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annotate mafft/core/setdirection.c @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include "mltaln.h"
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2
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3 #define DEBUG 0
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4
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5 char *directionfile;
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6 static int show_R_ = 1;
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7
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8 void arguments( int argc, char *argv[] )
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9 {
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10 int c;
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11
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12 inputfile = NULL;
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13 directionfile = NULL;
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14 show_R_ = 1;
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15
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16 while( --argc > 0 && (*++argv)[0] == '-' )
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17 {
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18 while ( (c = *++argv[0]) )
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19 {
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20 switch( c )
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21 {
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22 case 'd':
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23 directionfile = *++argv;
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24 fprintf( stderr, "directionfile = %s\n", directionfile );
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25 --argc;
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26 goto nextoption;
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27 case 'i':
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28 inputfile = *++argv;
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29 fprintf( stderr, "inputfile = %s\n", inputfile );
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30 --argc;
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31 goto nextoption;
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32 case 'r':
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33 show_R_ = 0;
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34 break;
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35 default:
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36 fprintf( stderr, "illegal option %c\n", c );
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37 argc = 0;
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38 break;
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39 }
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40 }
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41 nextoption:
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42 ;
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43 }
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44 if( argc != 0 )
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45 {
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46 fprintf( stderr, "options: Check source file !\n" );
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47 exit( 1 );
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48 }
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49 }
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50
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51
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52
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53 int main( int argc, char *argv[] )
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54 {
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55 FILE *infp;
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56 FILE *difp;
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57 int nlenmin;
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58 char **name;
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59 char **seq;
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60 char *tmpseq;
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61 char line[100];
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62 int *nlen;
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63 int i;
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64
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65 arguments( argc, argv );
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66
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67 if( inputfile )
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68 {
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69 infp = fopen( inputfile, "r" );
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70 if( !infp )
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71 {
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72 fprintf( stderr, "Cannot open %s\n", inputfile );
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73 exit( 1 );
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74 }
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75 }
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76 else
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77 infp = stdin;
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78
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79 if( directionfile )
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80 {
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81 difp = fopen( directionfile, "r" );
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82 if( !difp )
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83 {
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84 fprintf( stderr, "Cannot open %s\n", directionfile );
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85 exit( 1 );
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86 }
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87 }
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88 else
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89 {
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90 fprintf( stderr, "Give directionfile!\n" );
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91 }
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92
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93
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94 dorp = NOTSPECIFIED;
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95 getnumlen_casepreserve( infp, &nlenmin );
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96
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97 fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
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98
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99 seq = AllocateCharMtx( njob, nlenmax+1 );
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100 tmpseq = AllocateCharVec( MAX( B, nlenmax )+1 );
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101 name = AllocateCharMtx( njob, B+1 );
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102 nlen = AllocateIntVec( njob );
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103
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104 readData_pointer_casepreserve( infp, name, nlen, seq );
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105
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106 for( i=0; i<njob; i++ )
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107 {
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108 fgets( line, 99, difp );
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109 if( line[0] != '_' )
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110 {
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111 fprintf( stderr, "Format error!\n" );
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112 exit( 1 );
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113 }
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114 if( line[1] == 'R' )
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115 {
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116 sreverse( tmpseq, seq[i] );
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117 strcpy( seq[i], tmpseq );
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118
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119 strncpy( tmpseq, name[i]+1, B-3 );
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120 tmpseq[B-3] = 0;
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121 if( show_R_ )
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122 {
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123 strcpy( name[i]+1, "_R_" );
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124 strcpy( name[i]+4, tmpseq );
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125 }
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126 else
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127 {
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128 strcpy( name[i]+1, tmpseq );
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129 }
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130 }
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131 else if( line[1] == 'F' )
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132 {
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133 ;
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134 }
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135 else
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136 {
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137 fprintf( stderr, "Format error!\n" );
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138 exit( 1 );
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139 }
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140 }
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141
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142
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143 for( i=0; i<njob; i++ )
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144 {
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145 fprintf( stdout, ">%s\n", name[i]+1 );
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146 fprintf( stdout, "%s\n", seq[i] );
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147 }
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148
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149 free( nlen );
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150 FreeCharMtx( seq );
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151 FreeCharMtx( name );
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152 free( tmpseq );
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153
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154 return( 0 );
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155 }