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comparison 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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17:836fa4fe9494 18:e4d75f9efb90
1 #include <stdio.h>
2 #include <string.h>
3 #include <stdlib.h>
4 #include "mafft.h"
5
6 int report( int status, int progress, char *message )
7 {
8 fprintf( stderr, "status = %d\n", status );
9 fprintf( stderr, "progress = %d / 100\n", progress );
10 fprintf( stderr, "message = %s\n", message );
11 return( 0 );
12 }
13
14 int chudan( int status, int progress, char *message )
15 {
16 fprintf( stderr, "status = %d\n", status );
17 fprintf( stderr, "progress = %d / 100\n", progress );
18 fprintf( stderr, "message = %s\n", message );
19 return( 2 );
20 }
21 int main( void )
22 {
23 int i;
24 int argc;
25 char **argv;
26 char **seq;
27 char **name;
28 char *message;
29 int res;
30 int n, l, mlen;
31
32 // printf( "This is interface.\n" );
33
34
35 l = 10000;
36 n = 130;
37 seq = (char **)calloc( n, sizeof( char * ) );
38 name = (char **)calloc( n, sizeof( char * ) );
39 for( i=0; i<n; i++ ) seq[i] = calloc( l+1, sizeof( char ) );
40 for( i=0; i<n; i++ ) name[i] = calloc( 100, sizeof( char ) );
41
42 for( i=0; i<10; i++ )
43 {
44 strcpy( name[i*13+0], "name0" );
45 strcpy( name[i*13+1], "name1" );
46 strcpy( name[i*13+2], "name2" );
47 strcpy( name[i*13+3], "name3" );
48 strcpy( name[i*13+4], "name4" );
49 strcpy( name[i*13+5], "name5" );
50 strcpy( name[i*13+6], "name6" );
51 strcpy( name[i*13+7], "name7" );
52 strcpy( name[i*13+8], "name8" );
53 strcpy( name[i*13+9], "name9" );
54 strcpy( name[i*13+10], "name10" );
55 strcpy( name[i*13+11], "name11" );
56 strcpy( name[i*13+12], "name12" );
57
58
59 strcpy( seq[i*13+0], "TAATTAAAGGGCCGTGGTATACTGACCATGCGAAGGTAGCATAATCATTAGCCTTTTGATTTGAGGCTGGAATGAATGGTTTGACGAGAGATGGTCTGTCTCTTCGATTAAATTGAAGTTAATCTTTAAGTGAAAAAGCTTAAATGTACTTGGAGGGCGATAAGACCCTATAGATCTTTACATTTAATTCTTTTGTCTTGCGGTAGGTAATTAGACAGAGTAAAACAATGTTCGGTTGGGGCGACGGTAAGAACAGAATAAACACTTACAACATAAACACATCAATAAATGACCATTGATCCTTAGATGAATAAAGACCAAGTTACCTTAGGGATAACAGCGTAATTCTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-------------------" );
60 strcpy( seq[i*13+1], "GTGTTGAAGGGCCGCGGTATTTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTCGAATGAATGGTTGGACGAAAAACACACTGTTTCAGACAAAGAATTTGAATTTAACTTTTAAGTGAAAAGGCTTAAATGAATTAAAAAGACGATAAGACCCTATAAATCTTTACATTATGTTTTGTATTTTTAAAGTTGTTGTGTATTAAAAAGAAATATAAAGTAGATGTTGTGTTGGGGCAACGATAATATAATAAGATTAGCTGTTGGTAAAATTAAACAAATGTGTTTGTTAGGAGTAGTTAGATCCTTTTTAGAGATTTAAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCTTATCGAAGAAAAAGATTGCGACCTCGATG" );
61 strcpy( seq[i*13+2], "ATATTGAAGGGCCGCGGTATTTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGGAGGCTCGTATGAAAGGTCGAACGAGTGATAGACTGTCTCAGCAAAAAAAAAATTGAACTTAACTTTAAAGTGAAAAGGCTTTAATATTTCAGAAAGACGATAAGACCCTATAAATCTTCACACCACCTTTTATACTAAGCCAATCTGTTTGTATAAGGAGAAGTATAAAAAACGTGTTTTGTTGGGGCAACAAAGATATAATTAAATAACTGTTTTAATTTTAAAACAAAAATTTTTGAAAATAAATTGATCCTCTCTAAAGATTAAAAGATCAAGTTACTTTAGGGATAACAGCGTCATTTTTCTTGAGAGTTCCCATCGAAAGAAAAGTTTGCGACCTCGATG---" );
62 strcpy( seq[i*13+3], "AAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATAAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATCAAAAAGACGATAAGACCCTATAAATCTTTACAATAAATATATTTTATATTTTAGTTTATAAGTGAATGATATATAAAAATATAGGTTTGTTGCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATAGTTTAAATACAATAATCATTGCTTAATATAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG" );
63 strcpy( seq[i*13+4], "AAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATAAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATCAAAAAGACGATAAGACCCTATAAATCTTTACAATAAATATATTTTATATTTTAGCTTATAAGTGTATAAGAAATAAAAATATAGGTTTGTTGCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATAATTTAAATACAATAATCATTGCTTAATACAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG" );
64 strcpy( seq[i*13+5], "ATATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGAAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAATTGTATAAAATATTAAATTTGTAATTGTTTCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATTTATTAAATCCAGTAATTATTGATTAATAAAATTGATCCTTGAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
65 strcpy( seq[i*13+6], "ATATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGAAGGCTTGAATGAAAGGTTGGACAAAGAATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTTAAGTGAAAAGGCTTAAATAAATTAAAAAGACGATAAGACCCTATAAATCTTAACAATAAATAGACTTTATATTTTAATTTATAAGTGTGTAAGGTATAAATTTTATAATTGTTTCGCTGGGGCGGCGTAGATATATAAATAAACTGTCTATATATTATATCCAATAATTGTTGATTAATAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
66 strcpy( seq[i*13+7], "GTATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGGAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAAGTATATAAAATATTAAATTTGTATTTGTTTCGCTGGGGCGGCGTGGATATATAAATAAACTGTCTATGTGTTAAATCCAATAATTATTGATTAGTAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
67 strcpy( seq[i*13+8], "GTATTAAAGAGCCGCAGTATTCTGACTGTGCGAAGGTAGCATAATAAATTGTCTTTTAAATGGAGGCTTGAATGAAAGGTTGGACAAAGTATCATCTGTTTCTTAAATATTTATTGAATTTGACTTTCAAGTGAAAAGGCTTGAATAAATTAAAAAGACGATAAGACCCTATAAATCTTTACAATAAACATGTTCTATATTTTAATTTATAAGTGTATAAAGTATTAAATTTGTATTTGTTTCGCTGGGGCGGCGTGGATATATAAATAAACTGTCTATGTGTTAAATCCAATAATTATTGATTAATAAAATTGATCCTTAAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTTTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG--" );
68 strcpy( seq[i*13+9], "TGATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGTCTTTTAAATGGGGGCTAGAATGAATGGTTGGACAAAGTATCGTCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAAGTTATAATTTTATAAAATATAAAAGTATAGTTTTGTTGTGCTGGGGCGGCATAGATATATAAATAAACTGTCTATAAATTTGAATCAATGATTGTTGATTAATGTGGTTGATCCTTTAAGAGATTAGAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
69 strcpy( seq[i*13+10], "TGATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGTCTTTTAAATGGGGGCTAGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAATTTATAATTTTATAAAATATAAAAGTATAGTTTTGTTGTGCTGGGGCGGCATAGATATATAAATAAACTGTCTATAAATTTAAATCAATAGTTGTTGATTAATATAGTTGATCCTTTAAAAGATTAGAAGATTAAGTTACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
70 strcpy( seq[i*13+11], "TAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGGCTTTTAAATGGAGGCTGGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAACTTATAATTTTATAAAATATAAAAGTATAATTTTGTTGTGCTGGGGCGGCGTAGATATATAAATGAACTGTCTATGAAATTAAATCAATAATAGTTGATTATTAATATTGATCCTTTAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
71 strcpy( seq[i*13+12], "TAATTAAAGAGCCGCAGTATTTTGACTGTGCGAAGGTAGCATAATAGATTGGCTTTTAAATGGAGGCTGGAATGAATGGTTGGACAAAGTATCATCTGTTTCTTAAATAAATATTGAATTTGACTTTTAAGTTAAAAGGCTTAAATAAAATAAAAAGACGATAAGACCCTATAAATCTTTACATAAATTATATTTTAAATTTTAATTTATAATTTTATAAAATATAAAAGTATAATTTTGTTGTGCTGGGGCGGCGTAGATATATAAATGAACTGTCTATGAAATTAAATCAATAATAGTTGATTATTAATATTGATCCTTTAATAGATTAAAAGATTAAGATACTTTAGGGATAACAGCGTTATTTTTTCTGAGAGTTCAAATCGACAAAAGAGTTTGCGAGCCTCGATG-" );
72
73 }
74
75 argc = 20;
76 argv = (char **)calloc( argc, sizeof( char * ) );
77 for( i=0; i<argc; i++ ) argv[i] = calloc( 100, sizeof( char ) );
78 strcpy( argv[0], "disttbfast" );
79 strcpy( argv[1], "-W" );
80 strcpy( argv[2], "6" );
81 strcpy( argv[3], "-b" );
82 strcpy( argv[4], "62" );
83 strcpy( argv[5], "-Q" );
84 strcpy( argv[6], "100" );
85 strcpy( argv[7], "-h" );
86 strcpy( argv[8], "0" );
87 strcpy( argv[9], "-F" );
88 strcpy( argv[10], "-X" );
89 strcpy( argv[11], "-s" );
90 strcpy( argv[12], "0.0" );
91 strcpy( argv[13], "-f" );
92 strcpy( argv[14], "-1.53" );
93 strcpy( argv[15], "-C" );
94 strcpy( argv[16], "0" );
95 strcpy( argv[17], "-D" ); // Necessary. DNA -> -D; Protein -> -P
96 strcpy( argv[18], "-I" ); // --add
97 strcpy( argv[19], "2" ); // --add
98
99 #if 0
100 mlen = 5000;
101 message = (char *)calloc( mlen+1, sizeof( char ) );
102
103 fprintf( stderr, "first run\n" );
104 res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
105 fprintf( stderr, "second run\n" );
106 res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
107 fprintf( stderr, "third run\n" );
108 res = disttbfast( n, l, mlen, name, seq, &message, argc, argv, report );
109
110 fprintf( stderr, "\n\n\nmessage in interface = :%s:\n", message );
111 free( message );
112 #else
113 fprintf( stderr, "first run\n" );
114 res = disttbfast( n, l, name, seq, argc, argv, report );
115 fprintf( stderr, "second run\n" );
116 res = disttbfast( n, l, name, seq, argc, argv, chudan );
117 // fprintf( stderr, "third run\n" );
118 // res = disttbfast( n, l, name, seq, argc, argv, report );
119 #endif
120
121 if( res == GUI_LENGTHOVER )
122 {
123 fprintf( stderr, "length over!" );
124 }
125 else
126 {
127 fprintf( stderr, "res = %d\n", res );
128 fprintf( stdout, "Output:\n" );
129 for( i=0; i<n; i++ )
130 fprintf( stdout, "%s\n", seq[i] );
131 }
132 fprintf( stderr, "argv = \n" );
133 for( i=0; i<argc; i++ )
134 fprintf( stderr, "%s ", argv[i] );
135 fprintf( stderr, "\n" );
136
137 for( i=0; i<n; i++ ) free( seq[i] );
138 free( seq );
139 for( i=0; i<n; i++ ) free( name[i] );
140 free( name );
141 for( i=0; i<argc; i++ ) free( argv[i] );
142 free( argv );
143
144 }