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splittbfast2.c

#include "mltaln.h"

#define TREE 1
#define PICKSIZE 50 // must be >= 3
#define WEIGHT 0
#define TOKYORIPARA 0.70 // 0.70
#define TOKYORIPARA_A 0.10 
#define LENFAC 1
#define HUKINTOTREE 1
#define DIANA 0
#define MAX6DIST 10.0

// kouzoutai ni sasareru pointer ha static

#define DEBUG 0
#define IODEBUG 0
#define SCOREOUT 0

#define END_OF_VEC -1

static char *fastapath;
static int doalign = 'f';
static int doalign;
static int treeout;
static int classsize;
static int picksize;
static int maxl;
static int tsize;
static int numq;
static int reorder;
static int pid;
static int maxdepth = 0;
static double tokyoripara;

static double lenfaca, lenfacb, lenfacc, lenfacd;
#define PLENFACA 0.01
#define PLENFACB 10000
#define PLENFACC 10000
#define PLENFACD 0.1
#define DLENFACA 0.01
#define DLENFACB 2500
#define DLENFACC 2500
#define DLENFACD 0.1

static char datafile[1000];
static char queryfile[1000];
static char resultfile[1000];

typedef struct _scores
{
      double score;
      int selfscore;
      int orilen;
      int *pointt;
      int numinseq;
      char *name;
//    char *seq; // reallo
//    char **seqpt;
      int shimon;
} Scores;

int intcompare( const int *a, const int *b )
{
      return( *a - *b );
}

int dcompare( const Scores *a, const Scores *b )
{
      if( a->score > b->score ) return 1;
      else if( a->score < b->score ) return -1;
      else
      {
            if( a->selfscore < b->selfscore ) return 1;
            else if( a->selfscore > b->selfscore ) return -1;
            else 
            {
                  if( a->orilen < b->orilen ) return 1;
                  else if( a->orilen > b->orilen ) return -1;
                  else return 0;
            }
      }
}

static void gappickandx0( char *out, char *in )
{
      char c;
      if( scoremtx == -1 )
      {
            while( *in )
            {
                  if( (c=*in++) == '-' )
                        ;     
                  else if( c == 'u' )
                        *out++ = 't';
                  else if( amino_n[c] < 4 && amino_n[c] > -1 )
                        *out++ = c;
                  else
                        *out++ = 'n';
            }
      }
      else
      {
            while( *in )
            {
                  if( (c=*in++) == '-' )
                        ;     
                  else if( amino_n[c] < 20 && amino_n[c] > -1 )
                        *out++ = c;
                  else
                        *out++ = 'X';
            }
      }
      *out = 0;
}     

static int getkouho( int *pickkouho, double prob, int nin, Scores *scores, char **seq ) // 0 < prob < 1
{
      int nkouho = 0;
      int i, j;
      int *iptr = pickkouho;
      for( i=1; i<nin; i++ )
      {
            if( ( nkouho==0 || rnd() < prob ) && ( scores[i].shimon != scores->shimon || strcmp( seq[scores->numinseq], seq[scores[i].numinseq] ) ) )
            {
#if 0
                  for( j=0; j<nkouho; j++ )
                  {
                        if( scores[i].shimon == scores[pickkouho[j]].shimon || !strcmp( seq[scores[pickkouho[j]].numinseq], seq[scores[i].numinseq] ) ) 
                              break;
                  }
                  if( j == nkouho )
#endif
                  {
                        *iptr++ = i;
                        nkouho++;
//                      fprintf( stderr, "ok! nkouho=%d\n", nkouho );
                  }
            }
            else
            {
                  ;
//                fprintf( stderr, "no! %d-%d\n", 0, scores[i].numinseq );
            }
      }
      fprintf( stderr, "\ndone\n\n"  );
      return nkouho;
}

static void getfastascoremtx( int **tmpaminodis )
{
      FILE *qfp;
      FILE *dfp;
      FILE *rfp;
      int i, j;
      char aa;
      int slen;
      int res;
      char com[10000];
      static char *tmpseq;
      static char *tmpname;
      double *resvec;

      if( scoremtx == -1 )
      {
            tmpaminodis['a']['a'] = 5;
            tmpaminodis['g']['g'] = 5;
            tmpaminodis['c']['c'] = 5;
            tmpaminodis['t']['t'] = 5;
            tmpaminodis['n']['n'] = -1;

            return;
      }


      tmpseq = calloc( 2000, sizeof( char ) );
      tmpname = calloc( B, sizeof( char ) );
      resvec = calloc( 1, sizeof( double ) );

//    fprintf( stderr, "xformatting .. " );
      dfp = fopen( datafile, "w" );
      if( !dfp ) ErrorExit( "Cannot open datafile." );
      sprintf( tmpname, ">+===========+%d                      \0", 0 );
      strcpy( tmpseq, "AAAAAAXXXXXX" );
      strcat( tmpseq, "CCCCCCXXXXXX" );
      strcat( tmpseq, "DDDDDDXXXXXX" );
      strcat( tmpseq, "EEEEEEXXXXXX" );
      strcat( tmpseq, "FFFFFFXXXXXX" );
      strcat( tmpseq, "GGGGGGXXXXXX" );
      strcat( tmpseq, "HHHHHHXXXXXX" );
      strcat( tmpseq, "IIIIIIXXXXXX" );
      strcat( tmpseq, "KKKKKKXXXXXX" );
      strcat( tmpseq, "LLLLLLXXXXXX" );
      strcat( tmpseq, "MMMMMMXXXXXX" );
      strcat( tmpseq, "NNNNNNXXXXXX" );
      strcat( tmpseq, "PPPPPPXXXXXX" );
      strcat( tmpseq, "QQQQQQXXXXXX" );
      strcat( tmpseq, "RRRRRRXXXXXX" );
      strcat( tmpseq, "SSSSSSXXXXXX" );
      strcat( tmpseq, "TTTTTTXXXXXX" );
      strcat( tmpseq, "VVVVVVXXXXXX" );
      strcat( tmpseq, "WWWWWWXXXXXX" );
      strcat( tmpseq, "YYYYYYXXXXXX" );
      slen = strlen( tmpseq );
      writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
      fclose( dfp );
      fprintf( stderr, "done.\n" );

      for( i=0; i<20; i++ )
      {
            aa = amino[i];
//          fprintf( stderr, "checking %c\n", aa );
            *tmpseq = 0;
            sprintf( tmpname, ">+===========+%d                      \0", 0 );
            for( j=0; j<6; j++ )
                  sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
            qfp = fopen( queryfile, "w" );
            if( !qfp ) ErrorExit( "Cannot open queryfile." );
            writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
            fclose( qfp );

            if( scoremtx == -1 ) 
                  sprintf( com, "%s -z3 -m10  -n -Q -H -b%d -E%d -d%d %s %s %d > %s\0", fastapath,  M, M, 0, queryfile, datafile, 6, resultfile );
            else
                  sprintf( com, "%s -z3 -m10  -p -Q -H -b%d -E%d -d%d %s %s %d > %s\0", fastapath,  M, M, 0, queryfile, datafile, 2, resultfile );
            res = system( com );
            if( res )
            {
                  fprintf( stderr, "error in %s", fastapath );
                  exit( 1 );
            }

            rfp = fopen( resultfile, "r" );
            if( rfp == NULL )  
                  ErrorExit( "file 'fasta.$$' does not exist\n" );
            res = ReadFasta34m10_scoreonly( rfp, resvec, 1 );
            fprintf( stderr, "%c: %f\n", 'A'+i, *resvec/6 );
            fclose( rfp );
            if( ( (int)*resvec % 6 ) > 0.0 )
            {
                  fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
                  fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
                  exit( 1 );
            }
            tmpaminodis[aa][aa] = (int)( *resvec / 6 );
//          fprintf( stderr, "*resvec=%f, tmpaminodis[aa][aa] = %d\n", *resvec, tmpaminodis[aa][aa] );
      }
      tmpaminodis['X']['X'] = -1;
      free( tmpname );
      free( tmpseq );
      free( resvec );
}
static void getblastscoremtx( int **tmpaminodis )
{
      FILE *qfp;
      FILE *dfp;
      FILE *rfp;
      int i, j;
      char aa;
      int slen;
      int res;
      char com[10000];
      static char *tmpseq;
      static char *tmpname;
      double *resvec;

      if( scoremtx == -1 )
      {
            tmpaminodis['a']['a'] = 1;
            tmpaminodis['g']['g'] = 1;
            tmpaminodis['c']['c'] = 1;
            tmpaminodis['t']['t'] = 1;

            return;
      }


      tmpseq = calloc( 2000, sizeof( char ) );
      tmpname = calloc( B, sizeof( char ) );
      resvec = calloc( 1, sizeof( double ) );

//    fprintf( stderr, "xformatting .. " );
      dfp = fopen( datafile, "w" );
      if( !dfp ) ErrorExit( "Cannot open datafile." );
      sprintf( tmpname, "\0", i );
      strcpy( tmpseq, "AAAAAAXXXXXX" );
      strcat( tmpseq, "CCCCCCXXXXXX" );
      strcat( tmpseq, "DDDDDDXXXXXX" );
      strcat( tmpseq, "EEEEEEXXXXXX" );
      strcat( tmpseq, "FFFFFFXXXXXX" );
      strcat( tmpseq, "GGGGGGXXXXXX" );
      strcat( tmpseq, "HHHHHHXXXXXX" );
      strcat( tmpseq, "IIIIIIXXXXXX" );
      strcat( tmpseq, "KKKKKKXXXXXX" );
      strcat( tmpseq, "LLLLLLXXXXXX" );
      strcat( tmpseq, "MMMMMMXXXXXX" );
      strcat( tmpseq, "NNNNNNXXXXXX" );
      strcat( tmpseq, "PPPPPPXXXXXX" );
      strcat( tmpseq, "QQQQQQXXXXXX" );
      strcat( tmpseq, "RRRRRRXXXXXX" );
      strcat( tmpseq, "SSSSSSXXXXXX" );
      strcat( tmpseq, "TTTTTTXXXXXX" );
      strcat( tmpseq, "VVVVVVXXXXXX" );
      strcat( tmpseq, "WWWWWWXXXXXX" );
      strcat( tmpseq, "YYYYYYXXXXXX" );
      slen = strlen( tmpseq );
      writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
      fclose( dfp );
      if( scoremtx == -1 )
            sprintf( com, "formatdb  -p f -i %s -o F", datafile );
      else
            sprintf( com, "formatdb  -i %s -o F", datafile );
      system( com );
      fprintf( stderr, "done.\n" );

      for( i=0; i<20; i++ )
      {
            aa = amino[i];
            fprintf( stderr, "checking %c\n", aa );
            *tmpseq = 0;
            for( j=0; j<6; j++ )
                  sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
            qfp = fopen( queryfile, "w" );
            if( !qfp ) ErrorExit( "Cannot open queryfile." );
            writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
            fclose( qfp );

            sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7  -i %s -d %s >  %s\0", 1, queryfile, datafile, resultfile );
            res = system( com );
            if( res )
            {
                  fprintf( stderr, "error in %s", "blastall" );
                  exit( 1 );
            }

            rfp = fopen( resultfile, "r" );
            if( rfp == NULL )  
                  ErrorExit( "file 'fasta.$$' does not exist\n" );
            res = ReadBlastm7_scoreonly( rfp, resvec, 1 );
            fprintf( stdout, "%c: %f\n", 'A'+i, *resvec/6 );
            fclose( rfp );
            if( ( (int)*resvec % 6 ) > 0.0 )
            {
                  fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
                  fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
                  exit( 1 );
            }
            tmpaminodis[aa][aa] = (int)( *resvec / 6 );
      }
      tmpaminodis['X']['X'] = 0;
      free( tmpname );
      free( tmpseq );
      free( resvec );
      
}

static double *callfasta( char **seq, Scores *scores, int nin, int *picks, int query, int rewritedata )
{
      double *val;
      FILE *qfp;
      FILE *dfp;
      FILE *rfp;
      int i, j;
      char com[10000];
      static char datafile[1000];
      static char queryfile[1000];
      static char resultfile[1000];
      static int pid;
      static char *tmpseq;
      static char *tmpname;
      char *seqptr;
      int slen;
      int res;
      static Scores *scoresbk = NULL;
      static int ninbk = 0;

      if( pid == 0 )
      {
            pid = (int)getpid();
            sprintf( datafile, "/tmp/data-%d\0", pid );
            sprintf( queryfile, "/tmp/query-%d\0", pid );
            sprintf( resultfile, "/tmp/fasta-%d\0", pid );

            tmpseq = calloc( nlenmax+1, sizeof( char ) );
            tmpname = calloc( B+1, sizeof( char ) );
      }

      val = calloc( nin, sizeof( double ) );
//    fprintf( stderr, "nin=%d, q=%d\n", nin, query );

      if( rewritedata )
      {
            scoresbk = scores;
            ninbk = nin;
//          fprintf( stderr, "\nformatting .. " );
            dfp = fopen( datafile, "w" );
            if( !dfp ) ErrorExit( "Cannot open datafile." );
            if( picks == NULL ) for( i=0; i<nin; i++ )
            {
//                fprintf( stderr, "i=%d / %d / %d\n", i,  nin, njob );
//                fprintf( stderr, "nlenmax = %d\n", nlenmax );
//                fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
//                fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
                  gappick0( tmpseq, seq[scores[i].numinseq] );
                  sprintf( tmpname, ">+===========+%d                      \0", i );
                  slen = scores[i].orilen;
                  writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
            }
            else for( i=0; i<nin; i++ )
            {
                  gappick0( tmpseq, seq[scores[picks[i]].numinseq] );
                  sprintf( tmpname, ">+===========+%d                      \0", i );
                  slen = scores[picks[i]].orilen;
                  writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
            }
            fclose( dfp );
      }


      gappick0( tmpseq, seq[scores[query].numinseq] );
      sprintf( tmpname, ">+==========+%d                      \0", 0 );
      slen = scores[query].orilen;
      qfp = fopen( queryfile, "w" );
      if( !qfp ) ErrorExit( "Cannot open queryfile." );
      writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
      fclose( qfp );

//    fprintf( stderr, "calling fasta, nin=%d\n", nin );

      if( scoremtx == -1 ) 
            sprintf( com, "%s  -z3 -m10  -n -Q -H -b%d -E%d -d%d %s %s %d > %s\0",  fastapath, nin, nin, 0, queryfile, datafile, 6, resultfile );
      else
            sprintf( com, "%s  -z3 -m10  -p -Q -H -b%d -E%d -d%d %s %s %d > %s\0",  fastapath, nin, nin, 0, queryfile, datafile, 2, resultfile );
      res = system( com );
      if( res )
      {
            fprintf( stderr, "error in %s", fastapath );
            exit( 1 );
      }
//    fprintf( stderr, "fasta done\n" );

//exit( 1 );

      rfp = fopen( resultfile, "r" );
      if( rfp == NULL )  
            ErrorExit( "file 'fasta.$$' does not exist\n" );

//    fprintf( stderr, "reading fasta\n" );
      if( scoremtx == -1 ) 
            res = ReadFasta34m10_scoreonly_nuc( rfp, val, nin );
      else
            res = ReadFasta34m10_scoreonly( rfp, val, nin );
//    fprintf( stderr, "done. val[0] = %f\n", val[0] );


      fclose( rfp );

#if 0
      for( i=0; i<nin; i++ )
            fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
      exit( 1 );
#endif

      return( val );
}
static double *callblast( char **seq, Scores *scores, int nin, int query, int rewritedata )
{
      double *val;
      FILE *qfp;
      FILE *dfp;
      FILE *rfp;
      int i, j;
      char com[10000];
      static char datafile[1000];
      static char queryfile[1000];
      static char resultfile[1000];
      static int pid;
      static char *tmpseq;
      static char *tmpname;
      char *seqptr;
      int slen;
      int res;
      static Scores *scoresbk = NULL;
      static int ninbk = 0;

      if( pid == 0 )
      {
            pid = (int)getpid();
            sprintf( datafile, "/tmp/data-%d\0", pid );
            sprintf( queryfile, "/tmp/query-%d\0", pid );
            sprintf( resultfile, "/tmp/fasta-%d\0", pid );

            tmpseq = calloc( nlenmax+1, sizeof( char ) );
            tmpname = calloc( B+1, sizeof( char ) );
      }

      val = calloc( nin, sizeof( double ) );
//    fprintf( stderr, "nin=%d, q=%d\n", nin, query );

      if( rewritedata )
      {
            scoresbk = scores;
            ninbk = nin;
            fprintf( stderr, "\nformatting .. " );
            dfp = fopen( datafile, "w" );
            if( !dfp ) ErrorExit( "Cannot open datafile." );
            for( i=0; i<nin; i++ )
            {
//                fprintf( stderr, "i=%d / %d / %d\n", i,  nin, njob );
//                fprintf( stderr, "nlenmax = %d\n", nlenmax );
//                fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
//                fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
                  gappick0( tmpseq, seq[scores[i].numinseq] );
                  sprintf( tmpname, "+===========+%d                      \0", i );
                  slen = scores[i].orilen;
                  writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
            }
            fclose( dfp );
                  
            if( scoremtx == -1 )
                  sprintf( com, "formatdb  -p f -i %s -o F", datafile );
            else
                  sprintf( com, "formatdb  -i %s -o F", datafile );
            system( com );
//          fprintf( stderr, "done.\n" );
      }


      gappick0( tmpseq, seq[scores[query].numinseq] );
      sprintf( tmpname, "+==========+%d                      \0", 0 );
      slen = scores[query].orilen;
      qfp = fopen( queryfile, "w" );
      if( !qfp ) ErrorExit( "Cannot open queryfile." );
      writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
      fclose( qfp );
//    fprintf( stderr, "q=%s\n", tmpseq );

      fprintf( stderr, "\ncalling blast .. \n" );
      if( scoremtx == -1 ) 
            sprintf( com, "blastall -b %d -e 1e10 -p blastn -m 7  -i %s -d %s >  %s\0", nin, queryfile, datafile, resultfile );
      else
            sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7  -i %s -d %s >  %s\0", nin, queryfile, datafile, resultfile );
      res = system( com );
      if( res ) ErrorExit( "error in blast" );

      rfp = fopen( resultfile, "r" );
      if( rfp == NULL )  
            ErrorExit( "file 'fasta.$$' does not exist\n" );
      res = ReadBlastm7_scoreonly( rfp, val, nin );
      fclose( rfp );

#if 0
      for( i=0; i<nin; i++ )
            fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
#endif

      return( val );
}

static void selhead( int *ar, int n )
{
      int min = *ar;
      int *minptr = ar;
      int *ptr = ar;
      int tmp;
      n--;
      ar++;
      while( n-- )
      {
            if( ( tmp = *ptr++ ) < min )
            {
                  min = tmp;
                  minptr = ptr;
            }
      }
      if( minptr != ar )
      {
            tmp = *ar;
            *ar = min;
            *minptr = tmp;
      }
      return;
}

void arguments( int argc, char *argv[] )
{
    int c;

      doalign = 0;
      treeout = 0;
      reorder = 1;
      nevermemsave = 0;
      inputfile = NULL;
      fftkeika = 0;
      constraint = 0;
      nblosum = 62;
      fmodel = 0;
      calledByXced = 0;
      devide = 0;
      use_fft = 0;
      force_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;
      makedistmtx = 1;
      dorp = NOTSPECIFIED;
      ppenalty = -1530;
      ppenalty_ex = NOTSPECIFIED;
      poffset = -123;
      kimuraR = NOTSPECIFIED;
      pamN = NOTSPECIFIED;
      geta2 = GETA2;
      fftWinSize = NOTSPECIFIED;
      fftThreshold = NOTSPECIFIED;
      TMorJTT = JTT;
      classsize = NOTSPECIFIED;
      picksize = NOTSPECIFIED;
      tokyoripara = NOTSPECIFIED;

    while( --argc > 0 && (*++argv)[0] == '-' )
      {
        while ( c = *++argv[0] )
            {
            switch( c )
            {
                        case 'p':
                              picksize = atoi( *++argv );
                              fprintf( stderr, "picksize = %d\n", picksize );
                              --argc;
                              goto nextoption;
                        case 's':
                              classsize = atoi( *++argv );
                              fprintf( stderr, "groupsize = %d\n", classsize );
                              --argc;
                              goto nextoption;
                        case 'i':
                              inputfile = *++argv;
                              fprintf( stderr, "inputfile = %s\n", inputfile );
                              --argc;
                              goto nextoption;
                        case 'f':
                              ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
//                            fprintf( stderr, "ppenalty = %d\n", ppenalty );
                              --argc;
                              goto nextoption;
                        case 'g':
                              ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
                              fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
                              --argc;
                              goto nextoption;
                        case 'h':
                              poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
//                            fprintf( stderr, "poffset = %d\n", poffset );
                              --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 'T':
                              tokyoripara = (double)atof( *++argv );
                              --argc;
                              goto nextoption;
#if 0
                        case 'm':
                              fmodel = 1;
                              break;
#endif
                        case 'B':
                              doalign = 'f';
                              break;
                        case 'L':
                              doalign = 1;
                              break;
                        case 'x':
                              reorder = 0;
                              break;
                        case 't':
                              treeout = 1;
                              break;
                        case 'r':
                              fmodel = -1;
                              break;
                        case 'D':
                              dorp = 'd';
                              break;
                        case 'P':
                              dorp = 'p';
                              break;
                        case 'H':
                              makedistmtx = 0;
                              break;
                        case 'e':
                              fftscore = 0;
                              break;
                        case 'O':
                              fftNoAnchStop = 1;
                              break;
                        case 'R':
                              fftRepeatStop = 1;
                              break;
                        case 'Q':
                              calledByXced = 1;
                              break;
                        case 'a':
                              alg = 'a';
                              break;
                        case 'A':
                              alg = 'A';
                              break;
                        case 'N':
                              nevermemsave = 1;
                              break;
                        case 'M':
                              alg = 'M';
                              break;
                        case 'S':
                              alg = 'S';
                              break;
                        case 'C':
                              alg = 'C';
                              break;
                        case 'F':
                              use_fft = 1;
                              break;
                        case 'G':
                              use_fft = 1;
                              force_fft = 1;
                              break;
                        case 'v':
                              tbrweight = 3;
                              break;
                        case 'd':
                              disp = 1;
                              break;
                        case 'o':
                              outgap = 0;
                              break;
                        case 'J':
                              tbutree = 0;
                              break;
                        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 );
      }
      if( alg == 'C' && outgap == 0 )
      {
            fprintf( stderr, "conflicting options : C, o\n" );
            exit( 1 );
      }
}

static int maxl;
static int tsize;

int seq_grp_nuc( int *grp, char *seq )
{
      int tmp;
      int *grpbk = grp;
      while( *seq )
      {
            tmp = amino_grp[*seq++];
            if( tmp < 4 )
                  *grp++ = tmp;
            else
                  fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
      }
      *grp = END_OF_VEC;
      return( grp-grpbk );
}

int seq_grp( int *grp, char *seq )
{
      int tmp;
      int *grpbk = grp;
      while( *seq )
      {
            tmp = amino_grp[*seq++];
            if( tmp < 6 )
                  *grp++ = tmp;
            else
                  fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
      }
      *grp = END_OF_VEC;
      return( grp-grpbk );
}

void makecompositiontable_p( short *table, int *pointt )
{
      int point;

      while( ( point = *pointt++ ) != END_OF_VEC )
            table[point]++;
}

int commonsextet_p( short *table, int *pointt )
{
      int value = 0;
      short tmp;
      int point;
      static short *memo = NULL;
      static int *ct = NULL;
      static int *cp;

      if( !memo )
      {
            memo = (short *)calloc( tsize, sizeof( short ) );
            if( !memo ) ErrorExit( "Cannot allocate memo\n" );
            ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) );
            if( !ct ) ErrorExit( "Cannot allocate memo\n" );
      }

      cp = ct;
      while( ( point = *pointt++ ) != END_OF_VEC )
      {
            tmp = memo[point]++;
            if( tmp < table[point] )
                  value++;
            if( tmp == 0 ) *cp++ = point;
      }
      *cp = END_OF_VEC;
      
      cp =  ct;
      while( *cp != END_OF_VEC )
            memo[*cp++] = 0;

      return( value );
}

void makepointtable_nuc( int *pointt, int *n )
{
      int point;
      register int *p;

      p = n;
      point  = *n++ *  1024;
      point += *n++ *   256;
      point += *n++ *    64;
      point += *n++ *    16;
      point += *n++ *     4;
      point += *n++;
      *pointt++ = point;

      while( *n != END_OF_VEC )
      {
            point -= *p++ * 1024;
            point *= 4;
            point += *n++;
            *pointt++ = point;
      }
      *pointt = END_OF_VEC;
}

void makepointtable( int *pointt, int *n )
{
      int point;
      register int *p;

      p = n;
      point  = *n++ *  7776;
      point += *n++ *  1296;
      point += *n++ *   216;
      point += *n++ *    36;
      point += *n++ *     6;
      point += *n++;
      *pointt++ = point;

      while( *n != END_OF_VEC )
      {
            point -= *p++ * 7776;
            point *= 6;
            point += *n++;
            *pointt++ = point;
      }
      *pointt = END_OF_VEC;
}

#if 1
static void pairalign( int nseq, int *nlen, char **seq, int *mem1, int *mem2, double *weight, int *alloclen )
{
      int i;
      int l, len1, len2;
      int nlim;
      int clus1, clus2;
      float pscore, tscore;
      static int *fftlog;
      static char *indication1, *indication2;
      static double *effarr1 = NULL;
      static double *effarr2 = NULL;
      static char **mseq1, **mseq2;
      float dumfl = 0.0;
      int ffttry;
      int m1, m2;
#if 0
      int i, j;
#endif


      if( effarr1 == NULL ) 
      {
            fftlog = AllocateIntVec( nseq );
            effarr1 = AllocateDoubleVec( nseq );
            effarr2 = AllocateDoubleVec( nseq );
            indication1 = AllocateCharVec( 150 );
            indication2 = AllocateCharVec( 150 );
            mseq1 = AllocateCharMtx( nseq, 0 );
            mseq2 = AllocateCharMtx( nseq, 0 );
            for( l=0; l<nseq; l++ ) fftlog[l] = 1;
      }

      tscore = 0.0;
      m1 = mem1[0];
      m2 = mem2[0];
      len1 = strlen( seq[m1] );
      len2 = strlen( seq[m2] );
      if( *alloclen < len1 + len2 )
      {
            fprintf( stderr, "\nReallocating.." );
            *alloclen = ( len1 + len2 ) + 1000;
            ReallocateCharMtx( seq, nseq, *alloclen + 10 ); 
            fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
      }

#if WEIGHT
      clus1 = fastconjuction_noname( mem1, seq, mseq1, effarr1, weight, indication1 );
      clus2 = fastconjuction_noname( mem2, seq, mseq2, effarr2, weight, indication2 );
#else
      clus1 = fastconjuction_noweight( mem1, seq, mseq1, effarr1, indication1 );
      clus2 = fastconjuction_noweight( mem2, seq, mseq2, effarr2, indication2 );
#endif

#if 0
      for( i=0; i<clus1; i++ )
            fprintf( stderr, "in p seq[%d] = %s\n", mem1[i], seq[mem1[i]] );
      for( i=0; i<clus2; i++ )
            fprintf( stderr, "in p seq[%d] = %s\n", mem2[i], seq[mem2[i]] );
#endif

#if 0
      fprintf( stderr, "group1 = %.66s", indication1 );
      if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
      fprintf( stderr, "\n" );
      fprintf( stderr, "group2 = %.66s", indication2 );
      if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
      fprintf( stderr, "\n" );
#endif

//    fprintf( stdout, "mseq1 = %s\n", mseq1[0] );
//    fprintf( stdout, "mseq2 = %s\n", mseq2[0] );

      if( !nevermemsave && ( alg != 'M' && ( len1 > 10000 || len2 > 10000  ) ) )
      {
            fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode\n", len1, len2 );
            alg = 'M';
            if( commonIP ) FreeShortMtx( commonIP );
            commonAlloc1 = 0;
            commonAlloc2 = 0;
      }

      if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
      else                             ffttry = 0;

      if( force_fft || ( use_fft && ffttry ) )
      {
            fprintf( stderr, "\bf" );
            if( alg == 'M' )
            {
                  fprintf( stderr, "\bm" );
//                fprintf( stderr, "%d-%d", clus1, clus2 );
                  pscore = Falign_noudp( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
            }
            else
            {
//                fprintf( stderr, "%d-%d", clus1, clus2 );
                  pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
            }
      }
      else
      {
            fprintf( stderr, "\bd" );
            fftlog[m1] = 0;
            switch( alg )
            {
                  case( 'a' ):
                        pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
                        break;
                  case( 'M' ):
                        fprintf( stderr, "\bm" );
//                      fprintf( stderr, "%d-%d", clus1, clus2 );
                        pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL );
                        break;
                  case( 'A' ):
                        if( clus1 == 1 && clus2 == 1 )
                        {
//                            fprintf( stderr, "%d-%d", clus1, clus2 );
                              pscore = G__align11( mseq1, mseq2, *alloclen );
                        }
                        else
                        {
//                            fprintf( stderr, "%d-%d", clus1, clus2 );
                              pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
                        }
                        break;
                  default:
                        ErrorExit( "ERROR IN SOURCE FILE" );
            }
      }
#if SCOREOUT
      fprintf( stderr, "score = %10.2f\n", pscore );
#endif
      nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
      return;
}
#endif

static void treebase( int nseq, int *nlen, char **aseq, double *eff, int nalign, int ***topol, int *alloclen ) // topol
{
      int i, l;
      int nlim;
      int clus1, clus2;

      nlim = nalign-1;
      for( l=0; l<nlim; l++ )
      {
            fprintf( stderr, "in treebase, l = %d\n", l );
            fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
            fprintf( stderr, "aseq[topol[l][0][0]] = %s\n", aseq[topol[l][0][0]] );
            pairalign( nseq, nlen, aseq, topol[l][0], topol[l][1], eff, alloclen );
            free( topol[l][0] );
            free( topol[l][1] );
      }
}

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 );
}
       
#if 1
static int splitseq_mq( Scores *scores, int nin, int *nlen, char **seq, char **name, char *inputfile, int uniform, char **tree, int *alloclen, int *order, int *whichgroup, double *weight, int *depthpt )
{
      int val;
      int ii, jj, kk;
      int *mptr;
      int treelen;
      int thisgroup;
      static int groupid = 0;
      static int branchid = 0;
      static int uniformid = 0;
      int i, j, k, jlim;
      int selfscore0, selfscore1;
      double **dfromc;
      float **pickmtx;
      float **yukomtx;
      static short *table1;
      Scores **outs, *ptr;
      int *numin;
      int *tsukau;
      int belongto;
      FILE *outfp;
      char *outputfile;
      char **children;
      char **parttree;
      char *tmptree;
      int *optr;
      static int *orderpos = NULL;
      int rn;
      int npick;
      int nyuko;
      int *picks;
      int *yukos;
      int *s_p_map;
      int *p_o_map;
      int *s_y_map;
      int *y_o_map;
      int *closeh;
      int nkouho;
      int *pickkouho;
      int *iptr;
      int *jptr;
      int aligned;
      int ***topol;
      int *treeorder;
      int picktmp;
      float **len;
      double minscore;
//    double *minscoreinpick;
      float *hanni;
      double lenfac;
      double longer;
      double shorter;
      int off1, off2;
      static char **mseq1 = NULL;
      static char **mseq2 = NULL;
      double *blastresults;
      static int palloclen = 0;
      float maxdist;

      if( orderpos == NULL )
            orderpos = order;
      if( palloclen == 0 )
            palloclen = *alloclen * 2;
      if( mseq1 == NULL && doalign == 1 )
      {
            mseq1 = AllocateCharMtx( 1, palloclen );
            mseq2 = AllocateCharMtx( 1, palloclen );
      }



      if( nin == 0 ) 
      {
#if TREE
            if( treeout )
            {
                  *tree = (char *)calloc( 1, sizeof( char ) );
                  **tree = 0;
            }
#endif
            return 1;
      }

      if( nin < 2 || uniform == -1 ) // kokodato muda deha nai ga
      {
            fprintf( stderr, "\nLeaf  %d / %d                ", ++branchid, njob );
#if 0
            outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
            sprintf( outputfile, "%s-%d", inputfile, branchid );
            if( uniform > 0 )
                  sprintf( outputfile, "%su%d", outputfile, uniform );
            fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
            outfp = fopen( outputfile, "w" );
            free( outputfile );
            if( outfp == NULL )
            {
                  fprintf( stderr, "Cannot open %s\n", outputfile );
                  exit( 1 );
            }
            for( j=0; j<nin; j++ )
                  fprintf( outfp, ">G%d %s\n%s\n", branchid, scores[j].name+1, seq[scores[j].numinseq] );
            fclose( outfp );
#endif


#if TREE
            if( treeout )
            {
                  treelen = 0;
                  tmptree = calloc( 100, sizeof( char ) );
                  for( j=0; j<nin; j++ )
                  {
                        treelen += sprintf( tmptree, "%d", scores[j].numinseq+1 );
                  }
                  free( tmptree );
      
                  *tree = (char *)calloc( treelen + nin + 5, sizeof( char ) );
                  if( nin > 1 ) **tree = '(';
                  else          **tree = '\0';
//                **tree = '\0';
                  for( j=0; j<nin-1; j++ )
                  {
                        sprintf( *tree+strlen( *tree ), "%d,", scores[j].numinseq+1 );
                  }
                  sprintf( *tree+strlen( *tree ), "%d", scores[j].numinseq+1 );
                  if( nin > 1 ) strcat( *tree, ")" );
//                fprintf( stdout, "*tree = %s\n", *tree );
            }

#endif
            for( j=0; j<nin; j++ )
            {
                  *orderpos++ = scores[j].numinseq;
//                fprintf( stderr, "*order = %d\n", scores[j].numinseq );
            }

            return 1;
      }


#if 0
      okashii = 0;
      fprintf( stderr, "checking before swap!!\n" );
      for( i=0; i<nin; i++ )
      {
            fprintf( stderr, "scores[%d].seq (%d) = \n%s\n", i, scores[i].numinseq, scores[i].seq );
            if( strlen( seq[scores[i].numinseq] ) == 0 )
            {
                  okashii = 1;
                  fprintf( stderr, "OKASHII before swap!!\n" );
            }
      }
#endif
#if 0
      if( okashii == 1 )
      {
            for( i=0; i<njob; i++ )
            {
//                fprintf( stderr, "seq[%d] = \n%s\n", i,  seq[i] );
                  if( strlen( seq[i] ) == 0 )
                  {
                        fprintf( stderr, "OKASHII in seq!!\n" );
                  }
            }
            exit( 1 );
      }
#endif

      i = nin;
      ptr = scores;
      selfscore0 = scores->selfscore;
      belongto = 0;
      while( i-- )
      {
//          fprintf( stderr, "ptr-scores=%d, selfscore = %d, score = %f\n", ptr-scores, ptr->selfscore, ptr->score );
            if( ptr->selfscore > selfscore0 )
            {
                  selfscore0 = ptr->selfscore;
                  belongto = ptr-scores;
            }
            ptr++;
      } 
#if 1 
      if( belongto != 0 )
      {
//          fprintf( stderr, "swap %d %s\n<->\n%d %s\n", 0, scores->name, belongto, (scores+belongto)->name );
            ptr = calloc( 1, sizeof( Scores ) );
            *ptr = scores[belongto];
            scores[belongto] = *scores;
            *scores = *ptr;
            free( ptr );
      }
#endif


      if( doalign )
      {
            if( doalign == 'f' )
            {
                  blastresults = callfasta( seq, scores, nin, NULL, 0, 1 );
                  if( scores->selfscore != (int)blastresults[0] )
                  {
                        fprintf( stderr, "\n\nWARNING1: selfscore\n" );
                        fprintf( stderr, "scores->numinseq = %d\n", scores->numinseq+1 );
                        fprintf( stderr, "scores->orilen = %d\n", scores->orilen );
                        fprintf( stderr, "scores->selfscore = %d, but blastresults[0] = %f\n", scores->selfscore, blastresults[0] );
                        if( abs( scores->selfscore - (int)blastresults[0] ) > 2 )
                              exit( 1 );
//                      scores->selfscore = (int)blastresults[0]; //iinoka?

//                      exit( 1 );
                  }
            }
            else
                  gappick0( mseq1[0], seq[scores->numinseq] );
      }
      else
      {
            table1 = (short *)calloc( tsize, sizeof( short ) );
            if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
            makecompositiontable_p( table1, scores[0].pointt );
      }

      selfscore0 = scores[0].selfscore;
    for( i=0; i<nin; i++ ) 
      {
            if( scores->orilen > scores[i].orilen )
            {
                  longer = (double)scores->orilen;
                  shorter = (double)scores[i].orilen;
            }
            else
            {
                  longer = (double)scores[i].orilen; // nai
                  shorter = (double)scores->orilen; //nai
            }

#if LENFAC
            lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
//          lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
//          fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
#else
            lenfac = 1.0;
#endif

            if( doalign )
            {
                  if( doalign == 'f' )
                  {
                        scores[i].score = ( 1.0 - blastresults[i] / MIN( scores->selfscore, scores[i].selfscore ) ) * 1;
                  }
                  else
                  {
                        if( *depthpt == 0 ) fprintf( stderr, "\r%d / %d   ", i, nin );
                        gappick0( mseq2[0], seq[scores[i].numinseq] );
                        scores[i].score = ( 1.0 - (double)L__align11_noalign( mseq1, mseq2, palloclen, &off1, &off2, (i==0) ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
//                      fprintf( stderr, "scores[i] = %f\n", scores[i].score );
//                      fprintf( stderr, "m1=%s\n", seq[scores[0].numinseq] );
//                      fprintf( stderr, "m2=%s\n", seq[scores[i].numinseq] );
                  }
            }
            else
            {
                  scores[i].score = ( 1.0 - (double)commonsextet_p( table1, scores[i].pointt ) / MIN( selfscore0, scores[i].selfscore ) ) * lenfac;
                  if( scores[i].score > MAX6DIST ) scores[i].score = MAX6DIST;
            }
//          if( i ) fprintf( stderr, "%d-%d d %4.2f len %d %d\n", 1, i+1, scores[i].score, scores->orilen, scores[i].orilen );
      }
      if( doalign == 'f' ) free( blastresults );
      if( doalign == 0 ) free( table1 );
//exit( 1 );

//    fprintf( stderr, "sorting .. " );
      qsort( scores, nin, sizeof( Scores ), (int (*)())dcompare );
//    fprintf( stderr, "done.\n" );

      maxdist = scores[nin-1].score;
//    fprintf( stderr, "maxdist? = %f, nin=%d\n", scores[nin-1].score, nin );

      if( nin == 1 ) fprintf( stderr, "nin=1, scores[0].score = %f\n", scores[0].score );

// kokoni if( nin < 2 || ... )

      picks = AllocateIntVec( nin+1 );
      s_p_map = AllocateIntVec( nin+1 );
      s_y_map = AllocateIntVec( nin+1 );
      pickkouho = AllocateIntVec( nin+1 );
      closeh = AllocateIntVec( nin+1 );

//    nkouho = getkouho( pickkouho, (picksize+100)/nin, nin, scores, seq );
//    nkouho = getkouho( pickkouho, 1.0, nin, scores, seq ); // zenbu
//    fprintf( stderr, "selecting kouhos phase 2\n"  );
//    if( nkouho == 0 )
//    {
//          fprintf( stderr, "selecting kouhos, phase 2\n"  );
//          nkouho = getkouho( pickkouho, 1.0, nin, scores, seq );
//    }
//    fprintf( stderr, "\ndone\n\n"  );
      for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu



      iptr = picks;
      *iptr++ = 0;
      npick = 1;
      if( nkouho > 0 )
      {
//          fprintf( stderr, "pickkouho[0] = %d\n", pickkouho[0] );
//          fprintf( stderr, "pickkouho[nin-1] = %d\n", pickkouho[nin-1] );
//          fprintf( stderr, "\nMOST DISTANT kouho=%d, nin=%d, nkouho=%d\n", pickkouho[nkouho], nin, nkouho );
            picktmp = pickkouho[nkouho-1];
            nkouho--;
            if( ( scores[picktmp].shimon == scores[0].shimon ) && ( !strcmp( seq[scores[0].numinseq], seq[scores[picktmp].numinseq] ) ) )
            {
//                fprintf( stderr, "known, j=%d (%d inori)\n", 0, scores[picks[0]].numinseq );
//                fprintf( stderr, "%s\n%s\n", seq[scores[picktmp].numinseq], seq[scores[picks[0]].numinseq] );
                  ;
            }
            else
            {
                  *iptr++ = picktmp;
                  npick++;
//                fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
            }
      }
      i = 1;
      while( npick<picksize && nkouho>0 )
      {
            if( i )
            {
                  i = 0;
                  rn = nkouho * 0.5;
//                fprintf( stderr, "rn = %d\n", rn );
            }
            else
            {
                  rn = rnd() * (nkouho);
            }
            picktmp = pickkouho[rn];
//          fprintf( stderr, "rn=%d/%d (%d inori), kouho=%d, nin=%d, nkouho=%d\n", rn, nkouho, scores[pickkouho[rn]].numinseq, pickkouho[rn], nin, nkouho );

//          fprintf( stderr, "#kouho before swap\n" );
//          for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ",  pickkouho[i] ); fprintf( stderr, "\n" );

            nkouho--;
            pickkouho[rn] = pickkouho[nkouho];
#if 1
//          fprintf( stderr, "#kouho after swap\n" ); 
//          for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ",  pickkouho[i] ); fprintf( stderr, "\n" );
            for( j=0; j<npick; j++ )
            {
                  if( scores[picktmp].shimon == scores[picks[j]].shimon && !strcmp( seq[scores[picks[j]].numinseq], seq[scores[picktmp].numinseq] ) ) 
                        break;
            }
            if( j == npick )
#endif
            {
//                fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
                  npick++;
                  *iptr++ = picktmp;
            }
            else
            {
//                fprintf( stderr, "known, j=%d (%d inori)\n", j, scores[picks[j]].numinseq );
            }
      }
#if 0
      for( i=0; i<nin; i++ )
      {
            fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, nin, i, scores[i].score, scores[i].numinseq );
      }
      fprintf( stderr, "range:nin=%d scores[%d].score <= %f\n", nin, npick, scores[nin-1].score);
      for( i=0; i<npick; i++ )
      {
            fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, npick, picks[i], scores[picks[i]].score, scores[picks[i]].numinseq );
      }
exit( 1 );
#endif

//    fprintf( stderr, "\nnkouho=%d, defaultq2 = %d (%d inori)\n", nkouho, picks[npick-1], scores[picks[npick-1]].numinseq );

      qsort( picks, npick, sizeof( int ), (int (*)())intcompare );

//    fprintf( stderr, "allocating..\n" );

//    fprintf( stderr, "allocating outs, npick = %d\n", npick );
      numin = calloc( npick, sizeof( int ) );
      tsukau = calloc( npick, sizeof( int ) );
      outs = calloc( npick, sizeof( Scores * ) );
      for( i=0; i<npick; i++ ) outs[i] = NULL;
      topol = AllocateIntCub( npick, 2, 0 );
      treeorder = AllocateIntVec( npick + 1 );
      len = AllocateFloatMtx( npick, 2 );
      pickmtx = AllocateFloatHalfMtx( npick );
      yukomtx = AllocateFloatHalfMtx( npick );
//    minscoreinpick = AllocateDoubleVec( npick );
      yukos = AllocateIntVec( npick );
      p_o_map = AllocateIntVec( npick+1 );
      y_o_map = AllocateIntVec( npick+1 );
      hanni = AllocateFloatVec( npick );

      for( i=0; i<nin; i++ ) s_p_map[i] = -1;
//    fprintf( stderr, "npick = %d\n", npick );
//    fprintf( stderr, "picks =" );
      for( i=0; i<npick; i++ )
      {
            s_p_map[picks[i]] = i;
            p_o_map[i] = scores[picks[i]].numinseq;
//          fprintf( stderr, " %d\n", picks[i] );
      }
//    fprintf( stderr, "\n" );

#if 0
      fprintf( stderr, "p_o_map =" );
      for( i=0; i<npick; i++ )
      {
            fprintf( stderr, " %d", p_o_map[i] );
      }
      fprintf( stderr, "\n" );
#endif

      for( j=0; j<nin; j++ )
      {
            if( s_p_map[j] != -1 )
            {
                  pickmtx[0][s_p_map[j]] = (float)scores[j].score;
//                fprintf( stderr, "pickmtx[0][%d] = %f\n", s_p_map[j], pickmtx[0][s_p_map[j]] );
            }
      }

      for( j=1; j<npick; j++ )
      {
            if( doalign )
            {
                  if( doalign == 'f' )
                  {
//                      blastresults = callfasta( seq, scores, npick-j+1, picks+j-1, picks[j], 1 );
                        blastresults = callfasta( seq, scores, npick, picks, picks[j], (j==1) );
                        if( scores[picks[j]].selfscore != (int)blastresults[j] )
                        {
                              fprintf( stderr, "\n\nWARNING2: selfscore j=%d/%d\n", j, npick );
                              fprintf( stderr, "scores[picks[j]].numinseq = %d\n", scores[picks[j]].numinseq+1 );
                              fprintf( stderr, "scores[picks[j]].orilen = %d\n", scores[picks[j]].orilen );
                              fprintf( stderr, "scores[picks[j]].selfscore = %d, but blastresults[j] = %f\n", scores[picks[j]].selfscore, blastresults[j] );
                              if( abs( scores[picks[j]].selfscore - (int)blastresults[j] ) > 2 )
                                    exit( 1 );
//                            scores->selfscore = (int)blastresults[0]; //iinoka?
                        }
                  }
                  else
                        gappick0( mseq1[0], seq[scores[picks[j]].numinseq] );
            }
            else
            {
                  table1 = (short *)calloc( tsize, sizeof( short ) );
                  if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
                  makecompositiontable_p( table1, scores[picks[j]].pointt );
            }
      
            selfscore0 = scores[picks[j]].selfscore;
            pickmtx[j][0] = 0.0;
          for( i=j+1; i<npick; i++ ) 
            {
                  if( scores[picks[j]].orilen > scores[picks[i]].orilen )
                  {
                        longer = (double)scores[picks[j]].orilen;
                        shorter = (double)scores[picks[i]].orilen;
                  }
                  else
                  {
                        longer = (double)scores[picks[i]].orilen;
                        shorter = (double)scores[picks[j]].orilen;
                  }
      
      #if LENFAC
                  lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
      //          lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
      //          fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
      #else
                  lenfac = 1.0;
      #endif
      
                  if( doalign )
                  {
                        if( doalign == 'f' )
                        {
//                            fprintf( stderr, "blastresults[%d] = %f\n", i, blastresults[i] );
                              pickmtx[j][i-j] = ( 1.0 - blastresults[i] / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
                        }
                        else
                        {
//                            fprintf( stderr, "\r%d / %d   ", i, nin );
                              gappick0( mseq2[0], seq[scores[picks[i]].numinseq] );
                              pickmtx[j][i-j] = ( 1.0 - (double)L__align11_noalign( mseq1, mseq2, palloclen, &off1, &off2, (i==j+1) ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
      //                      fprintf( stderr, "scores[picks[i]] = %f\n", scores[picks[i]].score );
                        }
                  }
                  else
                  {
                        pickmtx[j][i-j] = ( 1.0 - (double)commonsextet_p( table1, scores[picks[i]].pointt ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * lenfac;
                        if( pickmtx[j][i-j] > MAX6DIST ) pickmtx[j][i-j] = MAX6DIST;
                  }

            }
            if( doalign == 'f' ) free( blastresults );
            if( doalign == 0 ) free( table1 );
      }

#if 0
      fprintf( stderr, "pickmtx = \n" );
      for( i=0; i<npick; i++ )
      {
            for( j=i; j<npick; j++ )
            {
                  fprintf( stderr, "pickmtx[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
            }
      }
      exit( 1 );
#endif


//    for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
//          fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );

      for( i=0; i<npick; i++ ) tsukau[i] = 1;
      for( i=0; i<nin; i++ ) closeh[i] = -1;
      for( i=0; i<npick; i++ ) 
      {
            closeh[picks[i]] = picks[i];
//          fprintf( stderr, "i=%d/%d, picks[i]=%d, %d inori, closeh[%d] = %d \n", i, npick, picks[i], p_o_map[i]+1, picks[i], closeh[picks[i]] );
      }
#if 0
      fprintf( stderr, "closeh = \n" );
      for( i=0; i<nin; i++ )
      {
            fprintf( stderr, "%d ", closeh[i] );
      }
      fprintf( stderr, "\n" );
#endif
#if DIANA
      for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
            fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
      fprintf( stderr, "DIANA!!\n" );
      if( npick > 2 )
      {
            float avdist;
            float avdist1;
            float avdist2;
            float maxavdist;
            int splinter;
            int count;
            int dochokoho;
            splinter = 0;
            int *docholist;
            int *docholistbk;
            maxavdist = 0.0;
            for( i=0; i<npick; i++ )
            {
                  avdist = 0.0;
                  for( j=i+1; j<npick; j++ )
                  {
                        avdist += pickmtx[i][j-i];
                  }
                  for( j=0; j<i; j++ )
                  {
                        avdist += pickmtx[j][i-j];
                  }
                  avdist /= (npick-1);
                  fprintf( stderr, "avdist[%d] = %f\n", p_o_map[i] + 1, avdist );
                  if( maxavdist < avdist ) 
                  {
                        maxavdist = avdist;
                        splinter = i;
                  }
            }
            fprintf( stderr, "splinter = %d (%d inori), maxavdist = %f\n", splinter, p_o_map[splinter]+1, maxavdist );

            docholist = AllocateIntVec( npick );
            docholistbk = AllocateIntVec( npick );
            for( i=0; i<npick; i++ ) docholist[i] = 0;
            docholist[splinter] = 1;
            while( 1 )
            {
                  for( i=0; i<npick; i++ ) docholistbk[i] = docholist[i]; 
                  for( dochokoho = 0; dochokoho<npick; dochokoho++ )
                  {
                        fprintf( stderr, "dochokoho=%d\n", dochokoho );
                        if( docholist[dochokoho] ) continue;
                        count = 0;
                        avdist1 = 0.0;
                        i=dochokoho;
                        {
                              for( j=i+1; j<npick; j++ )
                              {
                                    if( docholist[j] || j == dochokoho ) continue;
                                    avdist1 += pickmtx[i][j-i];
                                    count++;
                              }
                              for( j=0; j<i; j++ )
                              {
                                    if( docholist[j] || j == dochokoho ) continue;
                                    avdist1 += pickmtx[j][i-j];
                                    count++;
                              }
                        }
                        if( count < 1 ) avdist1 = 0.0;
                        else avdist1 /= (float)count;
                        fprintf( stderr, "docho %d (%dinori), avdist1 = %f\n", dochokoho, p_o_map[dochokoho] + 1, avdist1 );

                        count = 0;
                        avdist2 = 0.0;
                        i=dochokoho;
                        {
                              for( j=i+1; j<npick; j++ )
                              {
                                    if( !docholist[j] || j == dochokoho ) continue;
                                    avdist2 += pickmtx[i][j-i];
                                    count++;
                              }
                              for( j=0; j<i; j++ )
                              {
                                    if( !docholist[j] || j == dochokoho ) continue;
                                    avdist2 += pickmtx[j][i-j];
                                    count++;
                              }
                        }
                        if( count < 1 ) avdist2 = 0.0;
                        else avdist2 /= (float)count;
                        fprintf( stderr, "docho %d (%dinori), avdist2 = %f\n", dochokoho, p_o_map[dochokoho] + 1, avdist2 );

                        if( avdist2 < avdist1 ) 
                        {
                              docholist[dochokoho] = 1;
                              hanni[dochokoho] = avdist2;
                        }
                        else
                        {
                              docholist[dochokoho] = 0;
                              hanni[dochokoho] = avdist1;
                        }
                        fprintf( stderr, "avdist1=%f, avdist2=%f\n", avdist1, avdist2 );

                  }
                  for( i=0; i<npick; i++ ) if( docholist[i] != docholistbk[i] ) break;
                  if( i == npick ) break;

                  fprintf( stderr, "docholist = \n" );
                  for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", docholist[i] );
                  fprintf( stderr, "\n" );
            }
            fprintf( stderr, "docholist = \n" );
            for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", docholist[i] );
            fprintf( stderr, "\n" );

            for( i=0; i<npick; i++ ) if( docholist[i] == 0 ) break;
            yukos[0] = picks[i];
            for( i=0; i<npick; i++ ) if( docholist[i] == 1 ) break;
            yukos[1] = picks[splinter];

            for( i=0; i<npick; i++ ) 
            {
                  if( docholist[i] == 0 ) closeh[picks[i]] = yukos[0];
                  if( docholist[i] == 1 ) closeh[picks[i]] = yukos[1];
            }
//          for( i=0; i<npick; i++ ) closeh[picks[i]] = -1; // CHUUI !! iminai
            nyuko = 2;
            free( docholist );
            free( docholistbk );
      }
      else if( npick > 1 )
      {
            nyuko = 2;
            yukos[0] = picks[0]; yukos[1] = picks[1];
            closeh[picks[0]] = yukos[0];
            closeh[picks[1]] = yukos[1];
      }
      else
      {
            nyuko = 1;
            yukos[0] = picks[0];
            closeh[picks[0]] = yukos[0];
      }
#elif HUKINTOTREE
      if( npick > 2 )
      {
#if 0
            float avdist;
            float maxavdist;
            int count;
            int splinter;
            maxavdist = 0.0;
            splinter=0;
            for( i=0; i<npick; i++ )
            {
                  avdist = 0.0;
                  for( j=i+1; j<npick; j++ )
                  {
                        avdist += pickmtx[i][j-i];
                  }
                  for( j=0; j<i; j++ )
                  {
                        avdist += pickmtx[j][i-j];
                  }
                  avdist /= (npick-1);
                  fprintf( stderr, "avdist[%d] = %f\n", p_o_map[i] + 1, avdist );
                  if( maxavdist < avdist ) 
                  {
                        maxavdist = avdist;
                        splinter = i;
                  }
            }
            fprintf( stderr, "splinter = %d (%d inori), maxavdist = %f\n", splinter, p_o_map[splinter]+1, maxavdist );
#endif
//          fprintf( stderr, "check kaishi =>, npick=%d members = \n", npick );
//          for( i=0; i<npick; i++ ) fprintf( stderr, "%d (%d)", p_o_map[i]+1, picks[i] );
//          fprintf( stderr, "\n" );
            for( i=0; i<npick-1; i++ ) 
            {
                  if( tsukau[i] == 0 ) continue;
                  for( j=i+1; j<npick; j++ )
                  {
//                      float kijun = maxdist *  1/(npick-2);
//                      float kijun = maxavdist * tokyoripara;
                        float kijun;
                        kijun = maxdist * tokyoripara;  // atode kakunin
//                      fprintf( stderr, "%d-%d\n", i, j );
//                      fprintf( stderr, "maxdist = %f\n", maxdist );
//                      if( i==0 && j == 1 ) continue; // machigai!! CHUUI!!
//                      if( maxdist == pickmtx[i][j-i] ) continue;
                        if( tsukau[j] == 0 ) continue;
//                      fprintf( stderr, "checking %d-%d (%d-%d) %f, kijun=%f\n", p_o_map[i]+1, p_o_map[j]+1, i, j, pickmtx[i][j-i], kijun );
                        if( pickmtx[i][j-i] < kijun )
                        {
//                            fprintf( stderr, "dame!! %d => %d, because %f < %f\n", p_o_map[j]+1, p_o_map[i]+1, pickmtx[i][j-i], kijun );
#if 0
                              if( scores[picks[i]].orilen > scores[picks[j]].orilen )
                              {
                                    fprintf( stderr, "%d => %d\n", p_o_map[j]+1, p_o_map[i]+1 );
                                    tsukau[j] = 0;
                              }
                              else
                              {
                                    fprintf( stderr, "%d => %d\n", p_o_map[i]+1, p_o_map[j]+1 );
                                    tsukau[i] = 0;
                              }
                              if( 0 && j == npick-1 ) tsukau[i] = 0;
                              else                       tsukau[j] = 0;
                              fprintf( stderr, "tsukau[%d] = %d (%d inori)\n", j, tsukau[j], p_o_map[j]+1 );
#else
                              tsukau[j] = 0;
                              closeh[picks[j]] = closeh[picks[i]];
#endif
                        }
                  }
            }
      }

      for( ii=0,i=0; i<npick; i++ )
      {
            if( tsukau[i] )
            {
                  for( jj=ii,j=i; j<npick; j++ )
                  {
                        if( tsukau[j] )
                        {
                              yukomtx[ii][jj-ii] = pickmtx[i][j-i];
                              jj++;
                        }
                  }
                  ii++;
            }
      }
      for( ii=0,i=0; i<npick; i++ )
      {
            if( tsukau[i] )
            {
                  yukos[ii++] = picks[i];
            }
      }


      nyuko = ii;


      for( ii=0,i=0; i<npick; i++ )
      {
            if( tsukau[i] )
            {
                  for( jj=ii,j=i; j<npick; j++ )
                  {
                        if( tsukau[j] )
                        {
                              yukomtx[ii][jj-ii] = pickmtx[i][j-i];
                              jj++;
                        }
                  }
                  ii++;
            }
      }
      for( ii=0,i=0; i<npick; i++ )
      {
            if( tsukau[i] )
            {
                  yukos[ii++] = picks[i];
            }
      }

#endif
#if 0
      for( i=0; i<npick; i++ ) for( j=i; j<npick; j++ )
      {
            if( tsukau[i] == 1 && tsukau[j] == 1 )
                  fprintf( stderr, "dist[%d][%d] = %f (ok)\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i]  );
            else if( tsukau[i] == 0 && tsukau[j] == 0 )
                  fprintf( stderr, "dist[%d][%d] = %f (xx)\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i]  );
            else  
                  fprintf( stderr, "%d-%d, okashii\n", p_o_map[i]+1, p_o_map[j]+1 );
      }
#endif


      for( i=0; i<nin; i++ ) s_y_map[i] = -1;
//    fprintf( stderr, "npick = %d\n", npick );
//    fprintf( stderr, "yukos =" );
      for( i=0; i<nyuko; i++ )
      {
            s_y_map[yukos[i]] = i;
            y_o_map[i] = scores[yukos[i]].numinseq;
//          fprintf( stderr, " %d\n", yukos[i] );
      }
//    fprintf( stderr, "\n" );
#if 0
      for( i=0; i<nyuko; i++ )
      {
            fprintf( stderr, "y_o_map[%d] = %d\n", i, y_o_map[i]+1 );
      }
      for( i=0; i<nyuko; i++ ) for( j=i; j<nyuko; j++ )
      {
            fprintf( stderr, "yukodist[%d][%d] = %f (ok)\n", y_o_map[i]+1, y_o_map[j]+1, yukomtx[i][j-i]  );
      }
#endif

      for( i=0; i<nin; i++ )
      {
            if( closeh[i] != -1 )
            {
//                fprintf( stderr, "closeh[%d,%dinori] = %d,%dinori\n", i, scores[i].numinseq+1, closeh[i], scores[closeh[i]].numinseq+1 );
            }
      }

#if 0
            for( i=0; i<nyuko; i++ )
            {
                  minscoreinpick[i] = 99.9;
                  for( j=i+1; j<nyuko; j++ )
                  {
                        if( minscoreinpick[i] > yukomtx[i][j-i] )
                              minscoreinpick[i] = yukomtx[i][j-i];
                  }
                  for( j=0; j<i; j++ )
                  {
                        if( minscoreinpick[i] > yukomtx[j][i-j] )
                              minscoreinpick[i] = yukomtx[j][i-j];
                  }
                  fprintf( stderr, "minscoreinpick[%d(%dinori)] = %f\n", i, y_o_map[i]+1, minscoreinpick[i] );
            }
#endif


#if TREE
      if( treeout )
      {
            children = calloc( nyuko+1, sizeof( char * ) );
            for( i=0; i<nyuko+1; i++ ) children[i] = NULL;
      }
#endif
//    fprintf( stderr, "done..\n" );
      
//    fprintf( stderr, "classifying, pick=%d \n", nyuko );
      if( nyuko == 1 )
      {
            if( npick != 1 )
            {
                  fprintf( stderr, "okashii, nyuko = 1, shikashi npick = %d\n", npick );
                  exit( 1 );
            }
//          fprintf( stderr, "### itchi suru hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore );
//          fprintf( stderr, "seq[%d] = scores->seq = \n%s\n", scores->numinseq, seq[scores->numinseq] );

            uniform = -1;
            for( j=0; j<nin; j++ ) 
            {
                  belongto = 0;
                  outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
                  outs[belongto][numin[belongto]] = scores[j];
                  numin[belongto]++;
            }
      }
      else
      {
            dfromc = AllocateDoubleMtx( nyuko, nin );

            for( i=0; i<nyuko; i++ ) for( j=0; j<nin; j++ )
                  dfromc[i][j] = -0.5;
            for( j=0; j<nin; j++ )
            {
                  dfromc[0][j] = ( scores[j].score );
//                fprintf( stderr, "j=%d, s_p_map[j]=%d\n", j, s_p_map[j] );
            }

            fprintf( stderr, "\n\n%dx%d distance matrix\n", nyuko, nin );

#if 0
            fprintf( stderr, "yukos = \n" );
            for( i=0; i<nyuko; i++ ) fprintf( stderr, "%d ", y_o_map[i] + 1 );
            fprintf( stderr, "\n" );
#endif

            for( i=1; i<nyuko; i++ )
            {
                  fprintf( stderr, "%d / %d \r", i, nyuko );

                  if( doalign )
                  {
                        if( doalign == 'f' )
                        {
                              blastresults = callfasta( seq, scores, nin, NULL, yukos[i], (i==1) );
                        }
                        else
                              gappick0( mseq1[0], seq[scores[yukos[i]].numinseq] );
                  }
                  else
                  {
                        table1 = (short *)calloc( tsize, sizeof( short ) );
                        if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
                        makecompositiontable_p( table1, scores[yukos[i]].pointt );
                  }
            
                  selfscore0 = scores[yukos[i]].selfscore;
                  for( j=0; j<nin; j++ ) 
                  {
                        if( scores[yukos[i]].orilen > scores[j].orilen )
                        {
                              longer = scores[yukos[i]].orilen;
                              shorter = scores[j].orilen;
                        }
                        else
                        {
                              shorter = scores[yukos[i]].orilen;
                              longer = scores[j].orilen;
                        }

#if LENFAC
//                      lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
                        lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
//                      lenfac = 1.0 / ( shorter / longer * LENFACD + LENFACB / ( longer + LENFACC ) + LENFACA );
//                      fprintf( stderr, "lenfac = %f, l=%d, %d\n", lenfac, scores[yukos[i]].orilen, scores[j].orilen );
#else
                        lenfac = 1.0;
#endif
#if 1
                        ii = s_y_map[j]; jj=s_y_map[yukos[i]];
                        if( ii != -1 && jj != -1 )
                        {
                              if( dfromc[ii][yukos[jj]] != -0.5 )
                              {
                                    dfromc[i][j] = dfromc[ii][yukos[jj]];
                              }
                              else
                              {
                                    if( ii > jj )
                                    {
                                          kk = jj;
                                          jj = ii;
                                          ii = kk;
                                    }
                                    dfromc[ii][yukos[jj]] = 
                                    dfromc[i][j] = yukomtx[ii][jj-ii];
                              }
                        }
                        else
#endif
                        {
                              if( doalign )
                              {
                                    if( doalign == 'f' )
                                    {
                                          dfromc[i][j] = 
                                          ( 1.0 - blastresults[j] / MIN( selfscore0, scores[j].selfscore ) ) * 1;
                                    }
                                    else
                                    {
                                          gappick0( mseq2[0], seq[scores[j].numinseq] );
                                          dfromc[i][j] = ( 1.0 - (double)L__align11_noalign( mseq1, mseq2, palloclen, &off1, &off2, (j==0) ) / MIN( selfscore0, scores[j].selfscore ) ) * 1;
                                    }
                              }
                              else
                              {
                                    dfromc[i][j] = ( 1.0 - (double)commonsextet_p( table1, scores[j].pointt ) / MIN( selfscore0, scores[j].selfscore ) ) * lenfac;
                                    if( dfromc[i][j] > MAX6DIST ) dfromc[i][j] = MAX6DIST;
                              }
                        }
//                      fprintf( stderr, "i,j=%d,%d (%d,%d)/ %d,%d, dfromc[][]=%f \n", i, j, scores[yukos[i]].numinseq+1, scores[j].numinseq+1, nyuko, nin, dfromc[i][j] );

//                      if( i == 1 )
//                            fprintf( stdout, "&&& dfromc[%d][%d] (%d,%d) = %f\n", i, j, p_o_map[i], scores[j].numinseq, dfromc[i][j] );
                  }
//                fprintf( stderr, "i=%d, freeing\n", i );
                  if( !doalign ) free( table1 );
                  if( doalign && doalign == 'f' ) free( blastresults );
            }
            fprintf( stderr, "                \r" );




            for( i=0; i<nyuko; i++ ) numin[i] = 0;
//          fprintf( stderr, "### itchi shinai hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d, len=%d,%d, nin=%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore, scores->orilen, scores[nin-1].orilen, nin );
            for( j=0; j<nin; j++ ) 
            {
#if 0
                  belongto = s_y_map[j];
                  {
                        fprintf( stderr, "belongto = %d (%dinori)\n", belongto, y_o_map[belongto]+1 ); 
                  }
                  if( belongto == -1 && closeh[j] != -1 )
#endif
                  if( closeh[j] != -1 )
                  {
                        belongto = s_y_map[closeh[j]];
//                      if( belongto != -1 )
//                            fprintf( stderr, "known, %d(%dinori)->%d(%dinori)\n", j, scores[j].numinseq+1, belongto, y_o_map[belongto]+1 );
                  }
                  else
//                if( belongto == -1 )
                  {
                        belongto = 0;  // default ha horyu
                        minscore = dfromc[0][j];
                        for( i=0; i<nyuko; i++ )
                        {
//                            fprintf( stderr, "checking %d/%d,%d/%d (%d-%d inori) minscore=%f, dfromc[0][j]=%f, dfromc[i][j]=%f\n", i, nyuko, j, nin, y_o_map[i], scores[j].numinseq, minscore, dfromc[0][j], dfromc[i][j] );
                              if( scores[j].shimon == scores[yukos[i]].shimon && !strcmp( seq[scores[j].numinseq], seq[y_o_map[i]] ) ) 
                              {
//                                  fprintf( stderr, "yuko-%d (%d in ori) to score-%d (%d inori) ha kanzen itch\n", i, y_o_map[i], j, scores[j].numinseq );
                                    belongto = i;
                                    break;
                              }
                              if( dfromc[i][j] < minscore )
//                            if( dfromc[i][j] < minscore && minscore-dfromc[i][j] > ( minscoreinpick[yukos[i]] + minscoreinpick[j] ) * 1.0 )
//                            if( rnd() < 0.5 ) // CHUUI !!!!!
                              {
//                                  fprintf( stderr, "yuko-%d (%d in ori) to score-%d (%d inori) ha tikai, %f>%f\n", i, y_o_map[i]+1, j, scores[j].numinseq+1, minscore, dfromc[i][j] );
                                    minscore = dfromc[i][j];
                                    belongto = i;
                              }
                        }
                  }
#if 0
                  if( dfromc[belongto][j] > minscoreinpick[belongto] )
                  {
                        fprintf( stderr, "dame, %f > %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
                        belongto = npick;
                  }
                  else
                        fprintf( stderr, "ok, %f < %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
#endif
//                fprintf( stderr, "j=%d (%d inori) -> %d (%d inori) d=%f\n", j, scores[j].numinseq+1, belongto, y_o_map[belongto]+1, dfromc[belongto][j] );
//                fprintf( stderr, "numin = %d\n", numin[belongto] );
                  outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
                  outs[belongto][numin[belongto]] = scores[j];
                  numin[belongto]++;

            }
            FreeDoubleMtx( dfromc );

//          fprintf( stderr, "##### npick = %d\n", npick );
//          fprintf( stderr, "##### nyuko = %d\n", nyuko );


            if( nyuko > 2 )
            {
                  fprintf( stderr, "upgma       " );
                  veryfastsupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
                  fprintf( stderr, "\r                      \r" );
            }
            else
            {
                  topol[0][0] = (int *)realloc( topol[0][0], 2 * sizeof( int ) );
                  topol[0][1] = (int *)realloc( topol[0][1], 2 * sizeof( int ) );
                  topol[0][0][0] = 0;
                  topol[0][0][1] = -1;
                  topol[0][1][0] = 1;
                  topol[0][1][1] = -1;
            }

#if 0
            ii = nyuko-1;
            fprintf( stderr, "nyuko = %d, topol[][] = \n", nyuko );
            for( j=0; j<nyuko-1; j++ )
            {
                  fprintf( stderr, "STEP%d \n", j );
                  for( i=0; ; i++ )
                  {
                        fprintf( stderr, "%d ", ( topol[j][0][i] )+0 );
                        if( topol[j][0][i] == -1 ) break;
                  }
                  fprintf( stderr, "\n" );
                  for( i=0; ; i++ )
                  {
                        fprintf( stderr, "%d ", ( topol[j][1][i] )+0 );
                        if( topol[j][1][i] == -1 ) break;
                  }
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "\n" );
            }
            exit( 1 );
#endif
            jptr = treeorder; 
            iptr = topol[nyuko-2][0]; while( *iptr != -1 ) *jptr++ = *iptr++;
            iptr = topol[nyuko-2][1]; while( *iptr != -1 ) *jptr++ = *iptr++;
            *jptr++ = -1;
            for( j=0; j<nyuko; j++ )
            {
//                fprintf( stderr, "treeorder[%d] = %d\n", j, treeorder[j] );
                  if( treeorder[j] == -1 ) break;
            }
      }

      aligned = 1;
      for( i=0; i<nyuko; i++ )
      {
            ii = treeorder[i];
#if 0
            if( numin[ii] > 1 )
            {
                  fprintf( stderr, "\ncalling a child, pick%d (%d inori): # of mem=%d\n", i, p_o_map[ii]+1, numin[ii] );
                  for( j=0; j<numin[ii]; j++ )
                  {
                        fprintf( stderr, "%d ", outs[ii][j].numinseq+1 );
                  }
                  fprintf( stderr, "\n" );
            }
#endif
            aligned *= splitseq_mq( outs[ii], numin[ii], nlen, seq, name, inputfile, uniform, children+ii, alloclen, order, whichgroup, weight, depthpt );
      }


      for( i=0; i<nyuko; i++ )
      {
            if( !numin[i] )
            {
                  fprintf( stderr, "i=%d/%d, ERROR!\n", i, nyuko );
                  for( j=0; j<nyuko; j++ )
                        fprintf( stderr, "numin[%d] = %d (rep=%d inori)\n", j, numin[j], y_o_map[j] );
                  exit( 1 );
            }
      }

#if TREE
      if( treeout )
      {
            treelen = 0;
            for( i=0; i<nyuko; i++ )
                  treelen += strlen( children[i] );
            *tree = calloc( treelen + nin * 3, sizeof ( char ) );
      }
#endif


      if( nin >= classsize || !aligned )
            val = 0;
      else
            val = 1;

      if( nyuko > 1 )
      {
            int *mem1p, *mem2p;
            int mem1size, mem2size;
            int v1, v2, v3;
            int nlim;
            int l;
            int *mpt;
            static int *mem1 = NULL;
            static int *mem2 = NULL;
            char **parttree;

#if TREE
            if( treeout )
            {
                  parttree = (char **)calloc( nyuko, sizeof( char * ) );
                  for( i=0; i<nyuko; i++ )
                  {
//                      fprintf( stderr, "allocating parttree, size = %d\n", treelen + nin * 5 );
                        parttree[i] = calloc( treelen + nin * 5, sizeof ( char ) );
                        strcpy( parttree[i], children[i] );
                        free( children[i] );
                  }
                  free( children );
            }
#endif
            if( mem1 == NULL )
            {
                  mem1 = AllocateIntVec( njob+1 );
                  mem2 = AllocateIntVec( njob+1 );
            }

//          veryfastsupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
      
//          counteff_simple_float( nyuko, topol, len, eff );


            nlim = nyuko-1;
            for( l=0; l<nlim; l++ )
            {
                  mem1p = topol[l][0];
                  mptr = mem1;
                  mem1size = 0;
                  while( *mem1p != -1 )
                  {
//                      fprintf( stderr, "*mem1p = %d (%d inori), numin[]=%d\n", *mem1p, p_o_map[*mem1p], numin[*mem1p] );
                        i = numin[*mem1p]; ptr = outs[*(mem1p++)];
                        mem1size += i;
                        while( i-- )
                        {
                              *mptr++ = (ptr++)->numinseq;
                        }
                  }
                  *mptr = -1;

                  mem2p = topol[l][1];
                  mptr = mem2;
                  mem2size = 0;
                  while( *mem2p != -1 )
                  {
//                      fprintf( stderr, "*mem2p = %d (%d inori), numin[]=%d\n", *mem2p, p_o_map[*mem2p], numin[*mem2p] );
                        i = numin[*mem2p]; ptr = outs[*(mem2p++)];
                        mem2size += i;
                        while( i-- )
                        {
                              *mptr++ = (ptr++)->numinseq;
                        }
                  }
                  *mptr = -1;

                  qsort( mem1, mem1size, sizeof( int ), (int (*)())intcompare );
                  qsort( mem2, mem2size, sizeof( int ), (int (*)())intcompare );
//                selhead( mem1, numin[0] );
//                selhead( mem2, numin[1] );


#if 0
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "mem1 (nin=%d) = \n", nin );
                  for( i=0; ; i++ )
                  {
                        fprintf( stderr, "%d ", mem1[i]+1 );
                        if( mem1[i] == -1 ) break;
                  }
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "mem2 (nin=%d) = \n", nin );
                  for( i=0; ; i++ )
                  {
                        fprintf( stderr, "%d ", mem2[i]+1 );
                        if( mem2[i] == -1 ) break;
                  }
                  fprintf( stderr, "\n" );
#endif

#if 0
                  fprintf( stderr, "before pairalign, l = %d, nyuko=%d, mem1size=%d, mem2size=%d\n", l, nyuko, mem1size, mem2size );
                  fprintf( stderr, "before alignment\n" );
                  for( j=0; j<mem1size; j++ )
                        fprintf( stderr, "%s\n", seq[mem1[j]] );
                  fprintf( stderr, "----\n" );
                  for( j=0; j<mem2size; j++ )
                        fprintf( stderr, "%s\n", seq[mem2[j]] );
                  fprintf( stderr, "----\n\n" );
#endif

                  if( val )
                  {
                        fprintf( stderr, "\r  Alignment %d-%d                                 \r", mem1size, mem2size );
                        if( *mem1 < *mem2 )
                              pairalign( njob, nlen, seq, mem1, mem2, weight, alloclen );
                        else
                              pairalign( njob, nlen, seq, mem2, mem1, weight, alloclen );
                  }

#if TREE
                  if( treeout )
                  {
                        v1 = topol[l][0][0];
                        v2 = topol[l][1][0];
      
//                      fprintf( stderr, "nyuko=%d, v1=%d, v2=%d\n", nyuko, v1, v2 );
                        if( v1 > v2 )
                        {
                              v3 = v1;
                              v1 = v2;
                              v2 = v3;
                        }
//                      fprintf( stderr, "nyuko=%d, v1=%d, v2=%d after sort\n", nyuko, v1, v2 );
//                      fprintf( stderr, "nyuko=%d, v1=%d, v2=%d\n", nyuko, v1, v2 );
//                      fprintf( stderr, "v1=%d, v2=%d, parttree[v1]=%s, parttree[v2]=%s\n", v1, v2, parttree[v1], parttree[v2] );
                        sprintf( *tree, "(%s,%s)", parttree[v1], parttree[v2] );
                        strcpy( parttree[v1], *tree );
//                      fprintf( stderr, "parttree[%d] = %s\n", v1, parttree[v1] );
//                      fprintf( stderr, "*tree = %s\n", *tree );
                        free( parttree[v2] ); parttree[v2] = NULL;
                  }
#endif

#if 0
                  fprintf( stderr, "after alignment\n" );
                  for( j=0; j<mem1size; j++ )
                        fprintf( stderr, "%s\n", seq[mem1[j]] );
                  fprintf( stderr, "----\n" );
                  for( j=0; j<mem2size; j++ )
                        fprintf( stderr, "%s\n", seq[mem2[j]] );
                  fprintf( stderr, "----\n\n" );
#endif
            }
#if TREE
            if( treeout )
            {
                  free( parttree[v1] ); parttree[v1] = NULL;
//                fprintf( stderr, "*tree = %s\n", *tree );
//                FreeCharMtx( parttree );
                  free( parttree ); parttree = NULL;
            }
#endif

#if 0
            fprintf( stderr, "after alignment\n" );
            for( i=0; i<nyuko; i++ )
            {
                  for( j=0; j<numin[i]; j++ )
                        fprintf( stderr, "%s\n", seq[outs[i][j].numinseq] );
            }
#endif

            if( val )
            {
                  groupid++;
                  mptr = mem1; while( *mptr != -1 ) 
                  {
#if 0
                        fprintf( stdout, "==g1-%d \n", *mptr+1 );
                        fprintf( stdout, "%s \n", seq[*mptr] );
#endif
                        whichgroup[*mptr] = groupid;
                        weight[*mptr++] *= 0.5;
                  }
      
                  mptr = mem2; while( *mptr != -1 ) 
                  {
#if 0
                        fprintf( stdout, "=g2-%d ", *mptr+1 );
                        fprintf( stdout, "%s \n", seq[*mptr] );
#endif
                        whichgroup[*mptr] = groupid;
                        weight[*mptr++] *= 0.5;
                  }
      
                  if( numin[1] == 0 )
                  {
                        mptr = mem1; while( *mptr != -1 ) 
                        {
                              whichgroup[*mptr] = groupid;
                              weight[*mptr++] *= (double)2.0/numin[0];
                        }
                  }
            }
            {
                  if( *depthpt > maxdepth ) maxdepth = *depthpt;
                  (*depthpt)++;
            }
      }
      else
      {
#if TREE
            if( treeout )
            {
                  sprintf( *tree, "%s", children[0] );
                  free( children[0] );
                  free( children );
            }
#endif
      }
      for( i=0; i<npick; i++ ) free( (void *)outs[i] );
      FreeFloatHalfMtx( pickmtx, npick );
      FreeFloatHalfMtx( yukomtx, npick );
      FreeFloatMtx( len );
      FreeIntCub( topol );
      FreeIntVec( treeorder );
      free( outs );
      free( numin );
      free( picks );
      free( yukos );
      free( s_p_map );
      free( s_y_map );
      free( p_o_map );
      free( y_o_map );
      free( hanni );
      free( closeh );
      free( pickkouho );
      free( tsukau );
//    free( minscoreinpick );
      return val;
}
#endif

static void alignparaphiles( int nseq, int *nlen, double *weight, char **seq, int nmem, int *members, int *alloclen )
{
      int i, j, ilim;
      int *mem1 = AllocateIntVec( nmem );
      int *mem2 = AllocateIntVec( 2 );

      mem2[1] = -1;
      ilim = nmem-1;
      for( i=0; i<ilim; i++ )
      {
            mem1[i] = members[i];
            mem1[i+1] = -1;
            mem2[0] = members[i+1];
            pairalign( nseq, nlen, seq, mem1, mem2, weight, alloclen );
      }
      free( mem1 );
      free( mem2 );
}











int main( int argc, char *argv[] )
{
      static char **name, **seq;
      static int *grpseq;
      static char *tmpseq;
      static int  **pointt;
      static int *nlen;
      int i, j, st, en;
      FILE *prep;
      FILE *infp;
      FILE *treefp;
      char *treefile;
      char c;
      int alloclen;
      static int *order;
      static int *whichgroup;
      static double *weight;
      static char tmpname[B+100];
      int groupnum;
      int groupid;
      int pos;
      int *paramem;
      int npara;
      int completed;
      int orilen;
      int pscore;
      char *pt;
      int **tmpaminodis;
      double *blastresults;
      static char com[1000];
      int depth;
      int aan;

      static Scores *scores;
      static short *table1;
      static char **tree;



      arguments( argc, argv );

      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( tokyoripara == NOTSPECIFIED )
      {
            if( doalign ) tokyoripara = TOKYORIPARA_A;
            else tokyoripara = TOKYORIPARA;
      }

      if( picksize == NOTSPECIFIED || picksize < 2 )
            picksize = PICKSIZE;

      if( classsize == NOTSPECIFIED || classsize < 0 )
      {
            classsize = njob + 1;
      }
      else
      {
//          picksize = MIN( picksize, (int)sqrt( classsize ) + 1);
      }

      alloclen = nlenmax * 2;
      name = AllocateCharMtx( njob, B+1 );

      if( classsize == 1 )
            seq = AllocateCharMtx( njob, 0 );
      else
            seq = AllocateCharMtx( njob, alloclen+1 );

      nlen = AllocateIntVec( njob ); 
      tmpseq = calloc( nlenmax+1, sizeof( char )  );
      pointt = AllocateIntMtx( njob, 0 );
      grpseq = AllocateIntVec( nlenmax + 1 );
      order = (int *)calloc( njob + 1, sizeof( int ) );
      whichgroup = (int *)calloc( njob, sizeof( int ) );
      weight = (double *)calloc( njob, sizeof( double ) );

      fprintf( stderr, "alloclen = %d in main\n", alloclen );

      for( i=0; i<njob; i++ ) whichgroup[i] = 0;
      for( i=0; i<njob; i++ ) weight[i] = 1.0;
      for( i=0; i<njob; i++ ) order[i] = -1;

      if( classsize == 1 )
            readData_realloc( infp, name, nlen, seq );
      else
            readData_pointer( infp, name, nlen, seq );

      fclose( infp );

      constants( njob, seq );

      if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
      else              tsize = (int)pow( 6, 6 );

      if( dorp == 'd' )
      {
            lenfaca = DLENFACA;
            lenfacb = DLENFACB;
            lenfacc = DLENFACC;
            lenfacd = DLENFACD;
      }
      else
      {
            lenfaca = PLENFACA;
            lenfacb = PLENFACB;
            lenfacc = PLENFACC;
            lenfacd = PLENFACD;
      }

      maxl = 0;
      for( i=0; i<njob; i++ ) 
      {
            gappick0( tmpseq, seq[i] );
            nlen[i] = strlen( tmpseq );
            strcpy( seq[i], tmpseq );
            pointt[i] = AllocateIntVec( nlen[i]+1 ); // ??

            if( nlen[i] < 6 )
            {
                  fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
                  fprintf( stderr, "name = %s\n", name[i] );
                  fprintf( stderr, "seq = %s\n", seq[i] );
//                exit( 1 );
                  continue;
            }
            if( nlen[i] > maxl ) maxl = nlen[i];
            if( dorp == 'd' ) /* nuc */
            {
                  if( seq_grp_nuc( grpseq, tmpseq ) < 6 )
                  {
                        fprintf( stderr, "Seq %d, too short.\n", i+1 );
                        fprintf( stderr, "name = %s\n", name[i] );
                        fprintf( stderr, "seq = %s\n", seq[i] );
//                      exit( 1 );
                        continue;
                  }
                  makepointtable_nuc( pointt[i], grpseq );
            }
            else                 /* amino */
            {
                  if( seq_grp( grpseq, tmpseq ) < 6 )
                  {
                        fprintf( stderr, "Seq %d, too short.\n", i+1 );
                        fprintf( stderr, "name = %s\n", name[i] );
                        fprintf( stderr, "seq = %s\n", seq[i] );
//                      exit( 1 );
                        continue;
                  }
                  makepointtable( pointt[i], grpseq );
            }
            fprintf( stdout, ">%s\n", name[i] );
            fprintf( stdout, "%s\n", seq[i] );
      }
      exit( 1 );

#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 );
      }

      pid = (int)getpid();
      sprintf( datafile, "/tmp/data-%d\0", pid );
      sprintf( queryfile, "/tmp/query-%d\0", pid );
      sprintf( resultfile, "/tmp/fasta-%d\0", pid );

      scores = (Scores *)calloc( njob, sizeof( Scores ) );

//    fprintf( stderr, "\nCalculating i-i scores ... \n" );
      for( i=0; i<njob; i++ ) 
      {
            orilen = strlen( seq[i] );
            scores[i].numinseq = i; // irimasu
            scores[i].orilen = orilen;
      }

      if( doalign == 'f' )
      {
            fastapath = getenv( "FASTA_4_MAFFT" );
            if( !fastapath ) fastapath = "fasta34";
            fprintf( stderr, "fastapath=%s\n", fastapath );
            tmpaminodis = AllocateIntMtx( 0x80, 0x80 );
            getfastascoremtx( tmpaminodis );
      }
      else
            tmpaminodis = NULL;
      
      for( i=0; i<njob; i++ )
      {
            scores[i].pointt = pointt[i];
            scores[i].shimon = (int)pointt[i][0] + (int)pointt[i][1] + (int)pointt[i][scores[i].orilen-6];
            scores[i].name = name[i];
            if( doalign )
            {
                  fprintf( stderr, "\r %05d/%05d   ", i, njob );
                  free( scores[i].pointt );
                  if( doalign == 'f' )
                  {
#if 0
#define KIZAMI 100
                        int ipos = (int)( i / KIZAMI ) * KIZAMI;
                        int iposamari = i % KIZAMI;

                        fprintf( stderr, "%d / %d\r", i, njob );
//                      fprintf( stderr, "ipos = %d\n", ipos );
//                      fprintf( stderr, "iposamari = %d\n", iposamari );

//                      fprintf( stderr, " calling blast, i=%d\n", i );
//                      blastresults = callfasta( seq, scores+i, 1, 0, 1 );
                        blastresults = callfasta( seq, scores+ipos, MIN(KIZAMI,njob-ipos), NULL, iposamari, (iposamari==0)  );
//                      fprintf( stderr, "done., i=%d\n\n", i );
                        scores[i].selfscore = (int)blastresults[iposamari]; 
#if 0
                        for( j=0; j<100; j++ )
                        {
                              fprintf( stderr, "res[%d] = %f\n", j, blastresults[j] );
                        }
#endif
//                      fprintf( stderr, "%d->selfscore = %d\n", i, scores[i].selfscore );
                        free( blastresults );
#else
                        pscore = 0;
                        if( scoremtx == -1 )
                        {
                              st = 1;
                              en = 0;
                              for( pt=seq[i]; *pt; pt++ )
                              {
                                    if( *pt == 'u' ) *pt = 't';
                                    aan = amino_n[*pt];
                                    if( aan<0 || aan >= 4 ) *pt = 'n';

                                    if( *pt == 'n' ) 
                                    {
                                          en++;
                                          if( st ) continue;
                                          else pscore += tmpaminodis[(int)*pt][(int)*pt];
                                    }
                                    else
                                    {
                                          st = 0;
                                          en = 0;
                                          pscore += tmpaminodis[(int)*pt][(int)*pt];
                                    }
                              }
                              scores[i].selfscore = pscore - en * tmpaminodis['n']['n']; 
                        }
                        else
                        {
                              st = 1;
                              en = 0;
                              for( pt=seq[i]; *pt; pt++ )
                              {
                                    aan = amino_n[*pt];
                                    if( aan<0 || aan >= 20 ) *pt = 'X';
                                    if( *pt == 'X' ) 
                                    {
                                          en++;
                                          if( st ) continue;
                                          else pscore += tmpaminodis[(int)*pt][(int)*pt];
                                    }
                                    else
                                    {
                                          st = 0;
                                          en = 0;
                                          pscore += tmpaminodis[(int)*pt][(int)*pt];
                                    }
                              }
                              scores[i].selfscore = pscore - en * tmpaminodis['X']['X']; 
                        }
#endif
                  }
                  else
                  {
                        pscore = 0;
                        for( pt=seq[i]; *pt; pt++ )
                        {
                              pscore += amino_dis[(int)*pt][(int)*pt];
                        }
                        scores[i].selfscore = pscore; 
                  }
//                fprintf( stderr, "selfscore[%d] = %d\n", i+1, scores[i].selfscore );
            }
            else
            {
                  table1 = (short *)calloc( tsize, sizeof( short ) );
                  if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
                  makecompositiontable_p( table1, pointt[i] );
                  scores[i].selfscore = commonsextet_p( table1, pointt[i] );
                  free( table1 );
            }
      }
      if( tmpaminodis ) FreeIntMtx( tmpaminodis );

      depth = 0;
#if TREE
      if( treeout )
      {
            tree = (char **)calloc( 1, sizeof( char *) );
            *tree = NULL;
//          splitseq_bin( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight );
            completed = splitseq_mq( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth );
            treefile = (char *)calloc( strlen( inputfile ) + 10, sizeof( char ) );
            if( inputfile )
                  sprintf( treefile, "%s.tree", inputfile );
            else
                  sprintf( treefile, "splittbfast.tree" );
            treefp = fopen( treefile, "w" );
            fprintf( treefp, "%s\n", *tree );
            fclose( treefp );
      }
      else
            completed = splitseq_mq( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth );
#else
      completed = splitseq_mq( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth );
#endif

      fprintf( stderr, "\nDone.\n\n" );

#if 1
      groupnum = 0;
      groupid = -1;
      paramem = NULL;
      npara = 0;
      for( i=0; i<njob; i++ )
      {
            pos = order[i];
            if( whichgroup[pos] != groupid )
            {
                  groupnum++;
                  groupid = whichgroup[pos];
            }
            if( whichgroup[pos] )
            {
                  if( paramem )
                  {
                        paramem[npara] = -1;
                        if( npara > 1 && classsize > 2 ) 
                        {
                              qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
//                            selhead( paramem, npara );
                              alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
                        }
                        free( paramem ); paramem = NULL; npara = 0;
                  }
                  sprintf( tmpname, "Group-%d %s", groupnum, name[pos]+1 );
            }
            else
            {
                  paramem = realloc( paramem, sizeof( int) * ( npara + 2 ) );
                  paramem[npara++] = pos;
                  sprintf( tmpname, "Group-para %s", name[pos]+1 );
            }
            tmpname[B-1] = 0;
            strcpy( name[pos]+1, tmpname );
      }
      if( paramem )
      {
            paramem[npara] = -1;
            if( npara > 1 && classsize > 2 ) 
            {
                  qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
//                selhead( paramem, npara );
                  alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
            }
            free( paramem ); paramem = NULL; npara = 0;
      }
#else
      for( i=0; i<njob; i++ )
      {
            sprintf( tmpname, "Group-%d %s", whichgroup[i], name[i]+1 );
            strcpy( name[i]+1, tmpname );
      }
#endif


//    maketanni( name, seq,  njob, nlenmax, nlen );

      fclose( trap_g );

#if DEBUG
      fprintf( stderr, "writing alignment to stdout\n" );
#endif
      if( reorder )
            writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
      else
            writeData_pointer( stdout, njob, name, nlen, seq );
#if IODEBUG
      fprintf( stderr, "OSHIMAI\n" );
#endif
      if( classsize == 1 )
      {
            fprintf( stderr, "\n\n", njob );
            fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
            fprintf( stderr, "\n", njob );
            fprintf( stderr, "nseq = %d\n", njob );
            fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
            fprintf( stderr, "The input sequences have been sorted so that similar sequences are close.\n" );
            if( reorder )
                  fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
#if TREE
            if( treeout )
            {
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
            }
//          else
//          {
//                fprintf( stderr, "To output guide tree,\n" );
//                fprintf( stderr, "%% %s -t  -i %s\n", progName( argv[0] ), "inputfile" );
//          }
#endif
            if( !doalign )
            {
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
                  fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
            }
            fprintf( stderr, "\n" );
            fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
      }
      else if( groupnum > 1 )
      {
            fprintf( stderr, "\n\n" );
            fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
            fprintf( stderr, "\n" );
            fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
            fprintf( stderr, "The input sequences have been classified into %d groups + some paraphyletic groups\n", groupnum );
            fprintf( stderr, "Note that the alignment is not completed.\n" );
            if( reorder )
                  fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
#if TREE
            if( treeout )
            {
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
            }
//          else
//          {
//                fprintf( stderr, "To output guide tree,\n" );
//                fprintf( stderr, "%% %s -t  -i %s\n", progName( argv[0] ), "inputfile" );
//          }
#endif
            if( !doalign )
            {
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
                  fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
            }
            fprintf( stderr, "\n" );
            fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
      }                 
      else
      {
            fprintf( stderr, "\n\n" );
            fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
            fprintf( stderr, "\n", njob );
            fprintf( stderr, "nseq = %d\n", njob );
            fprintf( stderr, "groupsize = %d, partsize=%d\n", classsize, picksize );
//          fprintf( stderr, "A single alignment containing all the input sequences has been computed.\n" );
//          fprintf( stderr, "If the sequences are highly diverged and you feel there are too many gaps,\n" );
//          fprintf( stderr, "please try \n" );
//          fprintf( stderr, "%% mafft --parttree --groupsize 100 inputfile\n" );
//          fprintf( stderr, "which classifies the sequences into several groups with <~ 100 sequences\n" );
//          fprintf( stderr, "and performs only intra-group alignments.\n" );
            if( reorder )
                  fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
#if TREE
            if( treeout )
            {
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
            }
//          else
//          {
//                fprintf( stderr, "To output guide tree,\n" );
//                fprintf( stderr, "%% %s -t  -i %s\n", progName( argv[0] ), "inputfile" );
//          }
#endif
            if( !doalign )
            {
                  fprintf( stderr, "\n" );
                  fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
                  fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
            }
            fprintf( stderr, "\n" );
            fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
      }
#if TREE
      if( treeout ) free( treefile );
#endif

#if 0
      fprintf( stdout, "weight =\n" );
      for( i=0; i<njob; i++ )
            fprintf( stdout, "%d: %f\n", i+1, weight[i] );
#endif

      if( doalign == 'f' )
      {
            strcpy( com, "rm -f" );
            strcat( com, " " );
            strcat( com, datafile );
            strcat( com, "*  " );
            strcat( com, queryfile );
            strcat( com, " " );
            strcat( com, resultfile );
            fprintf( stderr, "%s\n", com );
            system( com );
      }

      SHOWVERSION;

      return( 0 );
}

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