1 | #include <unistd.h> |
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2 | #include <netdb.h> |
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3 | #include <sys/time.h> |
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4 | #include <sys/types.h> |
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5 | #include <sys/stat.h> |
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6 | #include <stdio.h> |
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7 | #include <stdlib.h> |
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8 | #include <string.h> |
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9 | //#include <xview/xview.h> |
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10 | //#include <xview/panel.h> |
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11 | #include <arbdb.h> |
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12 | #include <arbdbt.h> |
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13 | // #include <malloc.h> |
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14 | #include <aw_root.hxx> |
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15 | #include <aw_device.hxx> |
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16 | #include <aw_window.hxx> |
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17 | #include <awt.hxx> |
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18 | #include <awt_tree.hxx> |
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19 | #include <awt_sel_boxes.hxx> |
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20 | #include <gde.hxx> |
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21 | #include "GDE_menu.h" |
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22 | #include "GDE_def.h" |
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23 | #include "GDE_extglob.h" |
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24 | #include "GDE_awars.h" |
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25 | |
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26 | #include <string> |
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27 | #include <set> |
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28 | |
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29 | using namespace std; |
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30 | |
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31 | #define DEFAULT_COLOR 8 |
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32 | extern AW_CL agde_filtercd; |
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33 | |
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34 | /* |
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35 | ReplaceArgs(): |
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36 | Replace all command line arguements with the appropriate values |
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37 | stored for the chosen menu item. |
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38 | |
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39 | Copyright (c) 1989-1990, University of Illinois board of trustees. All |
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40 | rights reserved. Written by Steven Smith at the Center for Prokaryote Genome |
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41 | Analysis. Design and implementation guidance by Dr. Gary Olsen and Dr. |
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42 | Carl Woese. |
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43 | |
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44 | Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory. |
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45 | All rights reserved. |
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46 | |
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47 | */ |
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48 | |
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49 | |
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50 | static char *ReplaceArgs(AW_root *awr,char *Action,AWwindowinfo *AWinfo,int number) |
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51 | { |
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52 | /* |
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53 | * The basic idea is to replace all of the symbols in the method |
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54 | * string with the values picked in the dialog box. The method |
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55 | * is the general command line structure. All arguements have three |
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56 | * parts, a label, a method, and a value. The method never changes, and |
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57 | * is used to represent '-flag's for a given function. Values are the |
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58 | * associated arguements that some flags require. All symbols that |
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59 | * require argvalue replacement should have a '$' infront of the symbol |
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60 | * name in the itemmethod definition. All symbols without the '$' will |
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61 | * be replaced by their argmethod. There is currently no way to do a label |
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62 | * replacement, as the label is considered to be for use in the dialog |
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63 | * box only. An example command line replacement would be: |
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64 | * |
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65 | * itemmethod=> "lpr arg1 $arg1 $arg2" |
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66 | * |
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67 | * arglabel arg1=> "To printer?" |
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68 | * argmethod arg1=> "-P" |
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69 | * argvalue arg1=> "lw" |
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70 | * |
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71 | * arglabel arg2=> "File name?" |
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72 | * argvalue arg2=> "foobar" |
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73 | * argmethod arg2=> "" |
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74 | * |
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75 | * final command line: |
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76 | * |
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77 | * lpr -P lw foobar |
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78 | * |
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79 | * At this point, the chooser dialog type only supports the arglabel and |
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80 | * argmethod field. So if an argument is of type chooser, and |
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81 | * its symbol is "this", then "$this" has no real meaning in the |
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82 | * itemmethod definition. Its format in the .GDEmenu file is slighty |
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83 | * different as well. A choice from a chooser field looks like: |
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84 | * |
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85 | * argchoice:Argument_label:Argument_method |
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86 | * |
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87 | * |
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88 | */ |
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89 | const char *symbol=0; |
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90 | char *method=0; |
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91 | char *textvalue=0; |
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92 | char *temp; |
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93 | int i,newlen,type; |
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94 | symbol = AWinfo->gmenuitem->arg[number].symbol; |
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95 | //method = AWinfo->gmenuitem->arg[number]->method; |
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96 | //textvalue = AWinfo->gmenuitem->arg[number]->textvalue; |
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97 | type = AWinfo->gmenuitem->arg[number].type; |
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98 | if( (type == SLIDER) ) |
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99 | { |
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100 | char *awarname = GDE_makeawarname(AWinfo,number); |
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101 | textvalue = (char*)malloc(GBUFSIZ); |
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102 | char *awalue = awr->awar(awarname)->read_as_string(); |
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103 | sprintf(textvalue,"%s",awalue); |
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104 | free(awalue); |
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105 | } |
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106 | else if((type == CHOOSER) || |
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107 | (type == CHOICE_TREE) || |
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108 | (type == CHOICE_SAI) || |
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109 | (type == CHOICE_MENU) || |
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110 | (type == CHOICE_LIST) || |
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111 | (type == CHOICE_WEIGHTS) || |
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112 | (type == TEXTFIELD)) |
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113 | { |
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114 | char *awarname=GDE_makeawarname(AWinfo,number); |
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115 | method=awr->awar(awarname)->read_string(); |
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116 | textvalue=awr->awar(awarname)->read_string(); |
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117 | } |
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118 | |
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119 | if(textvalue == NULL) textvalue=(char *)calloc(1,sizeof(char)); |
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120 | if(method == NULL) method=(char *)calloc(1,sizeof(char)); |
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121 | if(symbol == NULL) symbol=""; |
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122 | |
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123 | set<string>warned_about; |
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124 | int conversion_warning = 0; |
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125 | int j = 0; |
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126 | |
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127 | for(; (i=Find2(Action+j,symbol)) != -1;) |
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128 | { |
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129 | i += j; |
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130 | ++j; |
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131 | if(i>0 && Action[i-1] == '$' ) |
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132 | { |
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133 | newlen = strlen(Action)-strlen(symbol) |
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134 | +strlen(textvalue); |
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135 | temp = (char *)calloc(newlen,1); |
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136 | if (temp == NULL) |
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137 | Error("ReplaceArgs():Error in calloc"); |
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138 | strncat(temp,Action,i-1); |
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139 | strncat(temp,textvalue,strlen(textvalue)); |
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140 | strcat( temp,&(Action[i+strlen(symbol)]) ); |
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141 | free(Action); |
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142 | Action = temp; |
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143 | } |
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144 | else |
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145 | { |
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146 | if (warned_about.find(symbol) == warned_about.end()) { |
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147 | fprintf(stderr, |
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148 | "old arb version converted '%s' to '%s' (now only '$%s' is converted)\n", |
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149 | symbol, textvalue, symbol); |
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150 | conversion_warning++; |
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151 | warned_about.insert(symbol); |
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152 | } |
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153 | // newlen = strlen(Action)-strlen(symbol) |
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154 | // +strlen(method)+1; |
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155 | // temp = (char *)calloc(newlen,1); |
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156 | // if (temp == NULL) |
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157 | // Error("ReplaceArgs():Error in calloc"); |
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158 | // strncat(temp,Action,i); |
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159 | // strncat(temp,method,strlen(method)); |
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160 | // strcat( temp,&(Action[i+strlen(symbol)]) ); |
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161 | // free(Action); |
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162 | // Action = temp; |
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163 | } |
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164 | } |
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165 | |
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166 | if (conversion_warning) { |
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167 | fprintf(stderr, |
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168 | "Conversion warnings occurred in Action:\n'%s'\n", |
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169 | Action); |
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170 | } |
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171 | |
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172 | free(textvalue); |
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173 | free(method); |
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174 | return(Action); |
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175 | } |
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176 | |
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177 | |
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178 | |
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179 | static long LMAX(long a,long b) |
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180 | { |
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181 | if(a>b) return a; |
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182 | return b; |
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183 | } |
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184 | |
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185 | static void GDE_free(void **p) |
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186 | { |
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187 | if(*p!=0) |
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188 | { |
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189 | //delete *p; |
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190 | free(*p); |
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191 | *p=0; |
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192 | } |
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193 | } |
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194 | |
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195 | /*void GDE_freemask(GMask *mask) |
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196 | { |
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197 | if(mask==0) return; |
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198 | GDE_free((void**)&mask->name); |
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199 | for(long i=0;i<mask->listlen;i++) |
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200 | { |
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201 | NumList numl=mask->list[i]; |
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202 | GDE_free((void**)&numl.valu); |
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203 | } |
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204 | GDE_free((void**)&mask->list); |
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205 | }*/ |
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206 | |
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207 | static char *ReplaceFile(char *Action,GfileFormat file) |
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208 | { |
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209 | char *symbol,*method,*temp; |
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210 | int i,newlen; |
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211 | symbol = file.symbol; |
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212 | method = file.name; |
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213 | |
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214 | for(; (i=Find2(Action,symbol)) != -1;) |
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215 | { |
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216 | newlen = strlen(Action)-strlen(symbol) + strlen(method)+1; |
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217 | temp = (char *)calloc(newlen,1); |
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218 | if (temp == NULL) |
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219 | Error("ReplaceFile():Error in calloc"); |
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220 | strncat(temp,Action,i); |
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221 | strncat(temp,method,strlen(method)); |
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222 | strcat( temp,&(Action[i+strlen(symbol)]) ); |
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223 | free(Action); |
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224 | Action = temp; |
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225 | } |
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226 | return(Action); |
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227 | } |
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228 | |
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229 | static char *ReplaceString(char *Action,const char *old,const char *news) |
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230 | { |
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231 | const char *symbol; |
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232 | const char *method; |
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233 | char *temp; |
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234 | int i,newlen; |
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235 | |
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236 | symbol = old; |
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237 | method = news; |
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238 | |
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239 | for(; (i=Find2(Action,symbol)) != -1;) |
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240 | { |
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241 | newlen = strlen(Action)-strlen(symbol) + strlen(method)+1; |
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242 | temp = (char *)calloc(newlen,1); |
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243 | if (temp == NULL) |
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244 | Error("ReplaceFile():Error in calloc"); |
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245 | strncat(temp,Action,i); |
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246 | strncat(temp,method,strlen(method)); |
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247 | strcat( temp,&(Action[i+strlen(symbol)]) ); |
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248 | free(Action); |
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249 | Action = temp; |
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250 | } |
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251 | return(Action); |
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252 | } |
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253 | |
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254 | |
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255 | static void GDE_freesequ(NA_Sequence *sequ) |
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256 | { |
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257 | if(sequ==0) return; |
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258 | GDE_free((void**)&sequ->comments); |
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259 | /* GDE_free((void**)&sequ->col_lut); OLIVER STRUNK */ |
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260 | GDE_free((void**)&sequ->cmask); |
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261 | /*GDE_freemask(sequ->mask);*/ |
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262 | GDE_free((void**)&sequ->baggage); |
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263 | GDE_free((void**)&sequ->sequence); |
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264 | /*if(sequ->groupf) |
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265 | { |
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266 | GDE_freesequ(sequ->groupf); |
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267 | GDE_free((void**)&sequ->groupf); |
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268 | }*/ |
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269 | } |
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270 | |
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271 | static void GDE_freeali(NA_Alignment *dataset) |
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272 | { |
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273 | if(dataset==0) return; |
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274 | GDE_free((void**)&dataset->id); |
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275 | GDE_free((void**)&dataset->description); |
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276 | GDE_free((void**)&dataset->authority); |
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277 | GDE_free((void**)&dataset->cmask); |
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278 | GDE_free((void**)&dataset->selection_mask); |
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279 | GDE_free((void**)&dataset->alignment_name); |
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280 | |
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281 | /* maybe not correct: |
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282 | GMask *mask=dataset->mask; |
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283 | GDE_freemask(dataset->mask); |
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284 | GDE_free((void**)&dataset->mask);*/ |
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285 | |
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286 | unsigned long i; |
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287 | // **maybe not correct: |
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288 | //NA_Sequence **group=dataset->group; |
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289 | //for(long i=0;i<dataset->numgroups;i++) |
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290 | // GDE_freesequ(dataset->group[i]); |
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291 | //GDE_free((void**)&dataset->group); |
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292 | // **correction: this was not correct |
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293 | |
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294 | for(i=0;i<dataset->numelements;i++) |
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295 | GDE_freesequ(&(dataset->element[i])); |
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296 | } |
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297 | |
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298 | static void GDE_export(NA_Alignment *dataset,char *align,long oldnumelements) |
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299 | { |
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300 | GB_begin_transaction(GLOBAL_gb_main); |
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301 | long maxalignlen=GBT_get_alignment_len(GLOBAL_gb_main,align); |
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302 | long isdefaultalign=0; |
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303 | int load_all = 0; |
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304 | if(maxalignlen<=0) |
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305 | { |
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306 | align=GBT_get_default_alignment(GLOBAL_gb_main); |
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307 | isdefaultalign=1; |
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308 | } |
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309 | |
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310 | maxalignlen=GBT_get_alignment_len(GLOBAL_gb_main,align); |
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311 | long lotyp=0; |
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312 | { |
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313 | GB_alignment_type at = GBT_get_alignment_type(GLOBAL_gb_main, align); |
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314 | |
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315 | switch (at) |
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316 | { |
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317 | case GB_AT_DNA: lotyp = DNA; break; |
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318 | case GB_AT_RNA: lotyp = RNA; break; |
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319 | case GB_AT_AA: lotyp = PROTEIN; break; |
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320 | case GB_AT_UNKNOWN: lotyp = DNA; break; |
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321 | } |
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322 | } |
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323 | |
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324 | GB_ERROR error = 0; |
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325 | unsigned long i; |
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326 | for(i=oldnumelements;!error && i<dataset->numelements;i++) |
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327 | { |
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328 | NA_Sequence *sequ=&(dataset->element[i]); |
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329 | int seqtyp,issame=0; |
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330 | seqtyp=sequ->elementtype; |
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331 | if( (seqtyp==lotyp)||((seqtyp==DNA)&&(lotyp==RNA))||((seqtyp==RNA)&&(lotyp==DNA)) ){ |
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332 | issame=1; |
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333 | }else{ |
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334 | aw_message(GBS_global_string("Warning: sequence type of species '%s' changed",sequ->short_name)); |
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335 | } |
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336 | |
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337 | if(sequ->tmatrix) { |
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338 | for(long j=0;j<sequ->seqlen;j++) { |
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339 | sequ->sequence[j] = (char)sequ->tmatrix[sequ->sequence[j]]; |
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340 | } |
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341 | } |
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342 | |
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343 | char *savename = GBS_string_2_key(sequ->short_name); |
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344 | sequ->gb_species = 0; |
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345 | |
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346 | if (!issame) /* save as extended */ |
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347 | { |
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348 | |
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349 | GBDATA *gb_extended = GBT_create_SAI(GLOBAL_gb_main,savename); |
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350 | sequ->gb_species=gb_extended; |
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351 | GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); |
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352 | error = GBT_write_sequence(gb_data,align,maxalignlen,(char *)sequ->sequence); |
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353 | } |
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354 | else /* save as sequence */ |
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355 | { |
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356 | GBDATA *gb_species_data = GB_search(GLOBAL_gb_main,"species_data",GB_CREATE_CONTAINER); |
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357 | GBDATA *gb_species; |
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358 | gb_species = GBT_find_species_rel_species_data(gb_species_data, savename); |
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359 | GB_push_my_security(GLOBAL_gb_main); |
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360 | |
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361 | if (gb_species) { /* new element that already exists !!!!*/ |
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362 | int select_mode; |
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363 | const char *msg = GBS_global_string( |
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364 | "You are (re-)importing a species '%s'.\n" |
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365 | "That species already exists in your database!\n" |
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366 | "\n" |
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367 | "Possible actions:\n" |
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368 | "\n" |
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369 | " - delete and overwrite the existing species\n" |
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370 | " - skip - don't change the species\n" |
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371 | " - reimport only the sequence of the existing species\n" |
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372 | " - reimport all sequences (don't ask again)\n" |
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373 | "\n" |
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374 | "Note: After aligning it's recommended to choose 'reimport all'.", |
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375 | savename); |
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376 | if (!load_all) { |
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377 | select_mode = aw_message(msg, |
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378 | "delete existing," // 0 |
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379 | "skip," // 1 |
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380 | "reimport sequence," // 2 |
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381 | "reimport all" // 3 |
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382 | ); |
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383 | |
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384 | if (select_mode == 3) { // load all sequences |
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385 | load_all = 1; |
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386 | } |
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387 | } |
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388 | |
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389 | if (load_all) { |
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390 | select_mode = 2; // reimport sequence |
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391 | } |
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392 | |
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393 | gde_assert(select_mode >= 0 && select_mode <= 2); |
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394 | |
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395 | switch(select_mode) { |
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396 | case 1: // skip |
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397 | gb_species = 0; |
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398 | continue; // continue with next species |
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399 | |
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400 | case 0: // delete existing species |
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401 | GB_delete(gb_species); |
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402 | // fall-through! |
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403 | case 2: // reimport sequence |
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404 | gb_species = GBT_create_species_rel_species_data(gb_species_data, savename); |
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405 | break; |
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406 | } |
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407 | } |
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408 | else { |
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409 | gb_species = GBT_create_species_rel_species_data(gb_species_data, savename); |
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410 | } |
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411 | if (!gb_species) continue; |
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412 | sequ->gb_species = gb_species; |
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413 | |
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414 | GBDATA *gb_old_data = GBT_read_sequence(gb_species, align); |
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415 | GBDATA *gb_data = GBT_add_data(gb_species, align,"data", GB_STRING); |
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416 | |
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417 | if (gb_old_data) { // we already have data -> compare checksums |
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418 | const char *old_seq = GB_read_char_pntr(gb_old_data); |
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419 | long old_checksum = GBS_checksum(old_seq, 1, "-."); |
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420 | long new_checksum = GBS_checksum((char*)sequ->sequence, 1, "-."); |
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421 | |
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422 | if (old_checksum != new_checksum) { |
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423 | aw_message(GBS_global_string("Warning: Sequence checksum for '%s' differs", savename)); |
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424 | } |
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425 | } |
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426 | |
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427 | error = GBT_write_sequence(gb_data,align,maxalignlen,(char *)sequ->sequence); |
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428 | GB_pop_my_security(GLOBAL_gb_main); |
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429 | |
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430 | } |
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431 | free(savename); |
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432 | } |
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433 | |
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434 | /* colormasks */ |
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435 | for(i=0;!error && i<dataset->numelements;i++) |
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436 | { |
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437 | NA_Sequence *sequ=&(dataset->element[i]); |
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438 | if(sequ->cmask) |
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439 | { |
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440 | GBDATA *gb_color; |
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441 | maxalignlen=LMAX(maxalignlen,sequ->seqlen); |
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442 | char *resstring=(char *)calloc((unsigned int)maxalignlen+1,sizeof(char)); |
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443 | |
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444 | char *dummy=resstring; |
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445 | for(long j=0;j<maxalignlen-sequ->seqlen;j++) |
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446 | *resstring++=DEFAULT_COLOR; |
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447 | |
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448 | for(long k=0;k<sequ->seqlen;k++) |
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449 | *resstring++=(char)sequ->cmask[i]; |
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450 | *resstring='\0'; |
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451 | |
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452 | GBDATA *gb_ali=GB_search(sequ->gb_species, |
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453 | align,GB_CREATE_CONTAINER); |
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454 | gb_color=GB_search(gb_ali,"colmask",GB_BYTES); |
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455 | error = GB_write_bytes(gb_color,dummy,maxalignlen); |
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456 | delete dummy; |
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457 | |
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458 | } |
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459 | } |
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460 | if(!error && dataset->cmask) |
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461 | { |
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462 | GBDATA *gb_color; |
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463 | maxalignlen=LMAX(maxalignlen,dataset->cmask_len); |
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464 | char *resstring=(char *)calloc((unsigned int)maxalignlen+1,sizeof(char)); |
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465 | |
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466 | char *dummy=resstring; |
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467 | long k; |
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468 | for(k=0;k<maxalignlen-dataset->cmask_len;k++) |
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469 | *resstring++=DEFAULT_COLOR; |
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470 | |
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471 | for(k=0;k<dataset->cmask_len;k++) |
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472 | *resstring++=(char)dataset->cmask[k]; |
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473 | *resstring='\0'; |
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474 | |
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475 | |
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476 | GBDATA *gb_extended = GBT_create_SAI(GLOBAL_gb_main,"COLMASK"); |
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477 | gb_color = GBT_add_data(gb_extended, align,"colmask", GB_BYTES); |
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478 | error = GB_write_bytes(gb_color,dummy,maxalignlen); |
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479 | |
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480 | delete dummy; |
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481 | } |
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482 | if (error) { |
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483 | GB_abort_transaction(GLOBAL_gb_main); |
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484 | aw_message(error); |
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485 | }else{ |
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486 | GB_commit_transaction(GLOBAL_gb_main); |
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487 | } |
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488 | if(isdefaultalign) delete align; |
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489 | } |
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490 | |
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491 | void GDE_startaction_cb(AW_window *aw,AWwindowinfo *AWinfo,AW_CL cd) |
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492 | { |
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493 | long oldnumelements=0; |
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494 | AWUSE(cd); |
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495 | AW_root *aw_root=aw->get_root(); |
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496 | |
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497 | GapCompression compress = static_cast<GapCompression>(aw_root->awar(AWAR_GDE_COMPRESSION)->read_int()); |
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498 | AP_filter *filter2 = awt_get_filter(aw_root,agde_filtercd); |
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499 | char *filter_name = 0; /* aw_root->awar(AWAR_GDE_FILTER_NAME)->read_string() */ |
---|
500 | char *alignment_name = strdup("ali_unknown"); |
---|
501 | bool marked = (aw_root->awar(AWAR_GDE_SPECIES)->read_int() != 0); |
---|
502 | long cutoff_stop_codon = aw_root->awar(AWAR_GDE_CUTOFF_STOPCODON)->read_int(); |
---|
503 | |
---|
504 | GmenuItem *current_item; |
---|
505 | current_item=AWinfo->gmenuitem; |
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506 | |
---|
507 | aw_openstatus(current_item->label); |
---|
508 | aw_status((double)0); |
---|
509 | |
---|
510 | int i,j,k,flag,select_mode =0; |
---|
511 | static int fileindx = 0; |
---|
512 | char *Action,buffer[GBUFSIZ]; |
---|
513 | i=0;k=0; |
---|
514 | if (current_item->numinputs>0) { |
---|
515 | DataSet->gb_main = GLOBAL_gb_main; |
---|
516 | GB_begin_transaction(DataSet->gb_main); |
---|
517 | delete DataSet->alignment_name; |
---|
518 | DataSet->alignment_name = GBT_get_default_alignment(DataSet->gb_main); |
---|
519 | free(alignment_name); |
---|
520 | alignment_name = strdup(DataSet->alignment_name); |
---|
521 | |
---|
522 | aw_status("reading database"); |
---|
523 | int stop; |
---|
524 | if (gde_cgss.get_sequences) { |
---|
525 | stop = ReadArbdb2(DataSet, filter2, compress, cutoff_stop_codon); |
---|
526 | } |
---|
527 | else { |
---|
528 | stop = ReadArbdb(DataSet, marked, filter2, compress, cutoff_stop_codon); |
---|
529 | } |
---|
530 | GB_commit_transaction(DataSet->gb_main); |
---|
531 | |
---|
532 | if(stop) goto startaction_end; |
---|
533 | |
---|
534 | if (DataSet->numelements==0) { |
---|
535 | aw_message("no sequences selected"); |
---|
536 | goto startaction_end; |
---|
537 | } |
---|
538 | } |
---|
539 | |
---|
540 | flag = AW_FALSE; |
---|
541 | for(j=0;j<current_item->numinputs;j++) { |
---|
542 | if(current_item->input[j].format != STATUS_FILE) { |
---|
543 | flag = AW_TRUE; |
---|
544 | } |
---|
545 | } |
---|
546 | if(flag && DataSet) select_mode = ALL; //TestSelection(); |
---|
547 | |
---|
548 | //chdir(current_dir); |
---|
549 | for(j=0;j<current_item->numinputs;j++) { |
---|
550 | sprintf(buffer,"/tmp/gde%d_%d",(int)getpid(),fileindx++); |
---|
551 | current_item->input[j].name = String(buffer); |
---|
552 | switch(current_item->input[j].format) { |
---|
553 | case COLORMASK: WriteCMask(DataSet,buffer,select_mode, current_item->input[j].maskable); break; |
---|
554 | case GENBANK: WriteGen(DataSet,buffer,select_mode, current_item->input[j].maskable); break; |
---|
555 | case NA_FLAT: WriteNA_Flat(DataSet,buffer,select_mode, current_item->input[j].maskable); break; |
---|
556 | case STATUS_FILE: WriteStatus(DataSet,buffer,select_mode); break; |
---|
557 | case GDE: WriteGDE(DataSet,buffer,select_mode, current_item->input[j].maskable); break; |
---|
558 | default: break; |
---|
559 | } |
---|
560 | } |
---|
561 | |
---|
562 | for(j=0;j<current_item->numoutputs;j++) |
---|
563 | { |
---|
564 | sprintf(buffer,"/tmp/gde%d_%d",(int)getpid(),fileindx++); |
---|
565 | current_item->output[j].name = String(buffer); |
---|
566 | } |
---|
567 | |
---|
568 | /* |
---|
569 | * Create the command line for external the function call |
---|
570 | */ |
---|
571 | Action = (char*)strdup(current_item->method); |
---|
572 | if(Action == NULL) Error("DO(): Error in duplicating method string"); |
---|
573 | |
---|
574 | while (1) { |
---|
575 | char *oldAction = strdup(Action); |
---|
576 | |
---|
577 | for(j=0;j<current_item->numargs;j++) Action = ReplaceArgs(aw_root,Action,AWinfo,j); |
---|
578 | bool changed = strcmp(oldAction, Action) != 0; |
---|
579 | free(oldAction); |
---|
580 | |
---|
581 | if (!changed) break; |
---|
582 | } |
---|
583 | |
---|
584 | for(j=0;j<current_item->numinputs;j++) Action = ReplaceFile(Action,current_item->input[j]); |
---|
585 | for(j=0;j<current_item->numoutputs;j++) Action = ReplaceFile(Action,current_item->output[j]); |
---|
586 | |
---|
587 | filter_name = AWT_get_combined_filter_name(aw_root, "gde"); |
---|
588 | Action = ReplaceString(Action,"$FILTER",filter_name); |
---|
589 | |
---|
590 | /* |
---|
591 | * call and go... |
---|
592 | */ |
---|
593 | |
---|
594 | aw_status("calling external program"); |
---|
595 | printf("Action: %s\n",Action); |
---|
596 | system(Action); |
---|
597 | free(Action); |
---|
598 | |
---|
599 | oldnumelements=DataSet->numelements; |
---|
600 | |
---|
601 | BlockInput = AW_FALSE; |
---|
602 | |
---|
603 | for(j=0;j<current_item->numoutputs;j++) |
---|
604 | { |
---|
605 | if(current_item->output[j].overwrite) |
---|
606 | { |
---|
607 | if(current_item->output[j].format == GDE) |
---|
608 | OVERWRITE = AW_TRUE; |
---|
609 | else |
---|
610 | Warning("Overwrite mode only available for GDE format"); |
---|
611 | } |
---|
612 | switch(current_item->output[j].format) |
---|
613 | { |
---|
614 | /* |
---|
615 | * The LoadData routine must be reworked so that |
---|
616 | * OpenFileName uses it, and so I can remove the |
---|
617 | * major kluge in OpenFileName(). |
---|
618 | */ |
---|
619 | case GENBANK: |
---|
620 | case NA_FLAT: |
---|
621 | case GDE: |
---|
622 | /*ARB-change:*/ |
---|
623 | /*OpenFileName(current_item->output[j].name,NULL);*/ |
---|
624 | LoadData(current_item->output[j].name); |
---|
625 | break; |
---|
626 | case COLORMASK: |
---|
627 | ReadCMask(current_item->output[j].name); |
---|
628 | break; |
---|
629 | case STATUS_FILE: |
---|
630 | ReadStatus(current_item->output[j].name); |
---|
631 | break; |
---|
632 | default: |
---|
633 | break; |
---|
634 | } |
---|
635 | OVERWRITE = AW_FALSE; |
---|
636 | } |
---|
637 | for(j=0;j<current_item->numoutputs;j++) |
---|
638 | { |
---|
639 | if(!current_item->output[j].save) |
---|
640 | { |
---|
641 | unlink(current_item->output[j].name); |
---|
642 | } |
---|
643 | } |
---|
644 | |
---|
645 | for(j=0;j<current_item->numinputs;j++) |
---|
646 | { |
---|
647 | if(!current_item->input[j].save) |
---|
648 | { |
---|
649 | unlink(current_item->input[j].name); |
---|
650 | } |
---|
651 | } |
---|
652 | |
---|
653 | aw_closestatus(); |
---|
654 | GDE_export(DataSet,alignment_name,oldnumelements); |
---|
655 | |
---|
656 | startaction_end: |
---|
657 | aw_closestatus(); |
---|
658 | free(alignment_name); |
---|
659 | delete filter2; |
---|
660 | free(filter_name); |
---|
661 | |
---|
662 | GDE_freeali(DataSet); |
---|
663 | free(DataSet); |
---|
664 | DataSet=0; |
---|
665 | DataSet = (NA_Alignment *) Calloc(1,sizeof(NA_Alignment)); |
---|
666 | DataSet->rel_offset = 0; |
---|
667 | |
---|
668 | // aw->hide(); |
---|
669 | } |
---|
670 | |
---|