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Dalignmm.c

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

#define MACHIGAI 0
#define OUTGAP0TRY 1
#define DEBUG 0
#define XXXXXXX    0
#define USE_PENALTY_EX  0
#define FASTMATCHCALC 1


static float **impmtx = NULL;
#if 0 // --> Salignmm.c
float imp_match_out_sc( int i1, int j1 )
{
//    fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
//    fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
      return( impmtx[i1][j1] );
}
#endif

static void imp_match_out_vead( float *imp, int i1, int lgth2 )
{
#if FASTMATCHCALC 
      float *pt = impmtx[i1];
      while( lgth2-- )
            *imp++ += *pt++;
#else
      int j;
      float *pt = impmtx[i1];
      for( j=0; j<lgth2; j++ )
            *imp++ += pt[j];
#endif
}
static void imp_match_out_vead_tate( float *imp, int j1, int lgth1 )
{
      int i;
      for( i=0; i<lgth1; i++ )
            *imp++ += impmtx[i][j1];
}

#if 0 // --> Salignmm.c
void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
{
      int i, j, k1, k2, tmpint, start1, start2, end1, end2;
      static int impalloclen = 0;
      float effij;
      double effijx;
      char *pt, *pt1, *pt2;
      static char *nocount1 = NULL;
      static char *nocount2 = NULL;
      LocalHom *tmpptr;

      if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
      {
            if( impmtx ) FreeFloatMtx( impmtx );
            if( nocount1 ) free( nocount1 );
            if( nocount2 ) free( nocount2 );
            impalloclen = MAX( lgth1, lgth2 ) + 2;
            impmtx = AllocateFloatMtx( impalloclen, impalloclen );
            nocount1 = AllocateCharVec( impalloclen );
            nocount2 = AllocateCharVec( impalloclen );
      }

      for( i=0; i<lgth1; i++ )
      {
            for( j=0; j<clus1; j++ )
                  if( seq1[j][i] == '-' ) break;
            if( j != clus1 ) nocount1[i] = 1; 
            else               nocount1[i] = 0;
      }
      for( i=0; i<lgth2; i++ )
      {
            for( j=0; j<clus2; j++ )
                  if( seq2[j][i] == '-' ) break;
            if( j != clus2 ) nocount2[i] = 1;
            else               nocount2[i] = 0;
      }

#if 0
fprintf( stderr, "nocount2 =\n" );
for( i = 0; i<impalloclen; i++ )
{
      fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
}
#endif



#if 0
      fprintf( stderr, "eff1 in _init_strict = \n" );
      for( i=0; i<clus1; i++ )
            fprintf( stderr, "eff1[] = %f\n", eff1[i] );
      for( i=0; i<clus2; i++ )
            fprintf( stderr, "eff2[] = %f\n", eff2[i] );
#endif

      for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
            impmtx[i][j] = 0.0;
      effijx =  fastathreshold;
      for( i=0; i<clus1; i++ )
      {
            for( j=0; j<clus2; j++ )
            {
                  effij = (float)( eff1[i] * eff2[j] * effijx );
                  tmpptr = localhom[i][j];
                  while( tmpptr )
                  {
//                      fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
//                      fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
//                      fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
//                      fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
                        pt = seq1[i];
                        tmpint = -1;
                        while( *pt != 0 )
                        {
                              if( *pt++ != '-' ) tmpint++;
                              if( tmpint == tmpptr->start1 ) break;
                        }
                        start1 = pt - seq1[i] - 1;
      
                        if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
                        else
                        {
#if MACHIGAI
                              while( *pt != 0 )
                              {
//                                  fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
                                    if( tmpint == tmpptr->end1 ) break;
                                    if( *pt++ != '-' ) tmpint++;
                              }
                              end1 = pt - seq1[i] - 0;
#else
                              while( *pt != 0 )
                              {
//                                  fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
                                    if( *pt++ != '-' ) tmpint++;
                                    if( tmpint == tmpptr->end1 ) break;
                              }
                              end1 = pt - seq1[i] - 1;
#endif
                        }
      
                        pt = seq2[j];
                        tmpint = -1;
                        while( *pt != 0 )
                        {
                              if( *pt++ != '-' ) tmpint++;
                              if( tmpint == tmpptr->start2 ) break;
                        }
                        start2 = pt - seq2[j] - 1;
                        if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
                        else
                        {
#if MACHIGAI
                              while( *pt != 0 )
                              {
                                    if( tmpint == tmpptr->end2 ) break;
                                    if( *pt++ != '-' ) tmpint++;
                              }
                              end2 = pt - seq2[j] - 0;
#else
                              while( *pt != 0 )
                              {
                                    if( *pt++ != '-' ) tmpint++;
                                    if( tmpint == tmpptr->end2 ) break;
                              }
                              end2 = pt - seq2[j] - 1;
#endif
                        }
//                      fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
//                      fprintf( stderr, "step 0\n" );
                        if( end1 - start1 != end2 - start2 )
                        {
//                            fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
                        }

#if 1
                        k1 = start1; k2 = start2;
                        pt1 = seq1[i] + k1;
                        pt2 = seq2[j] + k2;
                        while( *pt1 && *pt2 )
                        {
                              if( *pt1 != '-' && *pt2 != '-' )
                              {
// 重みを二重にかけないように注意して下さい。
//                                  impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
//                                  impmtx[k1][k2] += tmpptr->importance * effij;
                                    impmtx[k1][k2] += tmpptr->fimportance * effij;
//                                  fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
//                                  fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
//                                  fprintf( stderr, "%d (%c) - %d (%c)  - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
                                    k1++; k2++;
                                    pt1++; pt2++;
                              }
                              else if( *pt1 != '-' && *pt2 == '-' )
                              {
//                                  fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                    k2++; pt2++;
                              }
                              else if( *pt1 == '-' && *pt2 != '-' )
                              {
//                                  fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                    k1++; pt1++;
                              }
                              else if( *pt1 == '-' && *pt2 == '-' )
                              {
//                                  fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                    k1++; pt1++;
                                    k2++; pt2++;
                              }
                              if( k1 > end1 || k2 > end2 ) break;
                        }
#else
                        while( k1 <= end1 && k2 <= end2 )
                        {
                              fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
                              if( !nocount1[k1] && !nocount2[k2] )
                              {
                                    impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j]  * fastathreshold;
                                    fprintf( stderr, "marked\n" );
                              }
                              else
                                    fprintf( stderr, "no count\n" );
                              k1++; k2++;
                        }
#endif
                        tmpptr = tmpptr->next;
                  }
            }
      }
#if 0
      if( clus1 == 1 && clus2 == 6 )
      {
            fprintf( stderr, "\n" );
            fprintf( stderr, "seq1[0] =  %s\n", seq1[0] );
            fprintf( stderr, "seq2[0] =  %s\n", seq2[0] );
            fprintf( stderr, "impmtx = \n" );
            for( k2=0; k2<lgth2; k2++ )
                  fprintf( stderr, "%6.3f ", (double)k2 );
            fprintf( stderr, "\n" );
            for( k1=0; k1<lgth1; k1++ )
            {
                  fprintf( stderr, "%d ", k1 );
                  for( k2=0; k2<3; k2++ )
                        fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
                  fprintf( stderr, "\n" );
            }
            exit( 1 );
      }
#endif
}
#endif

#if 0
void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
{
      int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
      static int impalloclen = 0;
      char *pt;
      int allgap;
      static char *nocount1 = NULL;
      static char *nocount2 = NULL;

      if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
      {
            if( impmtx ) FreeFloatMtx( impmtx );
            if( nocount1 ) free( nocount1 );
            if( nocount2 ) free( nocount2 );
            impalloclen = MAX( lgth1, lgth2 ) + 2;
            impmtx = AllocateFloatMtx( impalloclen, impalloclen );
            nocount1 = AllocateCharVec( impalloclen );
            nocount2 = AllocateCharVec( impalloclen );
      }

      for( i=0; i<lgth1; i++ )
      {
            for( j=0; j<clus1; j++ )
                  if( seq1[j][i] == '-' ) break;
            if( j != clus1 ) nocount1[i] = 1; 
            else               nocount1[i] = 0;
      }
      for( i=0; i<lgth2; i++ )
      {
            for( j=0; j<clus2; j++ )
                  if( seq2[j][i] == '-' ) break;
            if( j != clus2 ) nocount2[i] = 1;
            else               nocount2[i] = 0;
      }

#if 0
fprintf( stderr, "nocount2 =\n" );
for( i = 0; i<impalloclen; i++ )
{
      fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
}
#endif

      for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
            impmtx[i][j] = 0;
      for( i=0; i<clus1; i++ )
      {
            fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
            for( j=0; j<clus2; j++ )
            {
                  fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
                  fprintf( stderr, "end1   = %d\n", localhom[i][j]->end1   );
                  fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
                  pt = seq1[i];
                  tmpint = -1;
                  while( *pt != 0 )
                  {
                        if( *pt++ != '-' ) tmpint++;
                        if( tmpint == localhom[i][j]->start1 ) break;
                  }
                  start1 = pt - seq1[i] - 1;

                  while( *pt != 0 )
                  {
//                      fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
                        if( *pt++ != '-' ) tmpint++;
                        if( tmpint == localhom[i][j]->end1 ) break;
                  }
                  end1 = pt - seq1[i] - 1;

                  pt = seq2[j];
                  tmpint = -1;
                  while( *pt != 0 )
                  {
                        if( *pt++ != '-' ) tmpint++;
                        if( tmpint == localhom[i][j]->start2 ) break;
                  }
                  start2 = pt - seq2[j] - 1;
                  while( *pt != 0 )
                  {
                        if( *pt++ != '-' ) tmpint++;
                        if( tmpint == localhom[i][j]->end2 ) break;
                  }
                  end2 = pt - seq2[j] - 1;
//                fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
                  k1 = start1;
                  k2 = start2;
                  fprintf( stderr, "step 0\n" );
                  while( k1 <= end1 && k2 <= end2 )
                  {
#if 0
                        if( !nocount1[k1] && !nocount2[k2] )
                              impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
                        k1++; k2++;
#else
                        if( !nocount1[k1] && !nocount2[k2] )
                              impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
                        k1++; k2++;
#endif
                  }

                  dif = ( end1 - start1 ) - ( end2 - start2 );
                  fprintf( stderr, "dif = %d\n", dif );
                  if( dif > 0 )
                  {
                        do
                        {
                              fprintf( stderr, "dif = %d\n", dif );
                              k1 = start1;
                              k2 = start2 - dif;
                              while( k1 <= end1 && k2 <= end2 )
                              {
                                    if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
                                          impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
                                    k1++; k2++;
                              }
                        }
                        while( dif-- );
                  }
                  else
                  {
                        do
                        {
                              k1 = start1 + dif;
                              k2 = start2;
                              while( k1 <= end1 )
                              {
                                    if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
                                          impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
                                    k1++; k2++;
                              }
                        }
                        while( dif++ );
                  }
            }
      }
#if 0
      fprintf( stderr, "impmtx = \n" );
      for( k2=0; k2<lgth2; k2++ )
            fprintf( stderr, "%6.3f ", (double)k2 );
      fprintf( stderr, "\n" );
      for( k1=0; k1<lgth1; k1++ )
      {
            fprintf( stderr, "%d", k1 );
            for( k2=0; k2<lgth2; k2++ )
                  fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
            fprintf( stderr, "\n" );
      }
#endif
}
#endif

static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
{
#if FASTMATCHCALC
      int j, l;
      float scarr[26];
      float **cpmxpd = floatwork;
      int **cpmxpdn = intwork;
      float *matchpt, *cpmxpdpt, **cpmxpdptpt;
      int *cpmxpdnpt, **cpmxpdnptpt;
      if( initialize )
      {
            int count = 0;
            for( j=0; j<lgth2; j++ )
            {
                  count = 0;
                  for( l=0; l<26; l++ )
                  {
                        if( cpmx2[l][j] )
                        {
                              cpmxpd[j][count] = cpmx2[l][j];
                              cpmxpdn[j][count] = l;
                              count++;
                        }
                  }
                  cpmxpdn[j][count] = -1;
            }
      }

      {
            for( l=0; l<26; l++ )
            {
                  scarr[l] = 0.0;
                  for( j=0; j<26; j++ )
                        scarr[l] += n_dis[j][l] * cpmx1[j][i1];
            }
            matchpt = match;
            cpmxpdnptpt = cpmxpdn;
            cpmxpdptpt = cpmxpd;
            while( lgth2-- )
            {
                  *matchpt = 0.0;
                  cpmxpdnpt = *cpmxpdnptpt++;
                  cpmxpdpt = *cpmxpdptpt++;
                  while( *cpmxpdnpt>-1 )
                        *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
                  matchpt++;
            } 
      }
#else
      int j, k, l;
      float scarr[26];
      float **cpmxpd = floatwork;
      int **cpmxpdn = intwork;
// simple
      if( initialize )
      {
            int count = 0;
            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] = 0.0;
            for( k=0; cpmxpdn[k][j]>-1; k++ )
                  match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
      } 
#endif
}

static void Atracking_localhom( float *impwmpt, 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, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
      float wm;
      char *gaptable1, *gt1bk;
      char *gaptable2, *gt2bk;
      lgth1 = strlen( seq1[0] );
      lgth2 = strlen( seq2[0] );
      gt1bk = AllocateCharVec( lgth1+lgth2+1 );
      gt2bk = AllocateCharVec( lgth1+lgth2+1 );

#if 0
      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 );
    }

      gaptable1 = gt1bk + lgth1+lgth2;
      *gaptable1 = 0;
      gaptable2 = gt2bk + lgth1+lgth2;
      *gaptable2 = 0;

      iin = lgth1; jin = lgth2;
      *impwmpt = 0.0;
      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 ) 
            {
                  *--gaptable1 = 'o';
                  *--gaptable2 = '-';
                  k++;
            }
            l= jin - jfi;
            while( --l )
            {
                  *--gaptable1 = '-';
                  *--gaptable2 = 'o';
                  k++;
            }
            if( iin == lgth1 || jin == lgth2 )
                  ;
            else
            {
                  *impwmpt += imp_match_out_sc( iin, jin );

//          fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
            }
            if( iin <= 0 || jin <= 0 ) break;
            *--gaptable1 = 'o';
            *--gaptable2 = 'o';
            k++;
            iin = ifi; jin = jfi;
      }

      for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
      for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );

      free( gt1bk );
      free( gt2bk );
}
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, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
      float wm;
      char *gaptable1, *gt1bk;
      char *gaptable2, *gt2bk;
      lgth1 = strlen( seq1[0] );
      lgth2 = strlen( seq2[0] );

      gt1bk = AllocateCharVec( lgth1+lgth2+1 );
      gt2bk = AllocateCharVec( lgth1+lgth2+1 );

#if 0
      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 );
    }

      gaptable1 = gt1bk + lgth1+lgth2;
      *gaptable1 = 0;
      gaptable2 = gt2bk + lgth1+lgth2;
      *gaptable2 = 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 ) 
            {
                  *--gaptable1 = 'o';
                  *--gaptable2 = '-';
                  k++;
            }
            l= jin - jfi;
            while( --l )
            {
                  *--gaptable1 = '-';
                  *--gaptable2 = 'o';
                  k++;
            }
            if( iin <= 0 || jin <= 0 ) break;
            *--gaptable1 = 'o';
            *--gaptable2 = 'o';
            k++;
            iin = ifi; jin = jfi;
      }

      for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
      for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );

      free( gt1bk );
      free( gt2bk );

      return( 0.0 );
}

float D__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
//    int k;
      register int i, j;
      int lasti, lastj;      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
      int lgth1, lgth2;
      int resultlen;
      float wm = 0.0;   /* int ?????? */
      float g;
      float *currentw, *previousw;
//    float fpenalty = (float)penalty;
#if USE_PENALTY_EX
      float fpenalty_ex = (float)penalty_ex;
#endif
#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 *ogcp1;
      static float *ogcp2;
      static float *fgcp1;
      static float *fgcp2;
      static float *digapfreq1;
      static float *digapfreq2;
      static float *gapfreq1;
      static float *gapfreq2;
      static float **gappat1;
      static float **gappat2;
      static float **cpmx1;
      static float **cpmx2;
      static int **intwork;
      static float **floatwork;
      static int orlgth1 = 0, orlgth2 = 0;
      float fpenalty = (float)penalty;
      float tmppenal;
      float *fgcp2pt;
      float *ogcp2pt;
      float fgcp1va;
      float ogcp1va;
      static int gappat1len;
      static int gappat2len;

#if 0
      fprintf( stderr, "####  eff in SA+++align\n" );
      fprintf( stderr, "####  seq1[0] = %s\n", seq1[0] );
      fprintf( stderr, "####  strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
      for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
#endif
      if( orlgth1 == 0 )
      {
            mseq1 = AllocateCharMtx( njob, 0 );
            mseq2 = AllocateCharMtx( njob, 0 );
      }


      lgth1 = strlen( seq1[0] );
      lgth2 = strlen( seq2[0] );
#if 0
      if( lgth1 == 0 || lgth2 == 0 )
      {
            fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
      }
#endif

      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 );

                  FreeFloatVec( ogcp1 );
                  FreeFloatVec( ogcp2 );
                  FreeFloatVec( fgcp1 );
                  FreeFloatVec( fgcp2 );
                  FreeFloatVec( gapfreq1 );
                  FreeFloatVec( gapfreq2 );
                  FreeFloatVec( digapfreq1 );
                  FreeFloatVec( digapfreq2 );
                  free( gappat1 );
                  free( gappat2 );


                  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 );

            ogcp1 = AllocateFloatVec( ll1+2 );
            ogcp2 = AllocateFloatVec( ll2+2 );
            fgcp1 = AllocateFloatVec( ll1+2 );
            fgcp2 = AllocateFloatVec( ll2+2 );
            gapfreq1 = AllocateFloatVec( ll1+2 );
            gapfreq2 = AllocateFloatVec( ll2+2 );
            digapfreq1 = AllocateFloatVec( ll1+2 );
            digapfreq2 = AllocateFloatVec( ll2+2 );
            gappat1 = (float **) calloc( ll1+2, sizeof( float * ) );
            gappat2 = (float **) calloc( ll2+2, sizeof( float * ) );
            gappat1len = ll1+2;
            gappat2len = ll2+2;

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

#if FASTMATCHCALC
            floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); 
            intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 ); 
#else
            floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); 
            intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); 
#endif

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

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


      for( i=0; i<icyc; i++ )
      {
            mseq1[i] = mseq[i];
            seq1[i][lgth1] = 0;
      }
      for( j=0; j<jcyc; j++ )
      {
            mseq2[j] = mseq[icyc+j];
            seq2[j][lgth2] = 0;
      }


      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
      {
            float t = 0.0;
            for( i=0; i<icyc; i++ )
                  t += eff1[i];
      fprintf( stderr, "## totaleff = %f\n", t );
      }
#endif

      cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
      cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );

      for( i=0; i<gappat1len; i++ ) gappat1[i] = NULL;
      for( i=0; i<gappat2len; i++ ) gappat2[i] = NULL;

      if( sgap1 )
      {
            new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
            new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
//          getGapPattern( gappat1, icyc, seq1, eff1, lgth1, egap1 );
//          getGapPattern( gappat2, jcyc, seq2, eff2, lgth2, egap2 );
      }
      else
      {
            st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
            st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
            st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
            st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
            st_getGapPattern( gappat1, gapfreq1, icyc, seq1, eff1, lgth1 );
            st_getGapPattern( gappat2, gapfreq2, jcyc, seq2, eff2, lgth2 );
      }



      for( i=0; i<lgth1; i++ ) 
      {
            if( gappat1[i] ) gappat1[i][i+2] = ( gappat1[i][i+2] ) * fpenalty;
//          if( gappat1[i] ) fprintf( stderr, "gappat1[%d][X] = %f (%f)\n", i, gappat1[i][i+2], fpenalty );
            if( gappat1[i] ) for( j=0,lastj=i+2; j<lastj; j++ ) 
            {
//                fprintf( stderr, "gappat1 (%c), %d-%d, %f\n", seq1[0][i], i, j, gappat1[i][j] );
                  gappat1[i][j] = ( 1.0 - gappat1[i][j] ) * fpenalty;
//                fprintf( stderr, "gappat1 (%c), %d-%d, %f\n", seq1[0][i], i, j, gappat1[i][j] );
            }
        ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
        fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
      }
      for( i=0; i<lgth2; i++ ) 
      {
            if( gappat2[i] ) gappat2[i][i+2] = ( gappat2[i][i+2] ) * fpenalty;
//          if( gappat2[i] ) fprintf( stderr, "gappat2[%d][X] = %f (%f)\n", i, gappat2[i][i+2], fpenalty );
            if( gappat2[i] ) for( j=0,lastj=i+2; j<lastj; j++ ) 
            {
//                fprintf( stderr, "gappat2 (%c), %d-%d, %f\n", seq2[0][i], i, j, gappat2[i][j] );
                  gappat2[i][j] = ( 1.0 - gappat2[i][j] ) * fpenalty;
            }
        ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
        fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
      }

#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, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
      if( localhom )
            imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306

      match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
      if( localhom )
            imp_match_out_vead( currentw, 0, lgth2 ); // 060306
#if 0 // -> tbfast.c
      if( localhom )
            imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );

#endif


#if 0
      for( i=0; i<lgth1+1; i++ )
            fprintf( stderr, "iv[%d] = %f\n", i, initverticalw[i] );
#endif

      if( outgap == 1 )
      {
            for( i=1; i<lgth1+1; i++ )
            {
//                initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
                  if( gappat1[i-1] ) 
                  {
                        initverticalw[i] += ( gappat1[i-1][i] ) ;
                  }
                  else initverticalw[i] += fpenalty;
            }
            for( j=1; j<lgth2+1; j++ )
            {
//                currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
                  if( gappat2[j-1]) 
                  {
                        currentw[j] += ( gappat2[j-1][j] ) ;
                  }
                  else currentw[j] += fpenalty;
            }
      }
#if OUTGAP0TRY
      else
      {
            for( j=1; j<lgth2+1; j++ )
                  currentw[j] -= offset * j / 2.0;
            for( i=1; i<lgth1+1; i++ )
                  initverticalw[i] -= offset * i / 2.0;
      }
#endif
#if 0
      for( i=0; i<lgth1+1; i++ )
            fprintf( stderr, "iv[%d] = %f\n", i, initverticalw[i] );
#endif

      for( j=1; j<lgth2+1; ++j ) 
      {
            m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
      }
      if( lgth2 == 0 )
            lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
      else
            lastverticalw[0] = currentw[lgth2-1];

      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" );
fprintf( stderr, "fcgp\n" );
for( i=0; i<lgth1; i++ ) 
      fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
for( i=0; i<lgth2; i++ ) 
      fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
#endif

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

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

            match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
#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( localhom )
            {
//                fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
#if  0
                  imp_match_out_vead( currentw, i, lgth2 );
#else
                  imp_match_out_vead( currentw, i, lgth2 );
#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] + ogcp2[1]; mpi = 0;
            mi = previousw[0]; mpi = 0;
            ijppt = ijp[i] + 1;
            mjpt = m + 1;
            prept = previousw;
            curpt = currentw + 1;
            mpjpt = mp + 1;
            fgcp2pt = fgcp2;
            ogcp2pt = ogcp2 + 1;
            fgcp1va = fgcp1[i-1];
            ogcp1va = ogcp1[i];
            lastj = lgth2+1;
            for( j=1; j<lastj; j++ )
            {
                  wm = *prept;

#if 1
//                if( !gappat1[i-1] && !gappat2[j-1] ) fprintf( stderr, "%c:%c match penal = 0.0\n", seq1[0][i], seq2[0][j] );
                  if( gappat1[i-1] ) 
                  {
//                      fprintf( stderr, "%c%c:%c%c match penal = %f\n", seq1[0][i-1], seq1[0][i], seq2[0][j-1], seq2[0][j], gappat1[i-1][i+1] );
                        wm += gappat1[i-1][i+1];
                  }
                  if( gappat2[j-1] ) 
                  {
//                      fprintf( stderr, "%c%c:%c%c match penal = %f\n", seq1[0][i-1], seq1[0][i], seq2[0][j-1], seq2[0][j], gappat2[j-1][j+1] );
                        wm += gappat2[j-1][j+1];
                  }
#endif
                  *ijppt = 0;

#if 0
                  fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
                  fprintf( stderr, "%5.0f?", g );
#endif
                  if( gappat2[j-1] ) tmppenal = gappat2[j-1][j-mpi-1];
                  else tmppenal = fpenalty;
                  tmppenal *= ( 1.0 - gapfreq2[j] );
                  tmppenal *= ( 1.0 - MIN( gapfreq1[i], gapfreq1[mpi] ) );
//                tmppenal *= ( 1.0 - 0.5 * ( gapfreq1[i] + gapfreq1[mpi] ) );
//                fprintf( stderr, "j-jump? i=%d, j=%d, j-mpi-1=%d, %c-%c, tmppenal = %f, mpi=%d, gf1=%f\n", i, j, j-mpi-1, seq1[0][i], seq2[0][j], tmppenal, mpi, gapfreq1[i] );
                  if( (g=mi+tmppenal) > wm )
//                if( (g=mi+*fgcp2pt) > wm )
                  {
//                      fprintf( stderr, "j-jump, %c->%c because wm=%f<g=%f\n", seq2[0][j], seq2[0][mpi], wm, g );
                        wm = g;
                        *ijppt = -( j - mpi );
                  }
//                if( (g=*prept+*ogcp2pt) >= mi )
                  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( gappat1[i-1] ) tmppenal = gappat1[i-1][i - *mpjpt-1];
                  else tmppenal = fpenalty;
                  tmppenal *= ( 1.0 - gapfreq1[i] );
                  tmppenal *= ( 1.0 - MIN( gapfreq2[j], gapfreq2[*mpjpt] ) );
//                tmppenal *= ( 1.0 - 0.5 * ( gapfreq2[j] + gapfreq2[*mpjpt] ) );
//                fprintf( stderr, "i-jump? i=%d, j=%d, i-*mpjpt-1=%d, %c-%c, tmppenal = %f, mpj=%d, gf2=%f\n", i, j, i-*mpjpt-1, seq1[0][i], seq2[0][j], tmppenal, *mpjpt, gapfreq2[j] );
                  if( (g=*mjpt+tmppenal) > wm )
//                if( (g=*mjpt+fgcp1va) > wm )
                  {
//                      fprintf( stderr, "i-jump, %c->%c, because wm=%f<g=%f\n", seq1[0][i], seq1[0][*mpjpt], wm, g );
                        wm = g;
                        *ijppt = +( i - *mpjpt );
                  }
//                if( (g=*prept+ogcp1va) >= *mjpt )
                  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++;
                  fgcp2pt++;
                  ogcp2pt++;
            }
            lastverticalw[i] = currentw[lgth2-1];
      }

//    fprintf( stderr, "wm = %f\n", wm );

#if OUTGAP0TRY
      if( !outgap )
      {
            for( j=1; j<lgth2+1; j++ )
                  currentw[j] -= offset * ( lgth2 - j ) / 2.0;
            for( i=1; i<lgth1+1; i++ )
                  lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
      }
#endif
            
      /*
      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] );
      */
      if( localhom )
      {
            Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
      }
      else
            Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );

//    fprintf( stderr, "### impmatch = %f\n", *impmatch );

      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] );
      */

//    fprintf( stderr, "wm = %f\n", wm );

      for( i=0; i<gappat1len; i++ ) 
      {
            if( gappat1[i] )
            {
                  free( gappat1[i] );
                  gappat1[i] = NULL;
            }
      }
      for( i=0; i<gappat2len; i++ )
      {
            if( gappat2[i] )
            {
                  free( gappat2[i] );
                  gappat2[i] = NULL;
            }
      }

      fprintf( stderr, "wm = %f\n", wm );

      return( wm );
}

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