1 | #include <stdio.h> |
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2 | #include <stdlib.h> // system |
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3 | #include <arbdb.h> |
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4 | #include <arbdbt.h> |
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5 | #include <aw_root.hxx> |
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6 | #include <aw_device.hxx> |
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7 | #include <aw_window.hxx> |
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8 | #include <aw_awars.hxx> |
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9 | #include <awt.hxx> |
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10 | #include <awt_sel_boxes.hxx> |
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11 | #include <iostream> |
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12 | #include <string.h> |
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13 | |
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14 | extern GBDATA *GLOBAL_gb_main; |
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15 | |
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16 | void aed_start_naligning(AW_window *aw) { |
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17 | AW_root *root = aw->get_root(); |
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18 | char *buffer; |
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19 | int i,j; |
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20 | |
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21 | GBS_strstruct *strstruct = GBS_stropen(1000); |
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22 | GBS_strcat(strstruct,"xterm -sl 1000 -sb -e sh -c 'LD_LIBRARY_PATH=\""); |
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23 | GBS_strcat(strstruct,GB_getenv("LD_LIBRARY_PATH")); |
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24 | GBS_strcat(strstruct,"\";export LD_LIBRARY_PATH;for i in "); |
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25 | if ( root->awar("naligner/what")->read_int() ) { |
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26 | GB_transaction dummy(GLOBAL_gb_main); |
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27 | for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL_gb_main); |
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28 | gb_species; |
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29 | gb_species = GBT_next_marked_species(gb_species)) |
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30 | { |
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31 | GBS_chrcat(strstruct, '\"'); |
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32 | GBS_strcat(strstruct, GBT_read_name(gb_species)); |
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33 | GBS_strcat(strstruct, "\" "); |
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34 | } |
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35 | }else{ |
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36 | char *species_name = root->awar( AWAR_SPECIES_NAME )->read_string(); |
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37 | GBS_strcat(strstruct,"\""); |
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38 | GBS_strcat(strstruct,species_name); |
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39 | GBS_strcat(strstruct,"\" "); |
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40 | delete species_name; |
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41 | } |
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42 | |
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43 | |
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44 | GBS_strcat(strstruct,"; do arb_naligner"); |
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45 | |
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46 | |
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47 | if ( root->awar("naligner/against")->read_int() ) { |
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48 | GBS_strcat(strstruct," -PARB_PT_SERVER"); |
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49 | GBS_intcat(strstruct, root->awar( "naligner/pt_server" )->read_int() ); |
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50 | }else{ |
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51 | GBS_strcat(strstruct," \"-f"); |
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52 | char *family = root->awar("naligner/sagainst")->read_string(); |
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53 | GBS_strcat(strstruct,family); |
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54 | delete family; |
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55 | GBS_strcat(strstruct,"\""); |
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56 | } |
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57 | GBS_strcat(strstruct," \"-s$i\" "); |
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58 | |
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59 | if (root->awar( "naligner/mark_profile" )->read_int() ) GBS_strcat(strstruct," -mf"); |
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60 | if (root->awar( "naligner/unmark_sequence" )->read_int() ) GBS_strcat(strstruct," -us"); |
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61 | |
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62 | GBS_strcat(strstruct," -minf"); GBS_intcat(strstruct,root->awar("naligner/minf")->read_int()); |
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63 | GBS_strcat(strstruct," -maxf"); GBS_intcat(strstruct,root->awar("naligner/maxf")->read_int()); |
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64 | GBS_strcat(strstruct," -minw"); GBS_floatcat(strstruct,root->awar("naligner/minw")->read_float()); |
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65 | GBS_strcat(strstruct," -maxew"); GBS_floatcat(strstruct,root->awar("naligner/maxew")->read_float()); |
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66 | GBS_strcat(strstruct," -ib"); GBS_intcat(strstruct,root->awar("naligner/det/ib")->read_int()); |
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67 | GBS_strcat(strstruct," -ic"); GBS_intcat(strstruct,root->awar("naligner/det/ic")->read_int()); |
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68 | |
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69 | GBS_strcat(strstruct," -cl"); GBS_floatcat(strstruct, root->awar("naligner/det/cl")->read_float()); |
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70 | |
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71 | |
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72 | |
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73 | |
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74 | GBS_strcat(strstruct," -cm"); GBS_floatcat(strstruct,root->awar("naligner/det/cm")->read_float()); |
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75 | GBS_strcat(strstruct," -ch"); GBS_floatcat(strstruct,root->awar("naligner/det/ch")->read_float()); |
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76 | GBS_strcat(strstruct," -mgf"); GBS_floatcat(strstruct,root->awar("naligner/igap_panelty")->read_float()); |
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77 | GBS_strcat(strstruct," -mma1"); |
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78 | GBS_strcat(strstruct," -msub"); |
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79 | for (i=0;i<5;i++){ |
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80 | for (j=0;j<5;j++) { |
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81 | char var[100]; |
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82 | if ( i==4 || j==4 ) { /* gap panelty */ |
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83 | if (i==4 && j==4) { |
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84 | GBS_floatcat(strstruct,0.0); |
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85 | }else{ |
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86 | GBS_floatcat(strstruct,root->awar("naligner/gap_panelty")->read_float()); |
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87 | GBS_chrcat(strstruct,','); |
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88 | } |
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89 | }else{ |
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90 | if (i<j) sprintf(var,"naligner/%c%c","acgt-"[i],"acgt-"[j]); |
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91 | else sprintf(var,"naligner/%c%c","acgt-"[j],"acgt-"[i]); |
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92 | GBS_floatcat(strstruct,root->awar(var)->read_float()); |
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93 | if (i<4 || j<4) GBS_chrcat(strstruct,','); |
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94 | } |
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95 | } |
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96 | } |
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97 | GBS_strcat(strstruct," || echo \"Aligner failed\";done;"); |
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98 | |
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99 | |
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100 | GBS_strcat(strstruct,"echo press \"(return)\" to close window;read a' &"); |
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101 | buffer = GBS_strclose(strstruct); |
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102 | system(buffer); |
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103 | printf("%s\n",buffer); |
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104 | delete buffer; |
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105 | } |
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106 | |
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107 | |
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108 | void create_naligner_variables(AW_root *root,AW_default db1) |
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109 | { |
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110 | root->awar_int( "naligner/what", 0 , db1); |
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111 | |
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112 | root->awar_int( "naligner/against", 0 , db1); |
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113 | root->awar_string( "naligner/sagainst", "" , db1); |
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114 | root->awar_int( "naligner/pt_server", -1 , db1); |
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115 | |
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116 | root->awar_int( "naligner/mark_profile", 1 , db1); |
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117 | root->awar_int( "naligner/unmark_sequence", 0 , db1); |
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118 | |
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119 | |
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120 | root->awar_float( "naligner/aa", 0.0 , db1); |
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121 | root->awar_float( "naligner/ac", 3.0 , db1); |
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122 | root->awar_float( "naligner/ag", 1.0 , db1); |
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123 | root->awar_float( "naligner/at", 3.0 , db1); |
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124 | root->awar_float( "naligner/cc", 0.0 , db1); |
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125 | root->awar_float( "naligner/cg", 3.0 , db1); |
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126 | root->awar_float( "naligner/ct", 1.0 , db1); |
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127 | root->awar_float( "naligner/gg", 0.0 , db1); |
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128 | root->awar_float( "naligner/gt", 3.0 , db1); |
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129 | root->awar_float( "naligner/tt", 0.0 , db1); |
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130 | root->awar_float( "naligner/gap_panelty", 5.0 , db1); |
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131 | root->awar_float( "naligner/igap_panelty", 0.2 , db1); |
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132 | root->awar_int( "naligner/minf", 3 , db1); |
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133 | root->awar_int( "naligner/maxf", 30 , db1); |
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134 | |
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135 | |
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136 | root->awar_float( "naligner/minw", .7 , db1); |
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137 | root->awar_float( "naligner/maxew", .2 , db1); |
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138 | |
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139 | root->awar_float( "naligner/det/cl", .25 , db1); |
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140 | root->awar_float( "naligner/det/cm", .5 , db1); |
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141 | root->awar_float( "naligner/det/ch", .8 , db1); |
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142 | root->awar_int( "naligner/det/ib", 5 , db1); |
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143 | root->awar_int( "naligner/det/ic", 5 , db1); |
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144 | |
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145 | } |
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146 | |
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147 | void ed_nalign_save(AW_window *aww) |
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148 | { |
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149 | AW_root *root = aww->get_root(); |
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150 | root->save_default("naligner/aa"); |
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151 | } |
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152 | |
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153 | AW_window *create_expert_naligner_window(AW_root *root) |
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154 | { |
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155 | const int mwidth = 5; |
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156 | AW_window_simple *aws = new AW_window_simple; |
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157 | aws->init( root, "ALIGNER_V2_EXPERT2", "ALIGNER V2.0 EXPERT 2"); |
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158 | aws->load_xfig("ed_al_ex.fig"); |
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159 | |
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160 | aws->at("close"); |
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161 | aws->callback ( (AW_CB0)AW_POPDOWN ); |
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162 | aws->create_button( "CLOSE", "CLOSE", "C" ); |
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163 | |
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164 | aws->at("save"); |
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165 | aws->callback(ed_nalign_save); |
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166 | aws->create_button("SAVE", "SAVE","S"); |
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167 | |
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168 | aws->at("minw"); |
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169 | aws->create_input_field("naligner/minw",mwidth); |
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170 | |
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171 | aws->at("maxew"); |
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172 | aws->create_input_field("naligner/maxew",mwidth); |
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173 | |
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174 | aws->at("ib"); |
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175 | aws->create_input_field("naligner/det/ib",mwidth); |
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176 | |
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177 | aws->at("ic"); |
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178 | aws->create_input_field("naligner/det/ic",mwidth); |
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179 | |
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180 | aws->at("cl"); |
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181 | aws->create_input_field("naligner/det/cl",mwidth); |
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182 | |
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183 | aws->at("cm"); |
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184 | aws->create_input_field("naligner/det/cm",mwidth); |
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185 | |
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186 | aws->at("ch"); |
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187 | aws->create_input_field("naligner/det/ch",mwidth); |
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188 | |
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189 | return (AW_window *)aws; |
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190 | } |
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191 | |
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192 | AW_window *create_special_naligner_window(AW_root *root, AW_CL cd2) |
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193 | { |
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194 | AW_window_simple *aws = new AW_window_simple; |
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195 | const int mwidth = 3; |
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196 | aws->init( root, "ALIGNER_V2_EXPERT", "ALIGNER V2.0 EXPERT"); |
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197 | aws->load_xfig("ed_al_sp.fig"); |
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198 | |
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199 | AWUSE(cd2); |
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200 | aws->label_length(22); |
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201 | |
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202 | aws->at("close"); |
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203 | aws->callback ( (AW_CB0)AW_POPDOWN ); |
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204 | aws->create_button( "CLOSE", "CLOSE", "C" ); |
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205 | |
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206 | aws->at("minr"); |
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207 | aws->create_input_field( "naligner/minf", 6); |
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208 | |
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209 | aws->at("maxr"); |
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210 | aws->create_input_field( "naligner/maxf", 6); |
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211 | |
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212 | aws->at("aa"); |
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213 | aws->create_input_field("naligner/aa",mwidth); |
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214 | aws->at("ac"); |
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215 | aws->create_input_field("naligner/ac",mwidth); |
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216 | aws->at("ag"); |
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217 | aws->create_input_field("naligner/ag",mwidth); |
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218 | aws->at("at"); |
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219 | aws->create_input_field("naligner/at",mwidth); |
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220 | |
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221 | aws->at("ca"); |
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222 | aws->create_input_field("naligner/ac",mwidth); |
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223 | aws->at("cc"); |
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224 | aws->create_input_field("naligner/cc",mwidth); |
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225 | aws->at("cg"); |
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226 | aws->create_input_field("naligner/cg",mwidth); |
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227 | aws->at("ct"); |
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228 | aws->create_input_field("naligner/ct",mwidth); |
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229 | |
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230 | aws->at("ga"); |
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231 | aws->create_input_field("naligner/ag",mwidth); |
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232 | aws->at("gc"); |
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233 | aws->create_input_field("naligner/cg",mwidth); |
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234 | aws->at("gg"); |
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235 | aws->create_input_field("naligner/gg",mwidth); |
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236 | aws->at("gt"); |
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237 | aws->create_input_field("naligner/gt",mwidth); |
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238 | |
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239 | aws->at("ta"); |
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240 | aws->create_input_field("naligner/at",mwidth); |
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241 | aws->at("tc"); |
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242 | aws->create_input_field("naligner/ct",mwidth); |
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243 | aws->at("tg"); |
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244 | aws->create_input_field("naligner/gt",mwidth); |
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245 | aws->at("tt"); |
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246 | aws->create_input_field("naligner/tt",mwidth); |
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247 | |
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248 | aws->at("gap"); |
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249 | aws->create_input_field("naligner/gap_panelty",4); |
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250 | |
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251 | aws->at("igap"); |
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252 | aws->create_input_field("naligner/igap_panelty",4); |
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253 | |
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254 | aws->at("expert"); |
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255 | aws->callback((AW_CB1)AW_POPUP,(AW_CL)create_expert_naligner_window); |
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256 | aws->create_button("EXPERT_OPTIONS", "EXPERT2","E"); |
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257 | |
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258 | aws->at("save"); |
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259 | aws->callback(ed_nalign_save); |
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260 | aws->create_button("SAAVE", "SAVE","S"); |
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261 | |
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262 | return (AW_window *)aws; |
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263 | } |
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264 | |
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265 | AW_window *create_naligner_window( AW_root *root, AW_CL cd2 ) { |
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266 | |
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267 | AW_window_simple *aws = new AW_window_simple; |
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268 | aws->init( root, "ALIGNER_V2","ALIGNER V2.0"); |
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269 | aws->load_xfig("awt/align.fig"); |
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270 | |
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271 | AWUSE(cd2); |
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272 | |
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273 | aws->label_length( 10 ); |
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274 | aws->button_length( 10 ); |
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275 | |
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276 | aws->at( "close" ); |
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277 | aws->callback ( (AW_CB0)AW_POPDOWN ); |
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278 | aws->create_button( "CLOSE", "CLOSE", "O" ); |
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279 | |
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280 | aws->at( "help" ); |
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281 | aws->callback ( AW_POPUP_HELP, (AW_CL) "ne_align_seq.hlp" ); |
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282 | aws->create_button( "HELP", "HELP" ); |
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283 | |
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284 | aws->at( "align" ); |
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285 | aws->callback ( aed_start_naligning ); |
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286 | aws->highlight(); |
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287 | aws->create_button( "GO", "GO", "G"); |
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288 | |
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289 | aws->at( "expert" ); |
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290 | aws->callback ( (AW_CB1)AW_POPUP,(AW_CL)create_special_naligner_window ); |
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291 | aws->create_button( "OPTIONS", "PARAMETERS", "E"); |
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292 | |
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293 | aws->at("what"); |
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294 | aws->create_toggle_field("naligner/what","Align","A"); |
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295 | aws->insert_toggle("Selected Species:","S",0); |
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296 | aws->insert_default_toggle("Marked Species","M",1); |
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297 | aws->update_toggle_field(); |
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298 | |
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299 | aws->at( "swhat" ); |
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300 | aws->create_input_field( AWAR_SPECIES_NAME, 2); |
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301 | |
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302 | aws->at("against"); |
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303 | aws->create_toggle_field("naligner/against","Reference","g"); |
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304 | aws->insert_toggle("Species by name","S",0); |
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305 | aws->insert_default_toggle("Auto search by pt_server","S",1); |
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306 | aws->update_toggle_field(); |
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307 | |
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308 | aws->at( "sagainst" ); |
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309 | aws->create_input_field( "naligner/sagainst", 2); |
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310 | |
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311 | aws->label_length( 25 ); |
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312 | |
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313 | aws->at( "pt_server" ); |
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314 | aws->label("PT_SERVER:"); |
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315 | awt_create_selection_list_on_pt_servers(aws, "naligner/pt_server", true); |
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316 | |
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317 | aws->at( "mark" ); |
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318 | aws->label_length(40); |
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319 | aws->label("Mark sequences found by the pt_server"); |
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320 | aws->create_toggle( "naligner/mark_profile"); |
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321 | |
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322 | return (AW_window *)aws; |
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323 | } |
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