+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-#define NODIST -9999
-
-static char *whereispairalign;
-static char *laraparams;
-static char foldalignopt[1000];
-static int stdout_align;
-static int stdout_dist;
-static int store_localhom;
-static int store_dist;
-
-typedef struct _jobtable
-{
- int i;
- int j;
-} Jobtable;
-
-#ifdef enablemultithread
-typedef struct _thread_arg
-{
- int thread_no;
- int njob;
- Jobtable *jobpospt;
- char **name;
- char **seq;
- LocalHom **localhomtable;
- double **distancemtx;
- double *selfscore;
- char ***bpp;
- int alloclen;
- pthread_mutex_t *mutex_counter;
- pthread_mutex_t *mutex_stdout;
-} thread_arg_t;
-#endif
-
-static void t2u( char *seq )
-{
- while( *seq )
- {
- if ( *seq == 'A' ) *seq = 'a';
- else if( *seq == 'a' ) *seq = 'a';
- else if( *seq == 'T' ) *seq = 'u';
- else if( *seq == 't' ) *seq = 'u';
- else if( *seq == 'U' ) *seq = 'u';
- else if( *seq == 'u' ) *seq = 'u';
- else if( *seq == 'G' ) *seq = 'g';
- else if( *seq == 'g' ) *seq = 'g';
- else if( *seq == 'C' ) *seq = 'c';
- else if( *seq == 'c' ) *seq = 'c';
- else *seq = 'n';
- seq++;
- }
-}
-
-static float recallpairfoldalign( char **mseq1, char **mseq2, int m1, int m2, int *of1pt, int *of2pt, int alloclen )
-{
- static FILE *fp = NULL;
- float value;
- char *aln1;
- char *aln2;
- int of1tmp, of2tmp;
-
- if( fp == NULL )
- {
- fp = fopen( "_foldalignout", "r" );
- if( fp == NULL )
- {
- fprintf( stderr, "Cannot open _foldalignout\n" );
- exit( 1 );
- }
- }
-
- aln1 = calloc( alloclen, sizeof( char ) );
- aln2 = calloc( alloclen, sizeof( char ) );
-
- readpairfoldalign( fp, *mseq1, *mseq2, aln1, aln2, m1, m2, &of1tmp, &of2tmp, alloclen );
-
- if( strstr( foldalignopt, "-global") )
- {
- fprintf( stderr, "Calling G__align11\n" );
- value = G__align11( mseq1, mseq2, alloclen, outgap, outgap );
- *of1pt = 0;
- *of2pt = 0;
- }
- else
- {
- fprintf( stderr, "Calling L__align11\n" );
- value = L__align11( mseq1, mseq2, alloclen, of1pt, of2pt );
- }
-
-// value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
-
- if( aln1[0] == 0 )
- {
- fprintf( stderr, "FOLDALIGN returned no alignment between %d and %d. Sequence alignment is used instead.\n", m1+1, m2+1 );
- }
- else
- {
- strcpy( *mseq1, aln1 );
- strcpy( *mseq2, aln2 );
- *of1pt = of1tmp;
- *of2pt = of2tmp;
- }
-
-// value = naivepairscore11( *mseq1, *mseq2, penalty ); // v6.511 ha kore wo tsukau, global nomi dakara.
-
-// fclose( fp ); // saigo dake yatta houga yoi.
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
-
- free( aln1 );
- free( aln2 );
-
- return( value );
-}
-
-static void callfoldalign( int nseq, char **mseq )
-{
- FILE *fp;
- int i;
- int res;
- static char com[10000];
-
- for( i=0; i<nseq; i++ )
- t2u( mseq[i] );
-
- fp = fopen( "_foldalignin", "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _foldalignin\n" );
- exit( 1 );
- }
- for( i=0; i<nseq; i++ )
- {
- fprintf( fp, ">%d\n", i+1 );
- fprintf( fp, "%s\n", mseq[i] );
- }
- fclose( fp );
-
- sprintf( com, "env PATH=%s foldalign210 %s _foldalignin > _foldalignout ", whereispairalign, foldalignopt );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in foldalign\n" );
- exit( 1 );
- }
-
-}
-
-static void calllara( int nseq, char **mseq, char *laraarg )
-{
- FILE *fp;
- int i;
- int res;
- static char com[10000];
-
-// for( i=0; i<nseq; i++ )
-
- fp = fopen( "_larain", "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _larain\n" );
- exit( 1 );
- }
- for( i=0; i<nseq; i++ )
- {
- fprintf( fp, ">%d\n", i+1 );
- fprintf( fp, "%s\n", mseq[i] );
- }
- fclose( fp );
-
-
-// fprintf( stderr, "calling LaRA\n" );
- sprintf( com, "env PATH=%s:/bin:/usr/bin mafft_lara -i _larain -w _laraout -o _lara.params %s", whereispairalign, laraarg );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in lara\n" );
- exit( 1 );
- }
-}
-
-static float recalllara( char **mseq1, char **mseq2, int alloclen )
-{
- static FILE *fp = NULL;
- static char *ungap1;
- static char *ungap2;
- static char *ori1;
- static char *ori2;
-// int res;
- static char com[10000];
- float value;
-
-
- if( fp == NULL )
- {
- fp = fopen( "_laraout", "r" );
- if( fp == NULL )
- {
- fprintf( stderr, "Cannot open _laraout\n" );
- exit( 1 );
- }
- ungap1 = AllocateCharVec( alloclen );
- ungap2 = AllocateCharVec( alloclen );
- ori1 = AllocateCharVec( alloclen );
- ori2 = AllocateCharVec( alloclen );
- }
-
-
- strcpy( ori1, *mseq1 );
- strcpy( ori2, *mseq2 );
-
- fgets( com, 999, fp );
- myfgets( com, 9999, fp );
- strcpy( *mseq1, com );
- myfgets( com, 9999, fp );
- strcpy( *mseq2, com );
-
- gappick0( ungap1, *mseq1 );
- gappick0( ungap2, *mseq2 );
- t2u( ungap1 );
- t2u( ungap2 );
- t2u( ori1 );
- t2u( ori2 );
-
- if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) )
- {
- fprintf( stderr, "SEQUENCE CHANGED!!\n" );
- fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
- fprintf( stderr, "ungap1 = %s\n", ungap1 );
- fprintf( stderr, "ori1 = %s\n", ori1 );
- fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
- fprintf( stderr, "ungap2 = %s\n", ungap2 );
- fprintf( stderr, "ori2 = %s\n", ori2 );
- exit( 1 );
- }
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
-// fclose( fp ); // saigo dake yatta houga yoi.
-
- return( value );
-}
-
-
-static float callmxscarna_giving_bpp( char **mseq1, char **mseq2, char **bpp1, char **bpp2, int alloclen, int i, int j )
-{
- FILE *fp;
- int res;
- char *com;
- float value;
- char *dirname;
-
-
- dirname = calloc( 100, sizeof( char ) );
- com = calloc( 1000, sizeof( char ) );
- sprintf( dirname, "_%d-%d", i, j );
- sprintf( com, "rm -rf %s", dirname );
- system( com );
- sprintf( com, "mkdir %s", dirname );
- system( com );
-
-
- sprintf( com, "%s/_bpporg", dirname );
- fp = fopen( com, "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot write to %s/_bpporg\n", dirname );
- exit( 1 );
- }
- fprintf( fp, ">a\n" );
- while( *bpp1 )
- fprintf( fp, "%s", *bpp1++ );
-
- fprintf( fp, ">b\n" );
- while( *bpp2 )
- fprintf( fp, "%s", *bpp2++ );
- fclose( fp );
-
- sprintf( com, "tr -d '\\r' < %s/_bpporg > %s/_bpp", dirname, dirname );
- system( com ); // for cygwin, wakaran
-
- t2u( *mseq1 );
- t2u( *mseq2 );
-
- sprintf( com, "%s/_mxscarnainorg", dirname );
- fp = fopen( com, "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open %s/_mxscarnainorg\n", dirname );
- exit( 1 );
- }
- fprintf( fp, ">1\n" );
-// fprintf( fp, "%s\n", *mseq1 );
- write1seq( fp, *mseq1 );
- fprintf( fp, ">2\n" );
-// fprintf( fp, "%s\n", *mseq2 );
- write1seq( fp, *mseq2 );
- fclose( fp );
-
- sprintf( com, "tr -d '\\r' < %s/_mxscarnainorg > %s/_mxscarnain", dirname, dirname );
- system( com ); // for cygwin, wakaran
-
-#if 0
- sprintf( com, "cd %s; %s/mxscarnamod -readbpp _mxscarnain > _mxscarnaout 2>_dum", dirname, whereispairalign );
-#else
- sprintf( com, "_mxscarnash%s", dirname );
- fp = fopen( com, "w" );
- fprintf( fp, "cd %s\n", dirname );
- fprintf( fp, "%s/mxscarnamod -readbpp _mxscarnain > _mxscarnaout 2>_dum\n", whereispairalign );
- fprintf( fp, "exit $tatus\n" );
- fclose( fp );
-
- sprintf( com, "tr -d '\\r' < _mxscarnash%s > _mxscarnash%s.unix", dirname, dirname );
- system( com ); // for cygwin, wakaran
-
- sprintf( com, "sh _mxscarnash%s.unix 2>_dum%s", dirname, dirname );
-#endif
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in mxscarna\n" );
- exit( 1 );
- }
-
- sprintf( com, "%s/_mxscarnaout", dirname );
-
- fp = fopen( com, "r" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open %s/_mxscarnaout\n", dirname );
- exit( 1 );
- }
-
- fgets( com, 999, fp );
- load1SeqWithoutName_new( fp, *mseq1 );
- fgets( com, 999, fp );
- load1SeqWithoutName_new( fp, *mseq2 );
-
- fclose( fp );
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
-#if 0
- sprintf( com, "rm -rf %s > /dev/null 2>&1", dirname );
- if( system( com ) )
- {
- fprintf( stderr, "retrying to rmdir\n" );
- usleep( 2000 );
- system( com );
- }
-#endif
-
- free( dirname );
- free( com );
-
-
- return( value );
-}
-
-#if 0
-static float callmxscarna_slow( char **mseq1, char **mseq2, int alloclen )
-{
- FILE *fp;
- int res;
- static char com[10000];
- float value;
-
-
- t2u( *mseq1 );
- t2u( *mseq2 );
- fp = fopen( "_mxscarnain", "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _mxscarnain\n" );
- exit( 1 );
- }
- fprintf( fp, ">1\n" );
- fprintf( fp, "%s\n", *mseq1 );
- fprintf( fp, ">2\n" );
- fprintf( fp, "%s\n", *mseq2 );
- fclose( fp );
-
- sprintf( com, "env PATH=%s mxscarnamod _mxscarnain > _mxscarnaout 2>_dum", whereispairalign );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in mxscarna\n" );
- exit( 1 );
- }
-
- fp = fopen( "_mxscarnaout", "r" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _mxscarnaout\n" );
- exit( 1 );
- }
-
- fgets( com, 999, fp );
- load1SeqWithoutName_new( fp, *mseq1 );
- fgets( com, 999, fp );
- load1SeqWithoutName_new( fp, *mseq2 );
-
- fclose( fp );
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
- return( value );
-}
-#endif
-
-static void readhat4( FILE *fp, char ***bpp )
-{
- char oneline[1000];
- int bppsize;
- int onechar;
-// double prob;
-// int posi, posj;
-
- bppsize = 0;
-// fprintf( stderr, "reading hat4\n" );
- onechar = getc(fp);
-// fprintf( stderr, "onechar = %c\n", onechar );
- if( onechar != '>' )
- {
- fprintf( stderr, "Format error\n" );
- exit( 1 );
- }
- ungetc( onechar, fp );
- fgets( oneline, 999, fp );
- while( 1 )
- {
- onechar = getc(fp);
- ungetc( onechar, fp );
- if( onechar == '>' || onechar == EOF )
- {
-// fprintf( stderr, "Next\n" );
- *bpp = realloc( *bpp, (bppsize+2) * sizeof( char * ) );
- (*bpp)[bppsize] = NULL;
- break;
- }
- fgets( oneline, 999, fp );
-// fprintf( stderr, "oneline=%s\n", oneline );
-// sscanf( oneline, "%d %d %f", &posi, &posj, &prob );
-// fprintf( stderr, "%d %d -> %f\n", posi, posj, prob );
- *bpp = realloc( *bpp, (bppsize+2) * sizeof( char * ) );
- (*bpp)[bppsize] = calloc( 100, sizeof( char ) );
- strcpy( (*bpp)[bppsize], oneline );
- bppsize++;
- }
-}
-
-static void preparebpp( int nseq, char ***bpp )
-{
- FILE *fp;
- int i;
-
- fp = fopen( "hat4", "r" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open hat4\n" );
- exit( 1 );
- }
- for( i=0; i<nseq; i++ )
- readhat4( fp, bpp+i );
- fclose( fp );
-}
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- nthread = 1;
- foldalignopt[0] = 0;
- laraparams = NULL;
- inputfile = 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;
- stdout_align = 0;
- stdout_dist = 0;
- store_dist = 1;
- store_localhom = 1;
- 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;
- RNAppenalty = NOTSPECIFIED;
- RNApthr = 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 'f':
- ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'g':
- ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'O':
- ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'E':
- ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'h':
- poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'k':
- kimuraR = atoi( *++argv );
-// fprintf( stderr, "kimuraR = %d\n", kimuraR );
- --argc;
- goto nextoption;
- case 'b':
- nblosum = atoi( *++argv );
- scoremtx = 1;
-// fprintf( stderr, "blosum %d\n", nblosum );
- --argc;
- goto nextoption;
- case 'j':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = JTT;
- fprintf( stderr, "jtt %d\n", pamN );
- --argc;
- goto nextoption;
- case 'm':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = TM;
- fprintf( stderr, "TM %d\n", pamN );
- --argc;
- goto nextoption;
- case 'l':
- ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
- pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
-// fprintf( stderr, "ppslocal = %d\n", ppslocal );
-// fprintf( stderr, "pslocal = %d\n", pslocal );
- --argc;
- goto nextoption;
- case 'd':
- whereispairalign = *++argv;
- fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
- --argc;
- goto nextoption;
- case 'p':
- laraparams = *++argv;
- fprintf( stderr, "laraparams = %s\n", laraparams );
- --argc;
- goto nextoption;
- case 'C':
- nthread = atoi( *++argv );
- fprintf( stderr, "nthread = %d\n", nthread );
- --argc;
- goto nextoption;
- case 'c':
- stdout_dist = 1;
- break;
- case 'n':
- stdout_align = 1;
- break;
- case 'x':
- store_localhom = 0;
- store_dist = 0;
- break;
-#if 1
- case 'a':
- fmodel = 1;
- break;
-#endif
- case 'r':
- fmodel = -1;
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- break;
- case 'e':
- fftscore = 0;
- break;
-#if 0
- case 'O':
- fftNoAnchStop = 1;
- break;
-#endif
- case 'Q':
- calledByXced = 1;
- break;
-#if 0
- case 'x':
- disp = 1;
- break;
- case 'a':
- alg = 'a';
- break;
-#endif
- case 'S':
- alg = 'S';
- break;
- case 't':
- alg = 't';
- store_localhom = 0;
- break;
- case 'L':
- alg = 'L';
- break;
- case 's':
- alg = 's';
- break;
- case 'B':
- alg = 'B';
- break;
- case 'T':
- alg = 'T';
- break;
- case 'H':
- alg = 'H';
- break;
- case 'M':
- alg = 'M';
- break;
- case 'R':
- alg = 'R';
- break;
- case 'N':
- alg = 'N';
- break;
- case 'K':
- alg = 'K';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'V':
- alg = 'V';
- break;
- case 'F':
- use_fft = 1;
- break;
- case 'v':
- tbrweight = 3;
- break;
- case 'y':
- divpairscore = 1;
- break;
-/* Modified 01/08/27, default: user tree */
- case 'J':
- tbutree = 0;
- break;
-/* modification end. */
- case 'o':
-// foldalignopt = *++argv;
- strcat( foldalignopt, " " );
- strcat( foldalignopt, *++argv );
- fprintf( stderr, "foldalignopt = %s\n", foldalignopt );
- --argc;
- goto nextoption;
- case 'z':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'Z':
- checkC = 1;
- 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 );
- }
-}
-
-int countamino( char *s, int end )
-{
- int val = 0;
- while( end-- )
- if( *s++ != '-' ) val++;
- return( val );
-}
-
-#if enablemultithread
-static void *athread( void *arg )
-{
- thread_arg_t *targ = (thread_arg_t *)arg;
- int i, j;
- int clus1, clus2;
- int off1, off2;
- int intdum;
- double bunbo;
- float pscore = 0.0; // by D.Mathog
- double *effarr;
- double *effarr1;
- double *effarr2;
- char **pair;
- char *indication1, *indication2;
- char **mseq1, **mseq2;
- char **aseq;
-
-// thread_arg
- int thread_no = targ->thread_no;
- int njob = targ->njob;
- Jobtable *jobpospt = targ->jobpospt;
- char **name = targ->name;
- char **seq = targ->seq;
- LocalHom **localhomtable = targ->localhomtable;
- double **distancemtx = targ->distancemtx;
- double *selfscore = targ->selfscore;
- char ***bpp = targ->bpp;
- int alloclen = targ->alloclen;
-
-// fprintf( stderr, "thread %d start!\n", thread_no );
-
- effarr = AllocateDoubleVec( njob );
- for( i=0; i<njob; i++ ) effarr[i] = 1.0;
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
- pair = AllocateCharMtx( njob, njob );
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
- for( i=0; i<njob; i++ ) pair[i][i] = 1;
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- aseq = AllocateCharMtx( njob, alloclen+10 );
-
- while( 1 )
- {
- pthread_mutex_lock( targ->mutex_counter );
- j = jobpospt->j;
- i = jobpospt->i;
- j++;
- if( j == njob )
- {
- i++;
- j = i + 1;
- if( i == njob-1 )
- {
-// fprintf( stderr, "thread %d end!\n", thread_no );
- pthread_mutex_unlock( targ->mutex_counter );
-
- if( commonIP ) FreeIntMtx( commonIP );
- commonIP = NULL;
- if( commonJP ) FreeIntMtx( commonJP );
- commonJP = NULL;
- Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
- G__align11_noalign( NULL, 0, 0, NULL, NULL, 0 );
- L__align11( NULL, NULL, 0, NULL, NULL );
- genL__align11( NULL, NULL, 0, NULL, NULL );
- free( effarr );
- free( effarr1 );
- free( effarr2 );
- free( indication1 );
- free( indication2 );
- FreeCharMtx( pair );
- free( mseq1 );
- free( mseq2 );
- FreeCharMtx( aseq );
- return( NULL );
- }
- }
- jobpospt->j = j;
- jobpospt->i = i;
- pthread_mutex_unlock( targ->mutex_counter );
-
-
- if( j == i+1 || j % 100 == 0 )
- {
- fprintf( stderr, "% 5d / %d (by thread %3d) \r", i, njob, thread_no );
-// fprintf( stderr, "% 5d - %5d / %d (thread %d)\n", i, j, njob, thread_no );
- }
-
-
- if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
- {
- if( store_dist ) distancemtx[i][j] = 2.0;
- if( stdout_dist)
- {
- pthread_mutex_lock( targ->mutex_stdout );
- fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, 2.0 );
- pthread_mutex_unlock( targ->mutex_stdout );
- }
- continue;
- }
-
- strcpy( aseq[i], seq[i] );
- strcpy( aseq[j], seq[j] );
- clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
- clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
-// fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
-// fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
-
-#if 0
- fprintf( stderr, "group1 = %.66s", indication1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "group2 = %.66s", indication2 );
- fprintf( stderr, "\n" );
-#endif
-// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
-
- if( use_fft )
- {
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
-// fprintf( stderr, "pscore (fft) = %f\n", pscore );
- off1 = off2 = 0;
- }
- else
- {
- switch( alg )
- {
- case( 'L' ):
- pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
- L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
- break;
- case( 'A' ):
- pscore = G__align11( mseq1, mseq2, alloclen, outgap, outgap );
- off1 = off2 = 0;
- break;
- case( 'N' ):
- pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
- genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
- break;
- case( 't' ):
- pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
- off1 = off2 = 0;
- break;
- case( 's' ):
- pscore = callmxscarna_giving_bpp( mseq1, mseq2, bpp[i], bpp[j], alloclen, i, j );
- off1 = off2 = 0;
- break;
-#if 0
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- off1 = off2 = 0;
- break;
- case( 'K' ):
- pscore = genG__align11( mseq1, mseq2, alloclen );
- off1 = off2 = 0;
- break;
- case( 'H' ):
- pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
- break;
- case( 'B' ):
- case( 'T' ):
- pscore = recalllara( mseq1, mseq2, alloclen );
- off1 = off2 = 0;
- break;
- case( 'M' ):
- pscore = MSalign11( mseq1, mseq2, alloclen );
- break;
-#endif
- default:
- ErrorExit( "\n\nERROR IN SOURCE FILE\n\n" );
- }
- }
-
- if( alg == 't' || ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) ) // 't' no jouken ha iranai to omou. if( ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) )
- {
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
-#endif
- if( !store_localhom )
- ;
- else if( alg == 'H' )
- putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
- else if( alg != 'S' && alg != 'V' )
- {
- putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
- }
-
- if( (bunbo=MIN( selfscore[i], selfscore[j] )) == 0.0 || bunbo < pscore )
- pscore = 2.0;
- else
- pscore = ( 1.0 - pscore / bunbo ) * 2.0;
- }
- else
- {
- pscore = 2.0;
- }
-
-#if 1 // mutex
- if( stdout_align )
- {
- pthread_mutex_lock( targ->mutex_stdout );
- if( alg != 't' )
- {
- fprintf( stdout, "sequence %d - sequence %d, pairwise distance = %10.5f\n", i+1, j+1, pscore );
- fprintf( stdout, ">%s\n", name[i] );
- write1seq( stdout, mseq1[0] );
- fprintf( stdout, ">%s\n", name[j] );
- write1seq( stdout, mseq2[0] );
- fprintf( stdout, "\n" );
- }
- pthread_mutex_unlock( targ->mutex_stdout );
- }
- if( stdout_dist )
- {
- pthread_mutex_lock( targ->mutex_stdout );
- if( j == i+1 ) fprintf( stdout, "%d %d d=%.3f\n", i+1, i+1, 0.0 );
- fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, pscore );
- pthread_mutex_unlock( targ->mutex_stdout );
- }
-#endif // mutex
- if( store_dist) distancemtx[i][j] = pscore;
- }
-}
-#endif
-
-static void pairalign( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen )
-{
- int i, j, ilim;
- int clus1, clus2;
- int off1, off2;
- float pscore = 0.0; // by D.Mathog
- static char *indication1, *indication2;
- FILE *hat2p, *hat3p;
- double **distancemtx;
- double *selfscore;
- double *effarr1;
- double *effarr2;
- char *pt;
- char *hat2file = "hat2";
- LocalHom **localhomtable = NULL, *tmpptr;
- static char **pair;
- int intdum;
- double bunbo;
- char ***bpp = NULL; // mxscarna no toki dake
-
- if( store_localhom )
- {
- 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;
- localhomtable[i][j].nokori = 0;
- }
- }
- }
-
- if( store_dist ) distancemtx = AllocateDoubleMtx( njob, njob );
- else distancemtx = NULL;
- selfscore = AllocateDoubleVec( njob );
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
-#if 0
-#else
- pair = AllocateCharMtx( njob, njob );
-#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 );
-
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
- for( i=0; i<njob; i++ ) pair[i][i] = 1;
-
- if( alg == 'H' )
- {
- fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
- callfoldalign( njob, seq );
- fprintf( stderr, "done.\n" );
- }
- if( alg == 'B' )
- {
- fprintf( stderr, "Running LARA (Bauer et al. http://www.planet-lisa.net/)\n" );
- calllara( njob, seq, "" );
- fprintf( stderr, "done.\n" );
- }
- if( alg == 'T' )
- {
- fprintf( stderr, "Running SLARA (Bauer et al. http://www.planet-lisa.net/)\n" );
- calllara( njob, seq, "-s" );
- fprintf( stderr, "done.\n" );
- }
- if( alg == 's' )
- {
- fprintf( stderr, "Preparing bpp\n" );
-// bpp = AllocateCharCub( njob, nlenmax, 0 );
- bpp = calloc( njob, sizeof( char ** ) );
- preparebpp( njob, bpp );
- fprintf( stderr, "done.\n" );
- fprintf( stderr, "Running MXSCARNA (Tabei et al. http://www.ncrna.org/software/mxscarna)\n" );
- }
-
- for( i=0; i<njob; i++ )
- {
- pscore = 0.0;
- for( pt=seq[i]; *pt; pt++ )
- pscore += amino_dis[(int)*pt][(int)*pt];
- selfscore[i] = pscore;
-
- }
-
-#if enablemultithread
- if( nthread > 0 )
- {
- Jobtable jobpos;
- pthread_t *handle;
- pthread_mutex_t mutex_counter;
- pthread_mutex_t mutex_stdout;
- thread_arg_t *targ;
-
- jobpos.i = 0;
- jobpos.j = 0;
-
- targ = calloc( nthread, sizeof( thread_arg_t ) );
- handle = calloc( nthread, sizeof( pthread_t ) );
- pthread_mutex_init( &mutex_counter, NULL );
- pthread_mutex_init( &mutex_stdout, NULL );
-
- for( i=0; i<nthread; i++ )
- {
- targ[i].thread_no = i;
- targ[i].njob = njob;
- targ[i].jobpospt = &jobpos;
- targ[i].name = name;
- targ[i].seq = seq;
- targ[i].localhomtable = localhomtable;
- targ[i].distancemtx = distancemtx;
- targ[i].selfscore = selfscore;
- targ[i].bpp = bpp;
- targ[i].alloclen = alloclen;
- targ[i].mutex_counter = &mutex_counter;
- targ[i].mutex_stdout = &mutex_stdout;
-
-// athread( (void *)targ );
- pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
-// pthread_create( handle+i, NULL, bthread, (void *)(targ+i) );
- }
-
-
- for( i=0; i<nthread; i++ )
- {
- pthread_join( handle[i], NULL );
- }
- pthread_mutex_destroy( &mutex_counter );
- pthread_mutex_destroy( &mutex_stdout );
- free( handle );
- free( targ );
- }
- else
-#endif
- {
- ilim = njob - 1;
- for( i=0; i<ilim; i++ )
- {
- if( stdout_dist) fprintf( stdout, "%d %d d=%.3f\n", i+1, i+1, 0.0 );
- fprintf( stderr, "% 5d / %d\r", i, njob );
- fflush( stderr );
- for( j=i+1; j<njob; j++ )
- {
-
- if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
- {
- if( store_dist ) distancemtx[i][j] = 2.0;
- if( stdout_dist) fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, 2.0 );
- continue;
- }
-
- strcpy( aseq[i], seq[i] );
- strcpy( aseq[j], seq[j] );
- clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
- clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
- // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
- // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
-
-#if 0
- fprintf( stderr, "group1 = %.66s", indication1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "group2 = %.66s", indication2 );
- fprintf( stderr, "\n" );
-#endif
- // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
-
- if( use_fft )
- {
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
-// fprintf( stderr, "pscore (fft) = %f\n", pscore );
- off1 = off2 = 0;
- }
- else
- {
- switch( alg )
- {
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- off1 = off2 = 0;
- break;
- case( 't' ):
- pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
- off1 = off2 = 0;
- break;
- case( 'A' ):
- pscore = G__align11( mseq1, mseq2, alloclen, outgap, outgap );
- off1 = off2 = 0;
- break;
- case( 'N' ):
- pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
- genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
- break;
- case( 'K' ):
- pscore = genG__align11( mseq1, mseq2, alloclen );
- off1 = off2 = 0;
- break;
- case( 'L' ):
- pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
- L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
- break;
- case( 'H' ):
- pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
- break;
- case( 'B' ):
- case( 'T' ):
- pscore = recalllara( mseq1, mseq2, alloclen );
- off1 = off2 = 0;
- break;
- case( 's' ):
- pscore = callmxscarna_giving_bpp( mseq1, mseq2, bpp[i], bpp[j], alloclen, i, j );
- off1 = off2 = 0;
- break;
- case( 'M' ):
- pscore = MSalign11( mseq1, mseq2, alloclen );
- break;
- default:
- ErrorExit( "ERROR IN SOURCE FILE" );
- }
- }
-
- if( alg == 't' || ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) ) // 't' no jouken ha iranai to omou. if( ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) )
- {
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
-#endif
- if( !store_localhom )
- ;
- else if( alg == 'H' )
- putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
- else if( alg != 'S' && alg != 'V' )
- putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
-
-
- if( (bunbo=MIN( selfscore[i], selfscore[j] )) == 0.0 || bunbo < pscore )
- pscore = 2.0;
- else
- pscore = ( 1.0 - pscore / bunbo ) * 2.0;
- }
- else
- {
- pscore = 2.0;
- }
-
- if( stdout_align )
- {
- if( alg != 't' )
- {
- fprintf( stdout, "sequence %d - sequence %d, pairwise distance = %10.5f\n", i+1, j+1, pscore );
- fprintf( stdout, ">%s\n", name[i] );
- write1seq( stdout, mseq1[0] );
- fprintf( stdout, ">%s\n", name[j] );
- write1seq( stdout, mseq2[0] );
- fprintf( stdout, "\n" );
- }
- }
- if( stdout_dist ) fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, pscore );
- if( store_dist) distancemtx[i][j] = pscore;
- }
- }
- }
-
-
- if( store_dist )
- {
- hat2p = fopen( hat2file, "w" );
- if( !hat2p ) ErrorExit( "Cannot open hat2." );
- WriteHat2_pointer( hat2p, njob, name, distancemtx );
- fclose( hat2p );
- }
-
- hat3p = fopen( "hat3", "w" );
- if( !hat3p ) ErrorExit( "Cannot open hat3." );
- if( store_localhom )
- {
- fprintf( stderr, "\n\n##### writing hat3\n" );
- 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;
-// tmptmptmptmptmp
-// if( alg == 'B' || alg == 'T' )
-// fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, 1.0, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
-// else
- fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d h\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
- }
- }
- }
-#if DEBUG
- fprintf( stderr, "calling FreeLocalHomTable\n" );
-#endif
- FreeLocalHomTable( localhomtable, njob );
-#if DEBUG
- fprintf( stderr, "done. FreeLocalHomTable\n" );
-#endif
- }
- fclose( hat3p );
-
- if( alg == 's' )
- {
- char **ptpt;
- for( i=0; i<njob; i++ )
- {
- ptpt = bpp[i];
- while( 1 )
- {
- if( *ptpt ) free( *ptpt );
- else break;
- ptpt++;
- }
- free( bpp[i] );
- }
- free( bpp );
- }
- free( selfscore );
- free( effarr1 );
- free( effarr2 );
- free( indication1 );
- free( indication2 );
- if( store_dist ) FreeDoubleMtx( distancemtx );
-}
-
-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
- fprintf( fp, "Unknown algorithm\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[] )
-{
- int nlen[M];
- char **name, **seq;
- char **mseq1, **mseq2;
- char **aseq;
- char **bseq;
- double *eff;
- int i;
- FILE *infp;
- char c;
- int alloclen;
-
- arguments( argc, argv );
-#ifndef enablemultithread
- nthread = 0;
-#endif
-
- if( inputfile )
- {
- infp = fopen( inputfile, "r" );
- if( !infp )
- {
- fprintf( stderr, "Cannot open %s\n", inputfile );
- exit( 1 );
- }
- }
- else
- infp = stdin;
-
- 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 );
- }
- if( njob > M )
- {
- fprintf( stderr, "The number of sequences must be < %d\n", M );
- fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
- exit( 1 );
- }
-
- alloclen = nlenmax*2;
- seq = AllocateCharMtx( njob, alloclen+10 );
- aseq = AllocateCharMtx( njob, alloclen+10 );
- bseq = AllocateCharMtx( njob, alloclen+10 );
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- name = AllocateCharMtx( njob, B );
-
- eff = AllocateDoubleVec( njob );
-
-#if 0
- Read( name, nlen, seq );
-#else
- readData_pointer( 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, "Illegal 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, aseq, mseq1, mseq2, eff, alloclen );
-
- fprintf( trap_g, "done.\n" );
-#if DEBUG
- fprintf( stderr, "closing trap_g\n" );
-#endif
- fclose( trap_g );
-
-// writePre( njob, name, nlen, aseq, !contin );
-#if 0
- writeData( stdout, njob, name, nlen, aseq );
-#endif
-#if IODEBUG
- fprintf( stderr, "OSHIMAI\n" );
-#endif
- SHOWVERSION;
-
- if( stdout_dist && nthread > 1 )
- {
- fprintf( stderr, "\nThe order of distances is not identical to that in the input file, because of the parallel calculation. Reorder them by yourself, using sort -n -k 2 | sort -n -k 1 -s\n" );
- }
- if( stdout_align && nthread > 1 )
- {
- fprintf( stderr, "\nThe order of pairwise alignments is not identical to that in the input file, because of the parallel calculation. Reorder them by yourself.\n" );
- }
- FreeCharMtx( seq );
- FreeCharMtx( aseq );
- FreeCharMtx( bseq );
- FreeCharMtx( name );
- free( mseq1 );
- free( mseq2 );
- free( eff );
-
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff