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getlag.c

#include "mltaln.h"

#define DEBUG 0
#define IODEBUG 0

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

      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 = 'C';
    mix = 0;
      tbitr = 0;
      scmtd = 5;
      tbweight = 0;
      tbrweight = 3;
      checkC = 0;
      treemethod = 'x';
      contin = 0;
      ppenalty = NOTSPECIFIED;
      ppenalty_ex = NOTSPECIFIED;
      poffset = NOTSPECIFIED;
      kimuraR = NOTSPECIFIED;
      pamN = NOTSPECIFIED;
      geta2 = GETA2;
      scoremtx = NOTSPECIFIED;

    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 'D':
                              scoremtx = -1;
                              break;
                        case 'P':
                              scoremtx = 0;
                              break;
                        case 'i':
                              contin = 1;
                              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':
                              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 );
      }
      readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
}


void treebase( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
{
      int i, j, l;
      int clus1, clus2;
      int s1, s2, r1, r2;
      float pscore;
      static char *indication1, *indication2;
      FILE *trap;
      static char name1[M][B], name2[M][B];
      static double **partialmtx = NULL;
      static int ***partialtopol = NULL;
      static double **partiallen = NULL;
      static double **partialeff = NULL;
      static double *effarr = NULL;
      static double *effarr1 = NULL;
      static double *effarr2 = NULL;
#if 0
      char pair[njob][njob];
#else
      static char **pair;
#endif
      if( partialtopol == NULL ) 
      {
            partialmtx = AllocateDoubleMtx( njob, njob );
            partialtopol = AllocateIntCub( njob, 2, njob );
            partialeff = AllocateDoubleMtx( njob, njob );
            partiallen = AllocateDoubleMtx( njob, 2 );
            effarr = AllocateDoubleVec( njob );
            effarr1 = AllocateDoubleVec( njob );
            effarr2 = AllocateDoubleVec( njob );
            indication1 = AllocateCharVec( njob*3+100 );
            indication2 = AllocateCharVec( njob*3+100 );
#if 0
#else
            pair = AllocateCharMtx( njob, njob );
#endif
      }

      if( checkC )
            for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );

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

      if( checkC )
            for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );

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

      for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
      for( i=0; i<njob; i++ ) pair[i][i] = 1;
      for( l=0; l<njob-1; l++ )
      {
            s1 = topol[l][0][0];
            for( i=0; (r1=topol[l][0][i])>-1; i++ ) 
                  if( pair[s1][r1] != 1 ) exit( 1 );
            s2 = topol[l][1][0];
            for( i=0; (r2=topol[l][1][i])>-1; i++ ) 
                  if( pair[s2][r2] != 1 ) exit( 1 );

            clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
            clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
            fprintf( trap_g, "\nSTEP-%d\n", l );
            fprintf( trap_g, "group1 = %s\n", indication1 );
            fprintf( trap_g, "group2 = %s\n", indication2 );

            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" );

            if( checkC )
                  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" );
*/

            pscore = Fgetlag( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );

            for( i=0; (r2=topol[l][1][i])>-1; i++ ) 
            {
                  pair[s1][r2] = 1;
                  pair[s2][r2] = 0;
            }

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

            if( disp ) display( aseq, njob );
            fprintf( stderr, "\n" );

      }
}

static void WriteOptions( FILE *fp )
{
      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" );
      }
      if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
      else if( scoremtx ==  1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
      else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
      else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );

    if( scoremtx == 0 || scoremtx == -1 )
        fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
    else
        fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );

      if( alg == 'a' )
            fprintf( fp, "Algorithm A\n" );
      else if( alg == 'A' ) 
            fprintf( fp, "Apgorithm 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( scoremtx == -1 )
            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 **mseq1, **mseq2;
      static char **aseq;
      static char **bseq;
      static double **pscore;
      static double **eff;
      static double **node0, **node1;
      int i, j;
      int identity;
      static int ***topol;
      static double **len;
      FILE *prep;
      char c;
      int alloclen;

      arguments( argc, argv );
      getnumlen( stdin );
      rewind( stdin );

      seq = AllocateCharMtx( njob, nlenmax*5+1 );
      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 = AllocateDoubleMtx( njob, njob );
      eff = AllocateDoubleMtx( njob, njob );
      node0 = AllocateDoubleMtx( njob, njob );
      node1 = AllocateDoubleMtx( njob, njob );

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


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

      treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );

      fprintf( trap_g, "done\n" );
      fclose( trap_g );

      writePre( njob, name, nlen, aseq, !contin );
      writeData( stdout, njob, name, nlen, aseq );
#if IODEBUG
      fprintf( stderr, "OSHIMAI\n" );
#endif
      SHOWVERSION;
      return( 0 );
}

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