+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 1
-#define TSUYOSAFACTOR 100
-
-
-static char *pairfile;
-static int nhomologs;
-
-void strip( char *s )
-{
- char *pt = s;
- while( *++pt )
- if( *pt == '\n' ) *pt = 0;
-}
-
-int searchused( char *q, char **keys, int n )
-{
- int i;
- for( i=0; i<n; i++ )
- {
-// fprintf( stderr, "%s ? %s\n", q, names[i] );
- if( !strcmp( q, keys[i] ) ) return( i );
- }
- return( -1 );
-}
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- nhomologs = 2;
- inputfile = NULL;
- pairfile = NULL;
- fftkeika = 0;
- pslocal = -1000.0;
- constraint = 0;
- nblosum = 62;
- fmodel = 0;
- calledByXced = 0;
- devide = 0;
- use_fft = 0;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- weight = 3;
- utree = 1;
- tbutree = 1;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- alg = 'A';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'x';
- contin = 0;
- scoremtx = 1;
- kobetsubunkatsu = 0;
- divpairscore = 0;
- dorp = NOTSPECIFIED;
- ppenalty = NOTSPECIFIED;
- ppenalty_OP = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- ppenalty_EX = NOTSPECIFIED;
- poffset = NOTSPECIFIED;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
-
- while( --argc > 0 && (*++argv)[0] == '-' )
- {
- while ( ( c = *++argv[0] ) )
- {
- switch( c )
- {
- case 'i':
- inputfile = *++argv;
- fprintf( stderr, "inputfile = %s\n", inputfile );
- --argc;
- goto nextoption;
- case 'p':
- pairfile = *++argv;
- fprintf( stderr, "pairfile = %s\n", pairfile );
- --argc;
- goto nextoption;
- case 't':
- nhomologs = atoi( *++argv );
- fprintf( stderr, "nhomologs = %d\n", nhomologs );
- --argc;
- goto nextoption;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- break;
- default:
- fprintf( stderr, "illegal option %c\n", c );
- argc = 0;
- break;
- }
- }
- nextoption:
- ;
- }
- if( argc == 1 )
- {
- cut = atof( (*argv) );
- argc--;
- }
- if( argc != 0 )
- {
- fprintf( stderr, "options: Check source file !\n" );
- exit( 1 );
- }
- if( tbitr == 1 && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : o, m or u\n" );
- exit( 1 );
- }
- if( alg == 'C' && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : C, o\n" );
- exit( 1 );
- }
-}
-
-int countamino( char *s, int end )
-{
- int val = 0;
- while( end-- )
- if( *s++ != '-' ) val++;
- return( val );
-}
-
-static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
-{
- FILE *tmpfp;
- static char dumm1[B], dumm0[B];
- int i, j;
- char *res;
- FILE *hat3p;
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
- static char **pseq;
- LocalHom **localhomtable, *tmpptr;
- float pscore = 0.0; // by D.Mathog, aguess
- char *aseq = NULL; // by D.Mathog
- char **usedseqs = NULL; // by D.Mathog
- char **usednames = NULL; // by D.Mathog
- int nused;
- double tsuyosa;
-
- tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
- fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
- localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
- for( i=0; i<njob; i++)
- {
- localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
- for( j=0; j<njob; j++)
- {
- localhomtable[i][j].start1 = -1;
- localhomtable[i][j].end1 = -1;
- localhomtable[i][j].start2 = -1;
- localhomtable[i][j].end2 = -1;
- localhomtable[i][j].opt = -1.0;
- localhomtable[i][j].next = NULL;
- }
- }
-
- if( effarr1 == NULL )
- {
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- pseq = AllocateCharMtx( 2, nlenmax*9+1 );
- aseq = AllocateCharVec( nlenmax*9+1 );
- usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
- usednames = AllocateCharMtx( njob, B );
-#if 0
-#else
-#endif
- }
-
-#if 0
- fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
-#endif
-
-#if 0
- for( i=0; i<njob; i++ )
- fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
-
-// writePre( njob, name, nlen, aseq, 0 );
-
- fprintf( stderr, "opening %s\n", pairfile );
- tmpfp = fopen( pairfile, "r" );
- if( !tmpfp )
- {
- fprintf( stderr, "Cannot open %s\n", pairfile );
- exit( 1 );
- }
- searchKUorWA( tmpfp );
- hat3p = fopen( "hat3", "w" );
- if( !hat3p ) ErrorExit( "Cannot open hat3." );
- nused = 0;
- while( 1 )
- {
- res = fgets( dumm0, B-1, tmpfp );
- strip( dumm0 );
- if( res == NULL )
- {
- break;
- }
- load1SeqWithoutName_new( tmpfp, pseq[0] );
- gappick0( aseq, pseq[0] );
- i = searchused( aseq, usedseqs, nused );
- if( i == -1 )
- {
- strcpy( usednames[nused], dumm0+1 );
- strcpy( usedseqs[nused], aseq );
- i = nused;
- nused++;
- }
- fprintf( stderr, "i = %d\n", i );
-
- res = fgets( dumm1, B-1, tmpfp );
- strip( dumm1 );
- if( res == NULL )
- {
- fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
- exit( 1 );
- }
- load1SeqWithoutName_new( tmpfp, pseq[1] );
- gappick0( aseq, pseq[1] );
- j = searchused( aseq, usedseqs, nused );
- if( j == -1 )
- {
- strcpy( usednames[nused], dumm1+1 );
- strcpy( usedseqs[nused], aseq );
- j = nused;
- nused++;
- }
- fprintf( stderr, "j = %d\n", j );
-
- if( strlen( pseq[0] ) != strlen( pseq[1] ) )
- {
- fprintf( stderr, "Not aligned, %s - %s\n", dumm0, dumm1 );
- exit( 1 );
- }
-
-
- fprintf( stderr, "adding %d-%d\n", i, j );
- putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
- for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
- }
- }
- fclose( tmpfp );
- fclose( hat3p );
-
- for( i=0; i<nused; i++ )
- fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );
-
-
-#if 0
- fprintf( stderr, "##### writing hat3\n" );
- hat3p = fopen( "hat3", "w" );
- if( !hat3p ) ErrorExit( "Cannot open hat3." );
- ilim = njob-1;
- for( i=0; i<ilim; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
- }
- }
- }
- fclose( hat3p );
-#endif
-#if DEBUG
- fprintf( stderr, "calling FreeLocalHomTable\n" );
-#endif
- FreeLocalHomTable( localhomtable, njob );
-#if DEBUG
- fprintf( stderr, "done. FreeLocalHomTable\n" );
-#endif
-}
-
-static void WriteOptions( FILE *fp )
-{
-
- if( dorp == 'd' ) fprintf( fp, "DNA\n" );
- else
- {
- if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
- else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
- else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
- }
- fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- if( use_fft ) fprintf( fp, "FFT on\n" );
-
- fprintf( fp, "tree-base method\n" );
- if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
- else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
- if( tbitr || tbweight )
- {
- fprintf( fp, "iterate at each step\n" );
- if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
- if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
- if( tbweight ) fprintf( fp, " weighted\n" );
- fprintf( fp, "\n" );
- }
-
- fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-
- if( alg == 'a' )
- fprintf( fp, "Algorithm A\n" );
- else if( alg == 'A' )
- fprintf( fp, "Algorithm A+\n" );
- else if( alg == 'S' )
- fprintf( fp, "Apgorithm S\n" );
- else if( alg == 'C' )
- fprintf( fp, "Apgorithm A+/C\n" );
- else
- fprintf( fp, "Unknown algorithm\n" );
-
- if( treemethod == 'x' )
- fprintf( fp, "Tree = UPGMA (3).\n" );
- else if( treemethod == 's' )
- fprintf( fp, "Tree = UPGMA (2).\n" );
- else if( treemethod == 'p' )
- fprintf( fp, "Tree = UPGMA (1).\n" );
- else
- fprintf( fp, "Unknown tree.\n" );
-
- if( use_fft )
- {
- fprintf( fp, "FFT on\n" );
- if( dorp == 'd' )
- fprintf( fp, "Basis : 4 nucleotides\n" );
- else
- {
- if( fftscore )
- fprintf( fp, "Basis : Polarity and Volume\n" );
- else
- fprintf( fp, "Basis : 20 amino acids\n" );
- }
- fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
- fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
- }
- else
- fprintf( fp, "FFT off\n" );
- fflush( fp );
-}
-
-
-int main( int argc, char *argv[] )
-{
- static int nlen[M];
- static char name[M][B], **seq;
- static char **bseq;
- static double *eff;
- int i;
- char c;
- int alloclen;
- FILE *infp;
-
- arguments( argc, argv );
-
- if( inputfile )
- {
- infp = fopen( inputfile, "r" );
- if( !infp )
- {
- fprintf( stderr, "Cannot open %s\n", inputfile );
- exit( 1 );
- }
- }
- else
- infp = stdin;
-
- if( !pairfile )
- {
- fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
- exit( 1 );
- }
-
- getnumlen( infp );
- rewind( infp );
-
- if( njob < 2 )
- {
- fprintf( stderr, "At least 2 sequences should be input!\n"
- "Only %d sequence found.\n", njob );
- exit( 1 );
- }
-
- seq = AllocateCharMtx( njob, nlenmax*9+1 );
- bseq = AllocateCharMtx( njob, nlenmax*9+1 );
- alloclen = nlenmax*9;
-
- eff = AllocateDoubleVec( njob );
-
-#if 0
- Read( name, nlen, seq );
-#else
- readData( infp, name, nlen, seq );
-#endif
- fclose( infp );
-
- constants( njob, seq );
-
-#if 0
- fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
- WriteOptions( trap_g );
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illeagal character %c\n", c );
- exit( 1 );
- }
-
-// writePre( njob, name, nlen, seq, 0 );
-
- for( i=0; i<njob; i++ ) eff[i] = 1.0;
-
-
- for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
-
- pairalign( name, nlen, bseq, eff, alloclen );
-
- fprintf( trap_g, "done.\n" );
-#if DEBUG
- fprintf( stderr, "closing trap_g\n" );
-#endif
- fclose( trap_g );
-
-#if IODEBUG
- fprintf( stderr, "OSHIMAI\n" );
-#endif
- SHOWVERSION;
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff