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setcore.c

#include "mltaln.h"

#define DEBUG 0
#define IODEBUG 0
#define SCOREOUT 1

double corethr;
int coreext;

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

      fftkeika = 1;
      constraint = 0;
      nblosum = 62;
      fmodel = 0;
      calledByXced = 0;
      devide = 0;
      use_fft = 0;
      fftscore = 1;
      fftRepeatStop = 0;
      fftNoAnchStop = 0;
    weight = 3;
    utree = 1;
      tbutree = 1;
    refine = 0;
    check = 1;
    cut = 0.0;
    disp = 0;
    outgap = 1;
    alg = 'A';
    mix = 0;
      tbitr = 0;
      scmtd = 5;
      tbweight = 0;
      tbrweight = 3;
      checkC = 0;
      treemethod = 'x';
      contin = 0;
      scoremtx = 0;
      kobetsubunkatsu = 0;
      dorp = NOTSPECIFIED;
      ppenalty = NOTSPECIFIED;
      ppenalty_ex = NOTSPECIFIED;
      poffset = NOTSPECIFIED;
      kimuraR = NOTSPECIFIED;
      pamN = NOTSPECIFIED;
      geta2 = GETA2;
      fftWinSize = NOTSPECIFIED;
      fftThreshold = NOTSPECIFIED;
      corethr = .5;
      coreext = 0;

    while( --argc > 0 && (*++argv)[0] == '-' )
      {
        while ( c = *++argv[0] )
            {
            switch( c )
            {
                        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;
                              fprintf( stderr, "jtt %d\n", pamN );
                              --argc;
                              goto nextoption;
                        case 'l':
                              fastathreshold = atof( *++argv );
                              constraint = 2;
                              fprintf( stderr, "weighti = %f\n", fastathreshold );
                              --argc;
                              goto nextoption;
                        case 'i':
                              corethr = atof( *++argv );
                              fprintf( stderr, "corethr = %f\n", corethr );
                              --argc;
                              goto nextoption;
                        case 'm':
                              fmodel = 1;
                              break;
                        case 'c':
                              coreext = 1;
                              break;
                        case 'r':
                              fmodel = -1;
                              break;
                        case 'D':
                              dorp = 'd';
                              break;
                        case 'P':
                              dorp = 'p';
                              break;
                        case 'e':
                              fftscore = 0;
                              break;
                        case 'O':
                              fftNoAnchStop = 1;
                              break;
                        case 'R':
                              fftRepeatStop = 1;
                              break;
                        case 'Q':
                              calledByXced = 1;
                              break;
                        case 's':
                              treemethod = 's';
                              break;
                        case 'x':
                              treemethod = 'x';
                              break;
                        case 'p':
                              treemethod = 'p';
                              break;
                        case 'a':
                              alg = 'a';
                              break;
                        case 'A':
                              alg = 'A';
                              break;
                        case 'S':
                              alg = 'S';
                              break;
                        case 'C':
                              alg = 'C';
                              break;
                        case 'F':
                              use_fft = 1;
                              break;
                        case 'v':
                              tbrweight = 3;
                              break;
                        case 'd':
                              disp = 1;
                              break;
                        case 'o':
                              outgap = 0;
                              break;
/* Modified 01/08/27, default: user tree */
                        case 'J':
                              tbutree = 0;
                              break;
/* modification end. */
                        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 void WriteOptions( FILE *fp )
{

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

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

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

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

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

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

int main( int argc, char *argv[] )
{
      static int  nlen[M];    
      static char name[M][B], **seq;
      static char **oseq;
      static double **pscore;
      static double *eff;
      static double **node0, **node1;
      static double *gapc;
      static double *avgap;
      double tmpavgap;
      int i, j, m, goffset;
      int identity;
      static int ***topol;
      static double **len;
      FILE *prep;
      char c;
      int corestart, coreend;
      int alloclen;
      double total;
      int winsize;
      char *pt, *ot, *stpt;
      double gapmin;
      LocalHom **localhomtable;

      arguments( argc, argv );

      getnumlen( stdin );
      rewind( stdin );

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

      seq = AllocateCharMtx( njob, nlenmax*9+1 );
      oseq = AllocateCharMtx( njob, nlenmax*9+1 );
      alloclen = nlenmax*9;

      topol = AllocateIntCub( njob, 2, njob );
      len = AllocateDoubleMtx( njob, 2 );
      pscore = AllocateDoubleMtx( njob, njob );
      eff = AllocateDoubleVec( njob );
      node0 = AllocateDoubleMtx( njob, njob );
      node1 = AllocateDoubleMtx( njob, njob );
      gapc = AllocateDoubleVec( alloclen );
      avgap = AllocateDoubleVec( alloclen );

#if 0
      Read( name, nlen, seq );
#else
      readData( stdin, name, nlen, seq );
#endif

      constants( njob, seq );

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

      initSignalSM();

      initFiles();

      WriteOptions( trap_g );

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

      writePre( njob, name, nlen, seq, 0 );

      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] = (double)substitution_hosei( seq[i], seq[j] );
            }
      }
      else
      {
            fprintf( stderr, "Loading 'hat2' ... " );
            prep = fopen( "hat2", "r" );
            if( prep == NULL ) ErrorExit( "Make hat2." );
            readhat2( prep, njob, name, pscore );
            fclose( prep );
            fprintf( stderr, "done.\n" );

#if 0
            prep = fopen( "hat2_check", "w" );
            WriteHat2( prep, njob, name, pscore );
            fclose( prep );
#endif

      }

      fprintf( stderr, "Constructing dendrogram ... " );
      if( treemethod == 'x' )
            supg( njob, pscore, topol, len );
      else if( treemethod == 's' )
            spg( njob, pscore, topol, len );
      else if( treemethod == 'p' )
            upg2( njob, pscore, topol, len );
      else 
            ErrorExit( "Incorrect tree\n" );
      fprintf( stderr, "done.\n" );

      countnode( njob, topol, node0 );
      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<nlenmax; i++ )
      {
            gapc[i] = 0.0;
            for( j=0; j<njob; j++ )
            {
                  if( seq[j][i] == '-' ) gapc[i] += eff[j];
            }
      }

      gapmin = 1.0;
      winsize = fftWinSize;
      goffset = winsize/2;
      tmpavgap = 0.0;
      corestart = coreend = -1;
      for( i=0; i<winsize; i++ )
      {
            tmpavgap += gapc[i];
      }
      for( i=winsize; i<nlenmax; i++ )
      {
            m = i - goffset;
            avgap[m] = tmpavgap / winsize;
//          fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
            if( avgap[m] < corethr )
            {
                  if( corestart == -1 )
                        corestart = i - winsize;
//                fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
                  if( avgap[m] < gapmin )
                  { 
                        gapmin = avgap[m];
                  }
                  coreend = i;
            }
            tmpavgap -= gapc[i-winsize];
            tmpavgap += gapc[i];
      }
      if( corestart == -1 || coreend == -1 )
      {
            corestart = 0;
            coreend = nlenmax-1;
      }

      for( i=0; i<njob; i++ )
      {
            pt = oseq[i];
            m = winsize;
            while( m-- ) *pt++ = '-';
            for( j=corestart; j<=coreend; j++ )
                  *pt++ = seq[i][j];
            m = winsize;
            while( m-- ) *pt++ = '-';
            *pt = 0;

            ot = oseq[i]+winsize-1;
            pt = seq[i]+corestart-1;
            if( coreext ) m = winsize;
            else m = 0;
            while( m && --pt > seq[i] )
                  if( *pt != '-' )
                  {
                        *ot-- = *pt;
                        m--;
                  }

            ot = oseq[i]+winsize+coreend-corestart+1;
            pt = seq[i]+coreend;
            if( coreext ) m = winsize;
            else m = 0;
            while( m && *(++pt) )
            {
                  if( *pt != '-' ) 
                  {
                        *ot++ = *pt;
                        m--;
                  }
            }
            fprintf( stdout, ">%s\n", name[i] );
            fprintf( stdout, "%s\n", oseq[i] );
      }

      exit( 1 );

      SHOWVERSION;
      return( 0 );
}

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