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annotate mafft/core/seq2regtable.c @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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 *weboutfile = NULL;
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6
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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 while( --argc > 0 && (*++argv)[0] == '-' )
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13 {
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14 while ( (c = *++argv[0]) )
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15 {
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16 switch( c )
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17 {
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18 case 'i':
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19 inputfile = *++argv;
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20 fprintf( stderr, "inputfile = %s\n", inputfile );
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21 --argc;
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22 goto nextoption;
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23 case 'w':
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24 weboutfile = *++argv;
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25 fprintf( stderr, "weboutfile = %s\n", weboutfile );
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26 --argc;
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27 goto nextoption;
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28 default:
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29 fprintf( stderr, "illegal option %c\n", c );
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30 argc = 0;
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31 break;
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32 }
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33 }
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34 nextoption:
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35 ;
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36 }
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37 if( argc != 0 )
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38 {
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39 fprintf( stderr, "options: Check source file !\n" );
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40 exit( 1 );
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41 }
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42 }
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43
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44
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45 int main( int argc, char *argv[] )
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46 {
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47 FILE *infp;
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48 FILE *weboutfp;
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49 int nlenmin;
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50 int isaligned = 0;
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51
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52 arguments( argc, argv );
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53
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54 if( inputfile )
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55 {
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56 infp = fopen( inputfile, "r" );
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57 if( !infp )
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58 {
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59 fprintf( stderr, "Cannot open %s\n", inputfile );
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60 exit( 1 );
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61 }
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62 }
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63 else
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64 infp = stdin;
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65
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66 if( weboutfile )
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67 {
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68 weboutfp = fopen( weboutfile, "w" );
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69 if( !weboutfp )
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70 {
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71 fprintf( stderr, "Cannot open %s\n", weboutfile );
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72 exit( 1 );
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73 }
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74 }
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75
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76 dorp = NOTSPECIFIED;
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77 if( weboutfile )
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78 {
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79 getnumlen_nogap_outallreg_web( infp, weboutfp, &nlenmin, &isaligned );
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80 if( isaligned ) fprintf( stdout, "Aligned\n" );
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81 else fprintf( stdout, "Not aligned\n" );
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82 }
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83 else
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84 getnumlen_nogap_outallreg( infp, &nlenmin );
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85
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86 return( 0 );
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87
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88 }