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annotate mafft/core/interface.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 <stdio.h>
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2 #include <string.h>
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3 #include <stdlib.h>
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4 #include "mafft.h"
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5
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6 int report( int status, int progress, char *message )
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7 {
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8 fprintf( stderr, "status = %d\n", status );
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9 fprintf( stderr, "progress = %d / 100\n", progress );
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10 fprintf( stderr, "message = %s\n", message );
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11 return( 0 );
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12 }
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13
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14 int chudan( int status, int progress, char *message )
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15 {
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16 fprintf( stderr, "status = %d\n", status );
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17 fprintf( stderr, "progress = %d / 100\n", progress );
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18 fprintf( stderr, "message = %s\n", message );
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19 return( 2 );
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20 }
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21 int main( void )
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22 {
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23 int i;
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24 int argc;
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25 char **argv;
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26 char **seq;
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27 char **name;
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28 char *message;
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29 int res;
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30 int n, l, mlen;
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32 // printf( "This is interface.\n" );
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34
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35 l = 10000;
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36 n = 130;
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37 seq = (char **)calloc( n, sizeof( char * ) );
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38 name = (char **)calloc( n, sizeof( char * ) );
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39 for( i=0; i<n; i++ ) seq[i] = calloc( l+1, sizeof( char ) );
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40 for( i=0; i<n; i++ ) name[i] = calloc( 100, sizeof( char ) );
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41
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42 for( i=0; i<10; i++ )
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43 {
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44 strcpy( name[i*13+0], "name0" );
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45 strcpy( name[i*13+1], "name1" );
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46 strcpy( name[i*13+2], "name2" );
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47 strcpy( name[i*13+3], "name3" );
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48 strcpy( name[i*13+4], "name4" );
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49 strcpy( name[i*13+5], "name5" );
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50 strcpy( name[i*13+6], "name6" );
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51 strcpy( name[i*13+7], "name7" );
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52 strcpy( name[i*13+8], "name8" );
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53 strcpy( name[i*13+9], "name9" );
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54 strcpy( name[i*13+10], "name10" );
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55 strcpy( name[i*13+11], "name11" );
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56 strcpy( name[i*13+12], "name12" );
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59 strcpy( seq[i*13+0], "TAATTAAAGGGCCGTGGTATACTGACCATGCGAAGGTAGCATAATCATTAGCCTTTTGATTTGAGGCTGGAATGAATGGTTTGACGAGAGATGGTCTGTCTCTTCGATTAAATTGAAGTTAATCTTTAAGTGAAAAAGCTTAAATGTACTTGGAGGGCGATAAGACCCTATAGATCTTTACATTTAATTCTTTTGTCTTGCGGTAGGTAATTAGACAGAGTAAAACAATGTTCGGTTGGGGCGACGGTAAGAACAGAATAAACACTTACAACATAAACACATCAATAAATGACCATTGATCCTTAGATGAATAAAGACCAAGTTACCTTAGGGATAACAGCGTAATTCTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-------------------" );
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60 strcpy( seq[i*13+1], "GTGTTGAAGGGCCGCGGTATTTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTCGAATGAATGGTTGGACGAAAAACACACTGTTTCAGACAAAGAATTTGAATTTAACTTTTAAGTGAAAAGGCTTAAATGAATTAAAAAGACGATAAGACCCTATAAATCTTTACATTATGTTTTGTATTTTTAAAGTTGTTGTGTATTAAAAAGAAATATAAAGTAGATGTTGTGTTGGGGCAACGATAATATAATAAGATTAGCTGTTGGTAAAATTAAACAAATGTGTTTGTTAGGAGTAGTTAGATCCTTTTTAGAGATTTAAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCTTATCGAAGAAAAAGATTGCGACCTCGATG" );
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61 strcpy( seq[i*13+2], "ATATTGAAGGGCCGCGGTATTTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGGAGGCTCGTATGAAAGGTCGAACGAGTGATAGACTGTCTCAGCAAAAAAAAAATTGAACTTAACTTTAAAGTGAAAAGGCTTTAATATTTCAGAAAGACGATAAGACCCTATAAATCTTCACACCACCTTTTATACTAAGCCAATCTGTTTGTATAAGGAGAAGTATAAAAAACGTGTTTTGTTGGGGCAACAAAGATATAATTAAATAACTGTTTTAATTTTAAAACAAAAATTTTTGAAAATAAATTGATCCTCTCTAAAGATTAAAAGATCAAGTTACTTTAGGGATAACAGCGTCATTTTTCTTGAGAGTTCCCATCGAAAGAAAAGTTTGCGACCTCGATG---" );
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62 strcpy( seq[i*13+3], "AAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATAAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATCAAAAAGACGATAAGACCCTATAAATCTTTACAATAAATATATTTTATATTTTAGTTTATAAGTGAATGATATATAAAAATATAGGTTTGTTGCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATAGTTTAAATACAATAATCATTGCTTAATATAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG" );
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63 strcpy( seq[i*13+4], "AAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATAAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATCAAAAAGACGATAAGACCCTATAAATCTTTACAATAAATATATTTTATATTTTAGCTTATAAGTGTATAAGAAATAAAAATATAGGTTTGTTGCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATAATTTAAATACAATAATCATTGCTTAATACAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG" );
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64 strcpy( seq[i*13+5], "ATATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAATTGTATAAAATATTAAATTTGTAATTGTTTCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATTTATTAAATCCAGTAATTATTGATTAATAAAATTGATCCTTGAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
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65 strcpy( seq[i*13+6], "ATATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGAAGGCTTGAATGAAAGGTTGGACAAAGAATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATTAAAAAGACGATAAGACCCTATAAATCTTAACAATAAATAGACTTTATATTTTAATTTATAAGTGTGTAAGGTATAAATTTTATAATTGTTTCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATATATTATATCCAATAATTGTTGATTAATAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
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66 strcpy( seq[i*13+7], "GTATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGGAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAAGTATATAAAATATTAAATTTGTATTTGTTTCGCTGGGGCGGCGTGGATATATAAATAAACTGTCTATGTGTTAAATCCAATAATTATTGATTAGTAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
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67 strcpy( seq[i*13+8], "GTATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGGAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAAGTGTATAAAGTATTAAATTTGTATTTGTTTCGCTGGGGCGGCGTGGATATATAAATAAACTGTCTATGTGTTAAATCCAATAATTATTGATTAATAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
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68 strcpy( seq[i*13+9], "TGATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGTCTTTTAAATGGGGGCTAGAATGAATGGTTGGACAAAGTATCGTCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAAGTTATAATTTTATAAAATATAAAAGTATAGTTTTGTTGTGCTGGGGCGGCATAGATATATAAATAAACTGTCTATAAATTTGAATCAATGATTGTTGATTAATGTGGTTGATCCTTTAAGAGATTAGAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
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69 strcpy( seq[i*13+10], "TGATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGTCTTTTAAATGGGGGCTAGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAATTTATAATTTTATAAAATATAAAAGTATAGTTTTGTTGTGCTGGGGCGGCATAGATATATAAATAAACTGTCTATAAATTTAAATCAATAGTTGTTGATTAATATAGTTGATCCTTTAAAAGATTAGAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
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70 strcpy( seq[i*13+11], "TAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGGCTTTTAAATGGAGGCTGGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAACTTATAATTTTATAAAATATAAAAGTATAATTTTGTTGTGCTGGGGCGGCGTAGATATATAAATGAACTGTCTATGAAATTAAATCAATAATAGTTGATTATTAATATTGATCCTTTAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
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71 strcpy( seq[i*13+12], "TAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGGCTTTTAAATGGAGGCTGGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAATTTATAATTTTATAAAATATAAAAGTATAATTTTGTTGTGCTGGGGCGGCGTAGATATATAAATGAACTGTCTATGAAATTAAATCAATAATAGTTGATTATTAATATTGATCCTTTAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
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72
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73 }
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74
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75 argc = 20;
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76 argv = (char **)calloc( argc, sizeof( char * ) );
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77 for( i=0; i<argc; i++ ) argv[i] = calloc( 100, sizeof( char ) );
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78 strcpy( argv[0], "disttbfast" );
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79 strcpy( argv[1], "-W" );
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80 strcpy( argv[2], "6" );
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81 strcpy( argv[3], "-b" );
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82 strcpy( argv[4], "62" );
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83 strcpy( argv[5], "-Q" );
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84 strcpy( argv[6], "100" );
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85 strcpy( argv[7], "-h" );
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86 strcpy( argv[8], "0" );
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87 strcpy( argv[9], "-F" );
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88 strcpy( argv[10], "-X" );
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89 strcpy( argv[11], "-s" );
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90 strcpy( argv[12], "0.0" );
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91 strcpy( argv[13], "-f" );
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92 strcpy( argv[14], "-1.53" );
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93 strcpy( argv[15], "-C" );
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94 strcpy( argv[16], "0" );
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95 strcpy( argv[17], "-D" ); // Necessary. DNA -> -D; Protein -> -P
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96 strcpy( argv[18], "-I" ); // --add
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97 strcpy( argv[19], "2" ); // --add
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98
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99 #if 0
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100 mlen = 5000;
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101 message = (char *)calloc( mlen+1, sizeof( char ) );
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102
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103 fprintf( stderr, "first run\n" );
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104 res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
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105 fprintf( stderr, "second run\n" );
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106 res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
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107 fprintf( stderr, "third run\n" );
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108 res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
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109
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110 fprintf( stderr, "\n\n\nmessage in interface = :%s:\n", message );
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111 free( message );
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112 #else
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113 fprintf( stderr, "first run\n" );
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114 res = disttbfast( n, l, name, seq, argc, argv, report );
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115 fprintf( stderr, "second run\n" );
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116 res = disttbfast( n, l, name, seq, argc, argv, chudan );
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117 // fprintf( stderr, "third run\n" );
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118 // res = disttbfast( n, l, name, seq, argc, argv, report );
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119 #endif
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120
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121 if( res == GUI_LENGTHOVER )
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122 {
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123 fprintf( stderr, "length over!" );
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124 }
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125 else
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126 {
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127 fprintf( stderr, "res = %d\n", res );
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128 fprintf( stdout, "Output:\n" );
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129 for( i=0; i<n; i++ )
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130 fprintf( stdout, "%s\n", seq[i] );
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131 }
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132 fprintf( stderr, "argv = \n" );
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133 for( i=0; i<argc; i++ )
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134 fprintf( stderr, "%s ", argv[i] );
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135 fprintf( stderr, "\n" );
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136
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137 for( i=0; i<n; i++ ) free( seq[i] );
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138 free( seq );
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139 for( i=0; i<n; i++ ) free( name[i] );
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140 free( name );
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141 for( i=0; i<argc; i++ ) free( argv[i] );
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142 free( argv );
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143
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144 }