← Back to branch summary

~ubuntu-branches/debian/sid/mafft/sid

« back to all changes in this revision

Viewing changes to core/replaceu.c

  • Committer: Bazaar Package Importer
  • Author(s): Andreas Tille
  • Date: 2011-03-12 00:02:43 UTC
  • mfrom: (1.1.7 upstream)
  • Revision ID: james.westby@ubuntu.com-20110312000243-1yx6ho40e2kf9nxw
Tags: 6.850-1
* New upstream version
* Adapted patch to new upstream
* Debhelper 8 (control + compat)
* debian/rules: Switch to dh
* debian/links: override broken symlinks created in Makefile

Show diffs side-by-side

added added

removed removed

Lines of Context:
core/replaceu.c
 
1
#include "mltaln.h"
 
2
 
 
3
#define DEBUG 0
 
4
 
 
5
static int seedoffset;
 
6
 
 
7
static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
 
8
{
 
9
        int i;
 
10
        char *pt;
 
11
        for( i=0; i<n; i++ )
 
12
        {
 
13
                pt = seq[i];
 
14
                while( *pt )
 
15
                {
 
16
                        if( !strchr( usual, *pt ) ) *pt = unknown;
 
17
                        else *pt = uporlow( *pt );
 
18
                        pt++;
 
19
                }
 
20
        }
 
21
}
 
22
 
 
23
 
 
24
void arguments( int argc, char *argv[] )
 
25
{
 
26
    int c;
 
27
 
 
28
        seedoffset = 0;
 
29
        inputfile = NULL;
 
30
 
 
31
    while( --argc > 0 && (*++argv)[0] == '-' )
 
32
        {
 
33
        while ( (c = *++argv[0]) )
 
34
                {
 
35
            switch( c )
 
36
            {
 
37
                                case 'o':
 
38
                                        seedoffset = atoi( *++argv );
 
39
                                        fprintf( stderr, "seedoffset = %d\n", seedoffset );
 
40
                                        --argc;
 
41
                                        goto nextoption;
 
42
                                case 'i':
 
43
                                        inputfile = *++argv;
 
44
                                        fprintf( stderr, "inputfile = %s\n", inputfile );
 
45
                                        --argc;
 
46
                                        goto nextoption;
 
47
                default:
 
48
                    fprintf( stderr, "illegal option %c\n", c );
 
49
                    argc = 0;
 
50
                    break;
 
51
            }
 
52
                }
 
53
                nextoption:
 
54
                        ;
 
55
        }
 
56
    if( argc != 0 ) 
 
57
    {
 
58
        fprintf( stderr, "options: Check source file !\n" );
 
59
        exit( 1 );
 
60
    }
 
61
}
 
62
 
 
63
 
 
64
 
 
65
int main( int argc, char *argv[] )
 
66
{
 
67
        FILE *infp;
 
68
        int nlenmin;
 
69
        char **name;
 
70
        char **seq;
 
71
        int *nlen;
 
72
        int i;
 
73
        char *usual;
 
74
 
 
75
        arguments( argc, argv );
 
76
 
 
77
        if( inputfile )
 
78
        {
 
79
                infp = fopen( inputfile, "r" );
 
80
                if( !infp )
 
81
                {
 
82
                        fprintf( stderr, "Cannot open %s\n", inputfile );
 
83
                        exit( 1 );
 
84
                }
 
85
        }
 
86
        else
 
87
                infp = stdin;
 
88
 
 
89
 
 
90
        dorp = NOTSPECIFIED;
 
91
        getnumlen_casepreserve( infp, &nlenmin );
 
92
 
 
93
        fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
 
94
 
 
95
        seq = AllocateCharMtx( njob, nlenmax+1 );
 
96
        name = AllocateCharMtx( njob, B+1 );
 
97
        nlen = AllocateIntVec( njob );
 
98
 
 
99
        readData_pointer_casepreserve( infp, name, nlen, seq );
 
100
 
 
101
//      for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
 
102
 
 
103
#if 0
 
104
        FILE *origfp;
 
105
        origfp = fopen( "_original", "w" );
 
106
        if( !origfp )
 
107
        {
 
108
                fprintf( stderr, "Cannot open _original\n" );
 
109
                exit( 1 );
 
110
        }
 
111
        for( i=0; i<njob; i++ )
 
112
        {
 
113
                nlen[i] = strlen( seq[i] );
 
114
                fprintf( origfp, ">%s\n", name[i]+1 );
 
115
                if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
 
116
                fprintf( origfp, "%s\n", seq[i] );
 
117
        }
 
118
        fclose( origfp );
 
119
#endif
 
120
 
 
121
        if( dorp == 'p' )
 
122
        {
 
123
                usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
 
124
                replace_unusual( njob, seq, usual, 'X', toupper );
 
125
        }
 
126
        else
 
127
        {
 
128
                usual = "ATGCUatgcu-";
 
129
                replace_unusual( njob, seq, usual, 'n', tolower );
 
130
        }
 
131
        
 
132
 
 
133
 
 
134
        for( i=0; i<njob; i++ )
 
135
        {
 
136
                fprintf( stdout, ">%d_oripos_%s\n", i+seedoffset, name[i] );
 
137
                fprintf( stdout, "%s\n", seq[i] );
 
138
        }
 
139
 
 
140
        free( nlen );
 
141
        FreeCharMtx( seq );
 
142
        FreeCharMtx( name );
 
143
 
 
144
        return( 0 );
 
145
}