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Viewing changes to core/f2cl.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

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Lines of Context:
core/f2cl.c
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static char *comment;
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static char *orderfile;
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static int format;
 
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static int namelen;
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static void fillspace( char *seq, int lenmax )
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{
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                        continue;
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                }
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                for( j=0; j<nseq; j++ )
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                        if( seq[0][i] != seq[j][i] ) break;
 
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                        if( toupper( seq[0][i] ) != toupper( seq[j][i] ) ) break;
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                if( j == nseq ) 
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                {
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                        mark[i] = '*';
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                {
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                        for( j=0; j<nseq; j++ )
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                        {
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                                if( !strchr( strong[k], seq[j][i] ) ) break;
 
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                                if( !strchr( strong[k], toupper( seq[j][i] ) ) ) break;
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                        }
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                        if( j == nseq ) break;
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                }
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                {
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                        for( j=0; j<nseq; j++ )
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                        {
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                                if( !strchr( weaker[k], seq[j][i] ) ) break;
 
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                                if( !strchr( weaker[k], toupper( seq[j][i] ) ) ) break;
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                        }
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                        if( j == nseq ) break;
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                }
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void arguments( int argc, char *argv[] )
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{
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    int c;
 
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        namelen = 15;
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        scoremtx = 1;
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        nblosum = 62;
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        dorp = NOTSPECIFIED;
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                                        fprintf( stderr, "orderfile = %s\n", orderfile );
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                                        --argc;
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                                        goto nextoption;
 
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                                case 'n':
 
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                                        namelen = atoi( *++argv );
 
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                                        fprintf( stderr, "namelen = %d\n", namelen );
 
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                                        --argc;
 
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                                        goto nextoption;
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                                case 'f':
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                                        format = 'f';
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                                        break;
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                                case 'm':
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                                        format = 'm';
 
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                                case 'y':
 
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                                        format = 'y';
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                                        break;
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                default:
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                    fprintf( stderr, "illegal option %c\n", c );
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        FILE *infp;
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        FILE *orderfp;
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        char gett[B];
 
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        int nlenmin;
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        arguments( argc, argv );
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        else
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                infp = stdin;
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        getnumlen( infp );
 
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        getnumlen_casepreserve( infp, &nlenmin );
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        rewind( infp );
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        seq = AllocateCharMtx( njob, nlenmax*2+1 );
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                for( i=0; i<njob; i++ ) order[i] = i;
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        }
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        readData_pointer( infp, name, nlen, seq );
 
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        readData_pointer_casepreserve( infp, name, nlen, seq );
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        fclose( infp );
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        if( format == 'c' ) for( i=0; i<njob; i++ ) fillspace( seq[i], nlenmax );
 
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        if( format == 'c' || format == 'y' ) for( i=0; i<njob; i++ ) fillspace( seq[i], nlenmax );
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        constants( njob, seq );
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//      initSignalSM();
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        if( format == 'f' )
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                writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
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        else if( format == 'c' )
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                clustalout_pointer( stdout, njob, nlenmax, seq, name, mark, comment, order );
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        else if( format == 'm' )
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                miyataout_reorder_pointer( stdout, njob, nlenmax, name, nlen, seq, order );
 
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                clustalout_pointer( stdout, njob, nlenmax, seq, name, mark, comment, order, namelen );
 
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        else if( format == 'y' )
 
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                phylipout_pointer( stdout, njob, nlenmax, seq, name, order );
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        else
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                fprintf( stderr, "Unknown format\n" );
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