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disttbfast_dummy.c

#include "mltaln.h"

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

#define END_OF_VEC -1


void arguments()
{
    int c;

      inputfile = NULL;
      fftkeika = 0;
      constraint = 0;
      nblosum = 62;
      fmodel = 0;
      calledByXced = 0;
      devide = 0;
      use_fft = 1;
      fftscore = 1;
      fftRepeatStop = 0;
      fftNoAnchStop = 0;
    weight = 3;
    utree = 1;
      tbutree = 1;
    refine = 0;
    check = 1;
    cut = 0.0;
    disp = 0;
    outgap = 1;
    alg = 'M';
    mix = 0;
      tbitr = 0;
      scmtd = 5;
      tbweight = 0;
      tbrweight = 3;
      checkC = 0;
      treemethod = 'x';
      contin = 0;
      kobetsubunkatsu = 0;
      makedistmtx = 1;
      ppenalty = -1530;
      ppenalty_ex = NOTSPECIFIED;
      poffset = -123;
      kimuraR = NOTSPECIFIED;
      pamN = NOTSPECIFIED;
      geta2 = GETA2;
      fftWinSize = NOTSPECIFIED;
      fftThreshold = NOTSPECIFIED;
      TMorJTT = JTT;
}

static int maxl;
static int tsize;

void seq_grp_nuc( int *grp, char *seq )
{
      int tmp;
      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;
}

void seq_grp( int *grp, char *seq )
{
      int tmp;
      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;
}

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 = calloc( tsize, sizeof( short ) );
            if( !memo ) ErrorExit( "Cannot allocate memo\n" );
            ct = 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;
}

void treebase( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double *effarr, int alloclen )
{
      int i, j, l;
      int clus1, clus2;
      int s1, s2, r1, r2;
      float pscore, tscore;
      static char *indication1, *indication2;
      FILE *trap;
      static char name1[M][B], name2[M][B];
      static double *effarr1 = NULL;
      static double *effarr2 = NULL;
      float dumfl = 0.0;
      double total;
      int intdum;


      if( effarr1 == NULL ) 
      {
            effarr1 = AllocateDoubleVec( njob );
            effarr2 = AllocateDoubleVec( njob );
            indication1 = AllocateCharVec( 150 );
            indication2 = AllocateCharVec( 150 );
      }

#if 0
      fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
#endif

#if 0
      for( i=0; i<njob; i++ )
            fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
#endif

      for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );



//    writePre( njob, name, nlen, aseq, 0 );

      tscore = 0.0;
      for( l=0; l<njob-1; l++ )
      {

            clus1 = fastconjuction( topol[l][0], aseq, mseq1, effarr1, effarr, name, name1, indication1 );
            clus2 = fastconjuction( topol[l][1], aseq, mseq2, effarr2, effarr, name, name2, indication2 );


            fprintf( stderr, "STEP %d /%d\r", l+1, njob-1 );
//          fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
//          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" );
//          for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );

/*
            fprintf( stderr, "before align all\n" );
            display( aseq, njob );
            fprintf( stderr, "\n" );
            fprintf( stderr, "before align 1 %s \n", indication1 );
            display( mseq1, clus1 );
            fprintf( stderr, "\n" );
            fprintf( stderr, "before align 2 %s \n", indication2 );
            display( mseq2, clus2 );
            fprintf( stderr, "\n" );
*/

            if( use_fft )
            {
                  if( alg == 'M' )
                        pscore = Falign_noudp( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
                  else
                        pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
            }
            else
            {
                  switch( alg )
                  {
                        case( 'a' ):
                              pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
                              break;
                        case( 'M' ):
                              pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
                              break;
                        case( 'A' ):
                              if( clus1 == 1 && clus2 == 1 )
                              {
                                    pscore = G__align11( mseq1, mseq2, alloclen );
                              }
                              else
                              {
                                    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
            tscore += pscore;
/*
            fprintf( stderr, "after align 1 %s \n", indication1 );
            display( mseq1, clus1 );
            fprintf( stderr, "\n" );
            fprintf( stderr, "after align 2 %s \n", indication2 );
            display( mseq2, clus2 );
            fprintf( stderr, "\n" );
*/

//          writePre( njob, name, nlen, aseq, 0 );

            if( disp ) display( aseq, njob );
//          fprintf( stderr, "\n" );
      }
#if SCOREOUT
      fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
#endif
}

static void WriteOptions( FILE *fp )
{

      if( dorp == 'd' ) fprintf( fp, "DNA\n" );
      else
      {
            if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
            else if( scoremtx ==  1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
            else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
      }
    fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
    if( use_fft ) fprintf( fp, "FFT on\n" );

      fprintf( fp, "tree-base method\n" );
      if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
      else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
      if( tbitr || tbweight ) 
      {
            fprintf( fp, "iterate at each step\n" );
            if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" ); 
            if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" ); 
            if( tbweight ) fprintf( fp, "  weighted\n" ); 
            fprintf( fp, "\n" );
      }

       fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );

      if( alg == 'a' )
            fprintf( fp, "Algorithm A\n" );
      else if( alg == 'A' ) 
            fprintf( fp, "Algorithm A+\n" );
      else if( alg == 'S' ) 
            fprintf( fp, "Apgorithm S\n" );
      else if( alg == 'C' ) 
            fprintf( fp, "Apgorithm A+/C\n" );
      else
            fprintf( fp, "Unknown algorithm\n" );

      if( treemethod == 'x' )
            fprintf( fp, "Tree = UPGMA (3).\n" );
      else if( treemethod == 's' )
            fprintf( fp, "Tree = UPGMA (2).\n" );
      else if( treemethod == 'p' )
            fprintf( fp, "Tree = UPGMA (1).\n" );
      else
            fprintf( fp, "Unknown tree.\n" );

    if( use_fft )
    {
        fprintf( fp, "FFT on\n" );
        if( dorp == 'd' )
            fprintf( fp, "Basis : 4 nucleotides\n" );
        else
        {
            if( fftscore )
                fprintf( fp, "Basis : Polarity and Volume\n" );
            else
                fprintf( fp, "Basis : 20 amino acids\n" );
        }
        fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
        fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
    }
      else
        fprintf( fp, "FFT off\n" );
      fflush( fp );
}
       

int disttbfast( char **in, int nlen[M], char name[M][B] )
{
      static char **seq;
      static char **mseq1, **mseq2;
      static char **aseq;
      static char **bseq;
      static int **pscore;
      static double *eff;
      int i, j;
      int identity;
      static int ***topol;
      static double **len;
      FILE *prep;
      FILE *infp;
      char c;
      int alloclen;
      double total;

      FILE *fp;
      FILE *orderfp;
      int *grpseq;
      char *tmpseq;
      int  **pointt;
      double **mtx;
      double **mtx2; 
      int score0; 
      static short *table1;
      char b[B];

      arguments();

      if( njob < 2 )
      {
            fprintf( stderr, "At least 2 sequences should be input!\n"
                                     "Only %d sequence found.\n", njob ); 
            exit( 1 );
      }

      seq = in;
      aseq = AllocateCharMtx( njob, nlenmax*5+1 );
      bseq = AllocateCharMtx( njob, nlenmax*5+1 );
      mseq1 = AllocateCharMtx( njob, 0 );
      mseq2 = AllocateCharMtx( njob, 0 );
      alloclen = nlenmax*5;

      topol = AllocateIntCub( njob, 2, njob );
      len = AllocateDoubleMtx( njob, 2 );
      pscore = AllocateIntMtx( njob, njob );
      eff = AllocateDoubleVec( njob );



      constants( njob, seq );


#if 0
      fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
#endif

      initSignalSM();

      initFiles();


      c = seqcheck( seq );
      if( c )
      {
            fprintf( stderr, "Illeagal character %c\n", c );
            exit( 1 );
      }

      fprintf( stderr, "\n" );

//    writePre( njob, name, nlen, seq, 0 );
      if( makedistmtx )
      {
            fprintf( stderr, "Making a distance matrix ..\n" );

          tmpseq = AllocateCharVec( nlenmax+1 );
            grpseq = AllocateIntVec( nlenmax+1 );
            pointt = AllocateIntMtx( njob, nlenmax+1 );
      mtx = AllocateDoubleMtx( njob, njob ); 
            if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
            else              tsize = (int)pow( 6, 6 );

            maxl = 0;
            for( i=0; i<njob; i++ ) 
            {
                  gappick0( tmpseq, seq[i] );
                  nlen[i] = strlen( tmpseq );
                  if( nlen[i] < 6 )
                  {
                        fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
                        exit( 1 );
                  }
                  if( nlen[i] > maxl ) maxl = nlen[i];
                  if( dorp == 'd' ) /* nuc */
                  {
                        seq_grp_nuc( grpseq, tmpseq );
                        makepointtable_nuc( pointt[i], grpseq );
                  }
                  else                 /* amino */
                  {
                        seq_grp( grpseq, tmpseq );
                        makepointtable( pointt[i], grpseq );
                  }
            }
            for( i=0; i<njob; i++ )
            {
                  table1 = calloc( tsize, sizeof( short ) );
                  if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
                  if( i % 10 == 0 )
                  {
                        fprintf( stderr, "%#4d / %#4d\r", i+1, njob );
                  }
                  makecompositiontable_p( table1, pointt[i] );
      
                  for( j=i; j<njob; j++ ) 
                  {
                        mtx[i][j] = commonsextet_p( table1, pointt[j] );
                  } 
                  free( table1 );
            }
            for( i=0; i<njob; i++ )
            {
                  score0 = mtx[i][i];
                  for( j=0; j<njob; j++ ) 
                        pscore[i][j] = (int)( ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3 * INTMTXSCALE + 0.5 );
            }
            for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) 
            {
                  pscore[i][j] = MIN( pscore[i][j], pscore[j][i] );
            }
      
            if( disopt )
            {
                  for( i=0; i<njob; i++ ) 
                  {
                        sprintf( b, "=lgth = %#04d", nlen[i] );
                        strins( b, name[i] );
                  }
            }
            FreeDoubleMtx( mtx );
            free( tmpseq );
            free( grpseq );
            FreeIntMtx( pointt );
            fprintf( stderr, "\ndone.\n\n" );
      }
      else if( tbutree == 0 )
      {
            for( i=1; i<njob; i++ ) 
            {
                  if( nlen[i] != nlen[0] ) 
                  {
                        fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
                        exit( 1 );
                  }
            }
            for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) 
            {
            /*
                  pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
            */
                  pscore[i][j] = (int)( substitution_hosei( seq[i], seq[j] ) * INTMTXSCALE + 0.5 );
            }
      }
      else
      {
#if 1
            fprintf( stderr, "Loading 'hat2' ... " );
            prep = fopen( "hat2", "r" );
            if( prep == NULL ) ErrorExit( "Make hat2." );
            readhat2_int( prep, njob, name, pscore );
            fclose( prep );
            fprintf( stderr, "done.\n" );
#endif
      }
#if 0
            prep = fopen( "hat2_check", "w" );
            WriteHat2_int( prep, njob, name, pscore );
            fclose( prep );
#endif

      fprintf( stderr, "Constructing dendrogram ... " );
      if( treemethod == 'x' )
      {
            veryfastsupg_int( njob, pscore, topol, len );
      }
      else 
            ErrorExit( "Incorrect tree\n" );
      fprintf( stderr, "\ndone.\n\n" );

      orderfp = fopen( "order", "w" );
      if( !orderfp )
      {
            fprintf( stderr, "Cannot open 'order'\n" );
            exit( 1 );
      }
      for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
      {
            fprintf( orderfp, "%d\n", j );
      }
      for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
      {
            fprintf( orderfp, "%d\n", j );
      }
      fclose( orderfp );
      

      for( i=0; i<njob; i++ )
      {
            len[i][0] /= INTMTXSCALE;
            len[i][1] /= INTMTXSCALE;
      }

      if( tbrweight )
      {
            weight = 3; 
#if 0
            utree = 0; counteff( njob, topol, len, eff ); utree = 1;
#else
            counteff_simple( njob, topol, len, eff );
#endif
      }
      else
      {
            for( i=0; i<njob; i++ ) eff[i] = 1.0;
      }


      for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );

      FreeIntMtx( pscore );
      FreeDoubleMtx( len );
      fprintf( stderr, "Progressive alignment ... \n" );
      treebase( name, nlen, bseq, aseq, mseq1, mseq2, topol, eff, alloclen );
      fprintf( stderr, "\ndone.\n\n" );

#if DEBUG
      fprintf( stderr, "writing alignment to stdout\n" );
#endif


      for( i=0; i<njob; i++ ) strcpy( seq[i], aseq[i] );

      fprintf( stderr, "mafft v%s\n", VERSION );
      return( 0 );
}

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