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Viewing changes to core/mltaln9.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/mltaln9.c
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                                fprintf( stderr, "========================================================================= \n" );
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                                fprintf( stderr, "========================================================================= \n" );
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                                fprintf( stderr, "========================================================================= \n" );
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                                fprintf( stderr, "=== \n" );
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                                fprintf( stderr, "=== Alphabet '%c' is unknown.\n", (*seq)[i] );
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                                fprintf( stderr, "=== Please check site %d in sequence %d.\n", i+1, (int)(seq-seqbk+1) );
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                                fprintf( stderr, "=== \n" );
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                                fprintf( stderr, "========================================================================= \n" );
 
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                                fprintf( stderr, "=== To make an alignment having unusual characters (U, @, #, etc), try\n" );
 
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                                fprintf( stderr, "=== %% mafft --anysymbol input > output\n" );
 
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                                fprintf( stderr, "=== \n" );
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                                fprintf( stderr, "========================================================================= \n" );
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                                fprintf( stderr, "========================================================================= \n" );
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                                return( (int)(*seq)[i] );
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        float *mindisfrom = NULL; // by D.Mathog, a guess
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        static char **tree;
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        static char *treetmp;
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        static char *nametmp;
 
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        static char *nametmp, *nameptr, *tmpptr;
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        FILE *fp;
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        float (*clusterfuncpt[1])(float,float);
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                nmemar = AllocateIntVec( njob );
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                mindisfrom = AllocateFloatVec( njob );
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                nearest = AllocateIntVec( njob );
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                treetmp = AllocateCharVec( njob*50 );
 
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                treetmp = AllocateCharVec( njob*150 );
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                nametmp = AllocateCharVec( 130 );
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                tree = AllocateCharMtx( njob, njob*50 );
 
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                tree = AllocateCharMtx( njob, njob*150 );
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        }
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                for( j=0; j<130; j++ ) nametmp[j] = 0;
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                for( j=0; j<130; j++ ) 
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                {
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                        if( isalnum( name[i][j] ) )
 
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                        if( name[i][j] == 0 )
 
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                                break;
 
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                        else if( isalnum( name[i][j] ) )
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                                nametmp[j] = name[i][j];
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                        else
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                                nametmp[j] = '_';
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                nametmp[129] = 0;
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//              sprintf( tree[i], "%d_l=%d_%.20s", i+1, nlen[i], nametmp+1 );
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                if( outnumber )
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                        sprintf( tree[i], "%d_%.20s", i+1, strstr( nametmp, "_numo_e" ) + 8 );
 
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                        nameptr = strstr( nametmp, "_numo_e" ) + 8;
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                else
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                        sprintf( tree[i], "%d_%.20s", i+1, nametmp+1 );
 
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                        nameptr = nametmp + 1;
 
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                if( (tmpptr=strstr( nameptr, "_oripos__" )) ) nameptr = tmpptr + 9; // = -> _ no tame
 
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                sprintf( tree[i], "%d_%.60s", i+1, nameptr );
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        }
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        for( i=0; i<nseq; i++ )
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        {
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        double *mindisfrom = NULL; // by D.Mathog, a guess
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        static char **tree;
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        static char *treetmp;
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        static char *nametmp;
 
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        static char *nametmp, *nameptr, *tmpptr;
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        FILE *fp;
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        double (*clusterfuncpt[1])(double,double);
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                nmemar = AllocateIntVec( njob );
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                mindisfrom = AllocateDoubleVec( njob );
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                nearest = AllocateIntVec( njob );
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                treetmp = AllocateCharVec( njob*50 );
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                nametmp = AllocateCharVec( 31 );
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                tree = AllocateCharMtx( njob, njob*50 );
 
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                treetmp = AllocateCharVec( njob*150 );
 
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                nametmp = AllocateCharVec( 91 );
 
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                tree = AllocateCharMtx( njob, njob*150 );
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        }
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    for( i=0; i<nseq; i++ )
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        {
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                for( j=0; j<30; j++ ) nametmp[j] = 0;
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                for( j=0; j<30; j++ ) 
 
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                for( j=0; j<90; j++ ) nametmp[j] = 0;
 
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                for( j=0; j<90; j++ ) 
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                {
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                        if( isalnum( name[i][j] ) )
 
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                        if( name[i][j] == 0 )
 
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                                break;
 
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                        else if( isalnum( name[i][j] ) )
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                                nametmp[j] = name[i][j];
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                        else
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                                nametmp[j] = '_';
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                }
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                nametmp[30] = 0;
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//              sprintf( tree[i], "%d_l=%d_%.20s", i+1, nlen[i], nametmp+1 );
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                sprintf( tree[i], "%d_%.20s", i+1, nametmp+1 );
 
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                nametmp[90] = 0;
 
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//              sprintf( tree[i], "%d_%.60s", i+1, nametmp+1 );
 
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                if( outnumber )
 
1759
                        nameptr = strstr( nametmp, "_numo_e" ) + 8;
 
1760
                else
 
1761
                        nameptr = nametmp + 1;
 
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1763
                if( (tmpptr=strstr( nameptr, "_oripos__" )) ) nameptr = tmpptr + 9; // = -> _ no tame
 
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                sprintf( tree[i], "%d_%.60s", i+1, nameptr );
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        }
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        for( i=0; i<nseq; i++ )
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        {
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        {
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                v += (double)naivepairscore11( s[i], s[j], penalty );
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        }
 
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        fprintf( stderr, "penalty = %d\n", penalty );
 
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        return( v );
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}
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