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SAalignmm.c

#include "mltaln.h"
#include "dp.h"

#define DEBUG 0

static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
{
      int j, k, l;
      float scarr[26];
      float **cpmxpd = floatwork;
      int **cpmxpdn = intwork;
      int count = 0;

      if( initialize )
      {
            for( j=0; j<lgth2; j++ )
            {
                  count = 0;
                  for( l=0; l<26; l++ )
                  {
                        if( cpmx2[l][j] )
                        {
                              cpmxpd[count][j] = cpmx2[l][j];
                              cpmxpdn[count][j] = l;
                              count++;
                        }
                  }
                  cpmxpdn[count][j] = -1;
            }
      }

      for( l=0; l<26; l++ )
      {
            scarr[l] = 0.0;
            for( k=0; k<26; k++ )
                  scarr[l] += n_dis[k][l] * cpmx1[k][i1];
      }
      for( j=0; j<lgth2; j++ )
      {
            match[j] = 0;
            for( k=0; cpmxpdn[k][j] > -1;  k++ )
                  match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
      } 
}

static float Atracking( float *lasthorizontalw, float *lastverticalw, 
                                    char **seq1, char **seq2, 
                        char **mseq1, char **mseq2, 
                        float **cpmx1, float **cpmx2, 
                        short **ijp, int icyc, int jcyc )
{
      int i, j, k, l, iin, jin, ifi, jfi, lgth1, lgth2;
      char gap[] = "-";
      float wm;
      lgth1 = strlen( seq1[0] );
      lgth2 = strlen( seq2[0] );

#if DEBUG
      for( i=0; i<lgth1; i++ ) 
      {
            fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
      }
#endif
 
      if( outgap == 1 )
            ;
      else
      {
            wm = lastverticalw[0];
            for( i=0; i<lgth1; i++ )
            {
                  if( lastverticalw[i] >= wm )
                  {
                        wm = lastverticalw[i];
                        iin = i; jin = lgth2-1;
                        ijp[lgth1][lgth2] = +( lgth1 - i );
                  }
            }
            for( j=0; j<lgth2; j++ )
            {
                  if( lasthorizontalw[j] >= wm )
                  {
                        wm = lasthorizontalw[j];
                        iin = lgth1-1; jin = j;
                        ijp[lgth1][lgth2] = -( lgth2 - j );
                  }
            }
      }

    for( i=0; i<lgth1+1; i++ ) 
    {
        ijp[i][0] = i + 1;
    }
    for( j=0; j<lgth2+1; j++ ) 
    {
        ijp[0][j] = -( j + 1 );
    }

      for( i=0; i<icyc; i++ )
      {
            mseq1[i] += lgth1+lgth2;
            *mseq1[i] = 0;
      }
      for( j=0; j<jcyc; j++ )
      {
            mseq2[j] += lgth1+lgth2;
            *mseq2[j] = 0;
      }
      iin = lgth1; jin = lgth2;
      for( k=0; k<=lgth1+lgth2; k++ ) 
      {
            if( ijp[iin][jin] < 0 ) 
            {
                  ifi = iin-1; jfi = jin+ijp[iin][jin];
            }
            else if( ijp[iin][jin] > 0 )
            {
                  ifi = iin-ijp[iin][jin]; jfi = jin-1;
            }
            else
            {
                  ifi = iin-1; jfi = jin-1;
            }
            l = iin - ifi;
            while( --l ) 
            {
                  for( i=0; i<icyc; i++ )
                        *--mseq1[i] = seq1[i][ifi+l];
                  for( j=0; j<jcyc; j++ ) 
                        *--mseq2[j] = *gap;
                  k++;
            }
            l= jin - jfi;
            while( --l )
            {
                  for( i=0; i<icyc; i++ ) 
                        *--mseq1[i] = *gap;
                  for( j=0; j<jcyc; j++ ) 
                        *--mseq2[j] = seq2[j][jfi+l];
                  k++;
            }
            if( iin <= 0 || jin <= 0 ) break;
            for( i=0; i<icyc; i++ ) 
                  *--mseq1[i] = seq1[i][ifi];
            for( j=0; j<jcyc; j++ ) 
                  *--mseq2[j] = seq2[j][jfi];
            k++;
            iin = ifi; jin = jfi;
      }
      return( 0.0 );
}


float Aalign( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
      register int i, j;
      int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
      int lgth1, lgth2;
      int resultlen;
      float wm;   /* int ?????? */
      float g;
      float x;
      static float mi, *m;
      static short **ijp;
      static int mpi, *mp;
      static float *currentw;
      static float *previousw;
      static float *match;
      static float *initverticalw;    /* kufuu sureba iranai */
      static float *lastverticalw;    /* kufuu sureba iranai */
      static char **mseq1;
      static char **mseq2;
      static char **mseq;
      static float **cpmx1;
      static float **cpmx2;
      static int **intwork;
      static float **floatwork;
      static int orlgth1 = 0, orlgth2 = 0;

#if DEBUG
      fprintf( stderr, "eff in SA+++align\n" );
      for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
#endif
      if( orlgth1 == 0 )
      {
            mseq1 = AllocateCharMtx( njob, 1 ); 
            mseq2 = AllocateCharMtx( njob, 1 ); /* by J. Thompson */
      }

      lgth1 = strlen( seq1[0] );
      lgth2 = strlen( seq2[0] );

      if( lgth1 > orlgth1 || lgth2 > orlgth2 )
      {
            int ll1, ll2;

            if( orlgth1 > 0 && orlgth2 > 0 )
            {
                  FreeFloatVec( currentw );
                  FreeFloatVec( previousw );
                  FreeFloatVec( match );
                  FreeFloatVec( initverticalw );
                  FreeFloatVec( lastverticalw );

                  FreeFloatVec( m );
                  FreeIntVec( mp );

                  FreeCharMtx( mseq );

                  FreeFloatMtx( cpmx1 );
                  FreeFloatMtx( cpmx2 );

                  FreeFloatMtx( floatwork );
                  FreeIntMtx( intwork );
            }

            ll1 = MAX( (int)(1.1*lgth1), orlgth1 ) + 100;
            ll2 = MAX( (int)(1.1*lgth2), orlgth2 ) + 100;

            fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );

            currentw = AllocateFloatVec( ll2+2 );
            previousw = AllocateFloatVec( ll2+2 );
            match = AllocateFloatVec( ll2+2 );

            initverticalw = AllocateFloatVec( ll1+2 );
            lastverticalw = AllocateFloatVec( ll1+2 );

            m = AllocateFloatVec( ll2+2 );
            mp = AllocateIntVec( ll2+2 );

            mseq = AllocateCharMtx( njob, ll1+ll2 );

            cpmx1 = AllocateFloatMtx( 26, ll1+2 );
            cpmx2 = AllocateFloatMtx( 26, ll2+2 );

            floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); 
            intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); 

            fprintf( stderr, "succeeded\n" );

            orlgth1 = ll1;
            orlgth2 = ll2;
      }

      for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
      for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];


      if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
      {
            int ll1, ll2;

            if( commonAlloc1 && commonAlloc2 )
            {
                  FreeShortMtx( commonIP );
            }

            ll1 = MAX( orlgth1, commonAlloc1 );
            ll2 = MAX( orlgth2, commonAlloc2 );

            fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );

            commonIP = AllocateShortMtx( ll1+10, ll2+10 );

            fprintf( stderr, "succeeded\n\n" );

            commonAlloc1 = ll1;
            commonAlloc2 = ll2;
      }
      ijp = commonIP;

      cpmx_calc( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
      cpmx_calc( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );

      match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
      match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );

      if( outgap == 1 )
      {
            for( i=1; i<lgth1+1; i++ )
            {
                  initverticalw[i] += penalty * 0.5;
            }
            for( j=1; j<lgth2+1; j++ )
            {
                  currentw[j] += penalty * 0.5;
            }
      }

      for( j=0; j<lgth2+1; ++j ) 
      {
            m[j] = currentw[j-1] + penalty * 0.5; mp[j] = 0;
      }

      lastverticalw[0] = currentw[lgth2-1];

      if( outgap ) lasti = lgth1+1; else lasti = lgth1;

      for( i=1; i<lasti; i++ )
      {

            floatncpy( previousw, currentw, lgth2+1 );
            previousw[0] = initverticalw[i-1];

            match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
            currentw[0] = initverticalw[i];

            mi = previousw[0] + penalty * 0.5; mpi = 0;
            for( j=1; j<lgth2+1; j++ )
            {
                  wm = previousw[j-1];
                  ijp[i][j] = 0;

                  g = penalty * 0.5;
                  x = mi + g;
                  if( x > wm )
                  {
                        wm = x;
                        ijp[i][j] = -( j - mpi );
                  }
                  g = penalty * 0.5;
                  x = previousw[j-1] + g;
                  if( mi <= x )
                  {
                        mi = x;
                        mpi = j-1;
                  }

                  g = penalty * 0.5;
                  x = m[j] + g;
                  if( x > wm )
                  {
                        wm = x;
                        ijp[i][j] = +( i - mp[j] );
                  }
                  g = penalty * 0.5;
                  x = previousw[j-1] + g;
                  if( m[j] <= x )
                  {
                        m[j] = x;
                        mp[j] = i-1;
                  }
                  currentw[j] += wm;
            }
            lastverticalw[i] = currentw[lgth2-1];
      }
      /*
      fprintf( stderr, "\n" );
      for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
      fprintf( stderr, "#####\n" );
      for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
      fprintf( stderr, "====>" );
      for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
      for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
      */
      Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );

      resultlen = strlen( mseq1[0] );
      if( alloclen < resultlen || resultlen > N )
      {
            fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
            ErrorExit( "LENGTH OVER!\n" );
      }

      for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
      for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
      /*
      fprintf( stderr, "\n" );
      for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
      fprintf( stderr, "#####\n" );
      for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
      */
      return( wm );
}

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