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Galign11.c

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

#define DEBUG 0
#define XXXXXXX    0
#define USE_PENALTY_EX  0


#if 1
static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 ) 
{
      char *seq2 = s2[0];
      int *intptr = amino_dis[s1[0][i1]];

      while( lgth2-- )
            *match++ = intptr[*seq2++];
}
#else
static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
{
      int j;

      for( j=0; j<lgth2; j++ )
            match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
}
#endif

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


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


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


float G__align11( char **seq1, char **seq2, int alloclen )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
//    int k;
      register int i, j;
      int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
      int lgth1, lgth2;
      int resultlen;
      float wm;   /* int ?????? */
      float g;
      float *currentw, *previousw;
      float fpenalty = (float)penalty;
      float fpenalty_ex = (float)penalty_ex;
#if 1
      float *wtmp;
      short *ijppt;
      float *mjpt, *prept, *curpt;
      int *mpjpt;
#endif
      static float mi, *m;
      static short **ijp;
      static int mpi, *mp;
      static float *w1, *w2;
      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;

      wm = 0.0;

      if( orlgth1 == 0 )
      {
            mseq1 = AllocateCharMtx( njob, 0 );
            mseq2 = AllocateCharMtx( njob, 0 );
      }


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



      if( lgth1 <= 0 || lgth2 <= 0 )
      {
            fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
      }

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

            if( orlgth1 > 0 && orlgth2 > 0 )
            {
                  FreeFloatVec( w1 );
                  FreeFloatVec( w2 );
                  FreeFloatVec( match );
                  FreeFloatVec( initverticalw );
                  FreeFloatVec( lastverticalw );

                  FreeFloatVec( m );
                  FreeIntVec( mp );

                  FreeCharMtx( mseq );


                  FreeFloatMtx( cpmx1 );
                  FreeFloatMtx( cpmx2 );

                  FreeFloatMtx( floatwork );
                  FreeIntMtx( intwork );
            }

            ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
            ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;

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

            w1 = AllocateFloatVec( ll2+2 );
            w2 = 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 ); 

#if DEBUG
            fprintf( stderr, "succeeded\n" );
#endif

            orlgth1 = ll1 - 100;
            orlgth2 = ll2 - 100;
      }


      mseq1[0] = mseq[0];
      mseq2[0] = mseq[1];


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

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

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

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

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

#if DEBUG
            fprintf( stderr, "succeeded\n\n" );
#endif

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


#if 0
      for( i=0; i<lgth1; i++ ) 
            fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif

      currentw = w1;
      previousw = w2;


      match_calc( initverticalw, seq2, seq1, 0, lgth1 );


      match_calc( currentw, seq1, seq2, 0, lgth2 );

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

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

      if( lgth2 == 0 )
            lastverticalw[0] = 0.0;               // lgth2==0 no toki error
      else
            lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error

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

#if XXXXXXX
fprintf( stderr, "currentw = \n" );
for( i=0; i<lgth1+1; i++ )
{
      fprintf( stderr, "%5.2f ", currentw[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "initverticalw = \n" );
for( i=0; i<lgth2+1; i++ )
{
      fprintf( stderr, "%5.2f ", initverticalw[i] );
}
fprintf( stderr, "\n" );
#endif

      for( i=1; i<lasti; i++ )
      {
            wtmp = previousw; 
            previousw = currentw;
            currentw = wtmp;

            previousw[0] = initverticalw[i-1];

            match_calc( currentw, seq1, seq2, i, lgth2 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
      fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
      fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
            currentw[0] = initverticalw[i];

            mi = previousw[0]; mpi = 0;

            ijppt = ijp[i] + 1;
            mjpt = m + 1;
            prept = previousw;
            curpt = currentw + 1;
            mpjpt = mp + 1;
            for( j=1; j<lgth2+1; j++ )
            {
                  wm = *prept;
                  *ijppt = 0;

#if 0
                  fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
                  fprintf( stderr, "%5.0f?", g );
#endif
                  if( (g=mi+fpenalty) > wm )
                  {
                        wm = g;
                        *ijppt = -( j - mpi );
                  }
                  if( (g=*prept) >= mi )
                  {
                        mi = g;
                        mpi = j-1;
                  }
#if USE_PENALTY_EX
                  mi += fpenalty_ex;
#endif

#if 0 
                  fprintf( stderr, "%5.0f?", g );
#endif
                  if( (g=*mjpt + fpenalty) > wm )
                  {
                        wm = g;
                        *ijppt = +( i - *mpjpt );
                  }
                  if( (g=*prept) >= *mjpt )
                  {
                        *mjpt = g;
                        *mpjpt = i-1;
                  }
#if USE_PENALTY_EX
                  m[j] += fpenalty_ex;
#endif

#if 0
                  fprintf( stderr, "%5.0f ", wm );
#endif
                  *curpt++ += wm;
                  ijppt++;
                  mjpt++;
                  prept++;
                  mpjpt++;
            }
            lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
      }

      Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );

      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" );
      }


      strcpy( seq1[0], mseq1[0] );
      strcpy( seq2[0], mseq2[0] );
#if 0
      fprintf( stderr, "\n" );
      fprintf( stderr, ">\n%s\n", mseq1[0] );
      fprintf( stderr, ">\n%s\n", mseq2[0] );
      fprintf( stderr, "wm = %f\n", wm );
#endif

      return( wm );
}


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