA_AWAR_ROOT "full_minlen" |
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54 | #define GA_AWAR_OVERHANG GA_AWAR_ROOT "overhang" |
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55 | #define GA_AWAR_THREADS GA_AWAR_ROOT "threads" |
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56 | #define GA_AWAR_QSIZE GA_AWAR_ROOT "qsize" |
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57 | |
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58 | void create_sina_variables(AW_root *root, AW_default db1) { |
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59 | root->awar_string(GA_AWAR_CMD, "sina", db1); |
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60 | root->awar_int(GA_AWAR_TGT, 2, db1); |
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61 | root->awar_int(AWAR_PT_SERVER, 0, db1); |
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62 | root->awar_string(GA_AWAR_SAI, "none", db1); |
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63 | root->awar_int(GA_AWAR_PROTECTION, 0, db1); |
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64 | root->awar_string(GA_AWAR_LOGLEVEL, "3", db1); |
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65 | root->awar_int(GA_AWAR_TURN_CHECK, 1, db1); |
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66 | root->awar_int(GA_AWAR_REALIGN, 1, db1); |
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67 | root->awar_int(GA_AWAR_PTLOAD, 0, db1); |
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68 | root->awar_int(GA_AWAR_COPYMARKREF, 0, db1); |
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69 | root->awar_float(GA_AWAR_GAP_PEN, 5.0, db1); |
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70 | root->awar_float(GA_AWAR_GAP_EXT, 2.0, db1); |
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71 | root->awar_int(GA_AWAR_ADVANCED, 0, db1); |
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72 | root->awar_int(GA_AWAR_FS_MIN, 15, db1); |
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73 | root->awar_int(GA_AWAR_FS_MAX, 40, db1); |
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74 | root->awar_float(GA_AWAR_FS_MSC, .7, db1); |
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75 | root->awar_int(GA_AWAR_MIN_FULL, 1, db1); |
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76 | root->awar_int(GA_AWAR_FULL_MINLEN, 1400, db1); |
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77 | root->awar_string(GA_AWAR_OVERHANG, "attach", db1); |
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78 | root->awar_int(GA_AWAR_THREADS, 1, db1); |
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79 | root->awar_int(GA_AWAR_QSIZE, 1, db1); |
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80 | } |
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81 | |
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82 | AW_active sina_mask(AW_root *root) { |
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83 | const char *sinaName = root->awar(GA_AWAR_CMD)->read_char_pntr(); |
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84 | char *sina = GB_executable(sinaName); |
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85 | const char *fail_reason = 0; |
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86 | |
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87 | if (sina) { |
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88 | int exitstatus = system(GBS_global_string("%s --has-cli-vers 1", sina)); |
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89 | exitstatus = WEXITSTATUS(exitstatus); |
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90 | |
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91 | switch (exitstatus) { |
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92 | case EXIT_SUCCESS: |
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93 | break; |
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94 | |
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95 | case EXIT_FAILURE: |
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96 | fail_reason = "Incompatible SINA and ARB versions"; |
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97 | break; |
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98 | |
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99 | case 127: // libs missing |
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100 | default: // unexpected |
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101 | fail_reason = GBS_global_string("Could execute SINA binary '%s' (exitstatus was %i)", |
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102 | sinaName, exitstatus); |
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103 | break; |
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104 | } |
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105 | free(sina); |
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106 | } |
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107 | else { |
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108 | fail_reason = GBS_global_string("%s not found", sinaName); |
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109 | } |
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110 | |
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111 | if (fail_reason) { |
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112 | fprintf(stderr, |
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113 | "Note: SINA (SILVA Aligner) disabled (Reason: %s)\n" |
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114 | " Visit http://www.ribocon.com/sina/ for more information.\n", |
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115 | fail_reason); |
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116 | } |
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117 | |
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118 | return fail_reason ? AWM_DISABLED : AWM_ALL; |
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119 | } |
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120 | |
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121 | static void sina_start(AW_window *window, AW_CL cd2) { |
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122 | GB_ERROR gb_error; |
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123 | AW_root *root = window->get_root(); |
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124 | cerr << "Starting SINA..." << endl; |
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125 | |
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126 | // make string from pt server selection |
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127 | int pt = root->awar(AWAR_PT_SERVER)->read_int(); |
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128 | const char *pt_server; |
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129 | std::stringstream ptnam; |
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130 | ptnam << "ARB_PT_SERVER" << pt; |
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131 | pt_server = GBS_read_arb_tcp(ptnam.str().c_str()); |
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132 | if (!pt_server) { |
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133 | aw_message("Unable to find definition for chosen PT-server"); |
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134 | return; |
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135 | } |
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136 | const char *pt_db = pt_server + strlen(pt_server) +1; |
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137 | pt_db += strlen(pt_db)+3; |
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138 | |
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139 | // start pt server if necessary |
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140 | gb_error = arb_look_and_start_server(AISC_MAGIC_NUMBER,ptnam.str().c_str(), |
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141 | GLOBAL_gb_main); |
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142 | if (gb_error) { |
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143 | std::stringstream tmp; |
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144 | tmp << "Cannot contact PT server. Aborting" << endl |
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145 | << " ID: \"" << tmp.str().c_str() |
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146 | << "\" PORT: \"" << pt_server |
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147 | << "\" DB: \"" << pt_db << endl |
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148 | << "\" GBERROR: \"" << gb_error << "\"" << endl; |
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149 | aw_message(tmp.str().c_str()); |
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150 | return; |
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151 | } |
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152 | |
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153 | // create temporary file |
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154 | char* tmpfile_tpl = GB_unique_filename("sina_select","tmp"); |
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155 | char* tmpfile; |
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156 | FILE* tmpfile_F = GB_fopen_tempfile(tmpfile_tpl,"w", &tmpfile); |
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157 | if (!tmpfile_F) { |
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158 | std::stringstream tmp; |
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159 | tmp << "Error: Unable to create temporary file \"" << tmpfile << "\"!"; |
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160 | aw_message(tmp.str().c_str()); |
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161 | return; |
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162 | } |
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163 | GB_remove_on_exit(tmpfile); |
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164 | |
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165 | std::vector<std::string> spec_names; |
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166 | switch(root->awar(GA_AWAR_TGT)->read_int()) { |
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167 | case 0: //current |
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168 | { |
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169 | char *spec_name = root->awar(AWAR_SPECIES_NAME)->read_string(); |
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170 | if (spec_name) { |
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171 | fwrite(spec_name, strlen(spec_name), 1, tmpfile_F); |
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172 | fwrite("\n", 1, 1, tmpfile_F); |
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173 | } else { |
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174 | aw_message("Unable to get name of currently active species"); |
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175 | return; |
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176 | } |
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177 | } |
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178 | break; |
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179 | case 1: //selected |
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180 | { |
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181 | struct AWTC_faligner_cd *cd = (struct AWTC_faligner_cd *)cd2; |
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182 | GB_begin_transaction(GLOBAL_gb_main); |
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183 | int num_selected = 0; |
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184 | for (GBDATA *gb_spec = cd->get_first_selected_species(&num_selected); |
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185 | gb_spec; gb_spec = cd->get_next_selected_species()) { |
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186 | GBDATA *gbd_name = GB_find(gb_spec, "name", down_level); |
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187 | if (gbd_name) { |
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188 | const char *str = GB_read_char_pntr(gbd_name); |
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189 | fwrite(str, strlen(str), 1, tmpfile_F); |
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190 | fwrite("\n", 1, 1, tmpfile_F); |
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191 | } |
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192 | } |
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193 | GB_commit_transaction(GLOBAL_gb_main); |
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194 | } |
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195 | break; |
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196 | case 2: //marked |
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197 | { |
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198 | GB_begin_transaction(GLOBAL_gb_main); |
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199 | for (GBDATA *gb_spec = GBT_first_marked_species(GLOBAL_gb_main); |
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200 | gb_spec; gb_spec = GBT_next_marked_species(gb_spec)) { |
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201 | GBDATA *gbd_name = GB_find(gb_spec, "name", down_level); |
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202 | if (gbd_name) { |
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203 | const char *str = GB_read_char_pntr(gbd_name); |
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204 | fwrite(str, strlen(str), 1, tmpfile_F); |
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205 | fwrite("\n", 1, 1, tmpfile_F); |
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206 | } |
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207 | } |
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208 | GB_commit_transaction(GLOBAL_gb_main); |
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209 | } |
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210 | break; |
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211 | } |
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212 | fclose(tmpfile_F); |
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213 | |
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214 | // build command line |
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215 | std::stringstream cmdline; |
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216 | cmdline << root->awar(GA_AWAR_CMD)->read_string() |
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217 | << " -i :" |
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218 | << " --queue-size " << root->awar(GA_AWAR_QSIZE)->read_as_string() |
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219 | << " --ncpu " << root->awar(GA_AWAR_THREADS)->read_as_string() |
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220 | << " --verbosity " << root->awar(GA_AWAR_LOGLEVEL)->read_as_string() |
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221 | << " --ptdb " << (root->awar(GA_AWAR_PTLOAD)->read_int()?pt_db:":") |
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222 | << " --ptport " << pt_server |
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223 | << " --turn " << (root->awar(GA_AWAR_TURN_CHECK)->read_int()?"all":"none") |
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224 | << (root->awar(GA_AWAR_REALIGN)->read_int()?" --realign":"") |
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225 | << " --overhang " << root->awar(GA_AWAR_OVERHANG)->read_string() |
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226 | << " --filter " << root->awar(GA_AWAR_SAI)->read_string() |
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227 | << " --fs-min " << root->awar(GA_AWAR_FS_MIN)->read_as_string() |
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228 | << " --fs-msc " << root->awar(GA_AWAR_FS_MSC)->read_as_string() |
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229 | << " --fs-max " << root->awar(GA_AWAR_FS_MAX)->read_as_string() |
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230 | << " --fs-req " << "1" |
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231 | << " --fs-req-full " << root->awar(GA_AWAR_MIN_FULL)->read_as_string() |
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232 | << " --fs-full-len " << root->awar(GA_AWAR_FULL_MINLEN)->read_as_string() |
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233 | << " --pen-gap " << root->awar(GA_AWAR_GAP_PEN)->read_as_string() |
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234 | << " --pen-gapext " << root->awar(GA_AWAR_GAP_EXT)->read_as_string() |
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235 | << (root->awar(GA_AWAR_COPYMARKREF)->read_int()?" --markcopy":"") |
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236 | << " --prot-level " << root->awar(GA_AWAR_PROTECTION)->read_as_string() |
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237 | << " --select-file " << tmpfile; |
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238 | |
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239 | gb_error = GB_xcmd(cmdline.str().c_str(), GB_TRUE, GB_FALSE); |
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240 | |
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241 | aw_message("SINA finished aligning."); |
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242 | } |
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243 | |
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244 | |
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245 | |
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246 | static char* filter_sai(GBDATA *gb_extended, AW_CL /*cd*/) { |
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247 | char *result = 0; |
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248 | GBDATA *gbd = GB_search(gb_extended, "ali_16s/_TYPE", GB_FIND); |
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249 | if (gbd) { |
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250 | const char* type = GB_read_char_pntr(gbd); |
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251 | if (type && strncmp("PV", type, 2) == 0) { |
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252 | gbd = GB_find(gb_extended, "name", down_level); |
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253 | result = GB_read_string(gbd); |
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254 | } |
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255 | } |
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256 | return result; |
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257 | } |
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258 | |
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259 | static AW_window* create_select_sai_window(AW_root *root) { |
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260 | static AW_window_simple *aws = 0; |
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261 | if (aws) return aws; |
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262 | |
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263 | aws = new AW_window_simple; |
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264 | |
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265 | aws->init(root, "SELECT_SAI", "Select Sai"); |
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266 | aws->load_xfig("selectSAI.fig"); |
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267 | |
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268 | aws->at("selection"); |
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269 | aws->callback((AW_CB0)AW_POPDOWN); |
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270 | |
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271 | awt_create_selection_list_on_extendeds(GLOBAL_gb_main, (AW_window*) aws, |
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272 | GA_AWAR_SAI, filter_sai, (AW_CL)root); |
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273 | |
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274 | aws->at("close"); |
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275 | aws->callback(AW_POPDOWN); |
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276 | aws->create_button("CLOSE", "CLOSE", "C"); |
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277 | |
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278 | aws->window_fit(); |
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279 | return (AW_window*) aws; |
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280 | } |
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281 | |
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282 | AW_window_simple* |
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283 | new_sina_simple(AW_root *root, AW_CL cd2, bool adv) { |
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284 | int closex, closey, startx, starty, winx, winy; |
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285 | const int hgap = 10; |
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286 | AW_window_simple *aws = new AW_window_simple; |
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287 | |
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288 | aws->init(root, "SINA", "SINA (SILVA Incremental Aligner)"); |
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289 | |
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290 | aws->button_length(12); |
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291 | aws->at(10,10); |
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292 | aws->auto_space(5,5); |
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293 | |
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294 | aws->callback(AW_POPDOWN); |
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295 | aws->create_button("CLOSE", "CLOSE", "O"); |
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296 | aws->get_at_position(&closex, &closey); |
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297 | |
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298 | aws->at_shift(10,0); |
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299 | aws->callback(show_sina_window, cd2, 0); |
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300 | aws->label_length(0); |
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301 | aws->label("Show advanced options"); |
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302 | aws->create_toggle(GA_AWAR_ADVANCED); |
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303 | |
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304 | aws->at_newline(); |
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305 | aws->at_shift(0,hgap); |
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306 | aws->label_length(15); |
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307 | aws->create_toggle_field(GA_AWAR_TGT, "Align what?", "A"); |
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308 | aws->insert_toggle("Current Species:", "C", 0); |
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309 | aws->insert_toggle("Selected Species", "S", 1); |
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310 | aws->insert_default_toggle("Marked Species", "M", 2); |
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311 | aws->update_toggle_field(); |
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312 | |
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313 | aws->at_shift(0,3); |
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314 | aws->create_input_field(AWAR_SPECIES_NAME, 20); |
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315 | |
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316 | aws->at_newline(); |
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317 | aws->at_shift(0,hgap); |
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318 | aws->button_length(24); |
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319 | aws->label("PT Server:"); |
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320 | awt_create_selection_list_on_pt_servers(aws, AWAR_PT_SERVER, true); |
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321 | |
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322 | aws->at_newline(); |
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323 | aws->callback(AW_POPUP, (AW_CL)create_select_sai_window, (AW_CL)0); |
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324 | aws->label("Pos. Var.:"); |
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325 | aws->create_button("SELECT_SAI", GA_AWAR_SAI); |
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326 | aws->button_length(12); |
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327 | |
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328 | |
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329 | aws->at_newline(); |
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330 | aws->label_length(0); |
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331 | aws->create_option_menu(GA_AWAR_OVERHANG, "Overhang placement"); |
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332 | aws->insert_option("keep attached", 0, "attach"); |
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333 | aws->insert_option("move to edge", 0, "edge"); |
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334 | aws->insert_option("remove", 0, "remove"); |
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335 | aws->update_option_menu(); |
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336 | |
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337 | if (adv) { |
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338 | aws->at_newline(); |
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339 | aws->at_shift(0,hgap); |
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340 | |
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341 | aws->label("Turn check"); |
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342 | aws->create_toggle(GA_AWAR_TURN_CHECK); |
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343 | |
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344 | aws->at_newline(); |
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345 | aws->label("Realign"); |
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346 | aws->create_toggle(GA_AWAR_REALIGN); |
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347 | |
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348 | aws->at_newline(); |
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349 | aws->label("Load reference sequences from PT-Server"); |
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350 | aws->create_toggle(GA_AWAR_PTLOAD); |
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351 | |
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352 | aws->at_newline(); |
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353 | aws->label("(Copy and) mark sequences used as reference"); |
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354 | aws->create_toggle(GA_AWAR_COPYMARKREF); |
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355 | |
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356 | aws->at_newline(); |
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357 | aws->at_shift(0,hgap); |
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358 | aws->label_length(0); |
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359 | |
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360 | aws->label("Gap insertion/extension penalties"); |
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361 | aws->create_input_field(GA_AWAR_GAP_PEN, 5); |
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362 | aws->create_input_field(GA_AWAR_GAP_EXT, 5); |
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363 | |
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364 | aws->at_newline(); |
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365 | aws->label("Family search min/min_score/max"); |
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366 | aws->create_input_field(GA_AWAR_FS_MIN, 3); |
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367 | aws->create_input_field(GA_AWAR_FS_MSC, 3); |
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368 | aws->create_input_field(GA_AWAR_FS_MAX, 3); |
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369 | |
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370 | aws->at_newline(); |
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371 | aws->label("Use at least"); |
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372 | aws->create_input_field(GA_AWAR_MIN_FULL, 3); |
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373 | aws->label("sequences with at least"); |
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374 | aws->create_input_field(GA_AWAR_FULL_MINLEN, 5); |
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375 | aws->label("bases as reference"); |
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376 | |
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377 | aws->at_newline(); |
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378 | aws->label("Max threads"); |
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379 | aws->create_input_field(GA_AWAR_THREADS,3); |
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380 | aws->label("Queue size"); |
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381 | aws->create_input_field(GA_AWAR_QSIZE,3); |
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382 | |
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383 | aws->at_newline(); |
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384 | aws->label("SINA command"); |
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385 | aws->create_input_field(GA_AWAR_CMD,20); |
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386 | |
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387 | aws->at_shift(0,hgap); |
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388 | } |
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389 | |
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390 | aws->at_newline(); |
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391 | aws->at_shift(0,hgap); |
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392 | |
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393 | aws->label_length(17); |
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394 | aws->create_option_menu(GA_AWAR_PROTECTION, "Protection Level", "P"); |
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395 | aws->insert_option("0", 0, 0); |
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396 | aws->insert_option("1", 0, 1); |
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397 | aws->insert_option("2", 0, 2); |
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398 | aws->insert_option("3", 0, 3); |
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399 | aws->insert_option("4", 0, 4); |
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400 | aws->insert_option("5", 0, 5); |
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401 | aws->insert_option("6", 0, 6); |
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402 | aws->update_option_menu(); |
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403 | |
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404 | aws->at_newline(); |
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405 | aws->create_option_menu(GA_AWAR_LOGLEVEL, "Logging level", "L"); |
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406 | aws->insert_option("silent", 0, "1"); |
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407 | aws->insert_option("quiet", 0, "2"); |
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408 | aws->insert_default_option("normal", 0, "3"); |
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409 | aws->insert_option("verbose", 0, "4"); |
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410 | aws->insert_option("debug", 0, "5"); |
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411 | aws->insert_option("debug more", 0, "6"); |
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412 | aws->update_option_menu(); |
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413 | |
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414 | aws->get_window_size(winx, winy); |
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415 | aws->get_at_position(&startx, &starty); |
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416 | |
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417 | aws->at(winx-closex+5,closey); |
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418 | aws->callback(AW_POPUP_HELP, (AW_CL) "sina_main.hlp"); |
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419 | aws->create_button("HELP", "HELP"); |
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420 | |
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421 | aws->at(winx-closex+5, starty); |
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422 | aws->callback(sina_start, cd2); |
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423 | aws->highlight(); |
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424 | aws->create_button("Start", "Start", "S"); |
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425 | |
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426 | return aws; |
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427 | } |
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428 | |
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429 | void show_sina_window(AW_window *aw, AW_CL cd2, AW_CL) { |
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430 | static AW_window_simple *ga_aws = 0; |
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431 | static AW_window_simple *ga_aws_adv = 0; |
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432 | |
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433 | AW_root *root = aw->get_root(); |
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434 | if (root->awar(GA_AWAR_ADVANCED)->read_int()) { |
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435 | if (!ga_aws_adv) ga_aws_adv = new_sina_simple(root, cd2, true); |
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436 | ga_aws_adv->show(); |
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437 | if (ga_aws) ga_aws->hide(); |
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438 | } |
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439 | else { |
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440 | if (!ga_aws) ga_aws = new_sina_simple(root, cd2, false); |
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441 | ga_aws->show(); |
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442 | if (ga_aws_adv) ga_aws_adv->hide(); |
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443 | } |
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444 | } |
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445 | |
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446 | /* |
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447 | Local Variables: |
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448 | mode:c++ |
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449 | c-file-style:"stroustrup" |
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450 | c-file-offsets:((innamespace . 0)(inline-open . 0)(case-label . 0)) |
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451 | indent-tabs-mode:nil |
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452 | fill-column:99 |
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453 | End: |
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454 | */ |
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455 | // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=99 : |
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456 | |
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