Logo Search packages:      
Sourcecode: mafft version File versions  Download package

partQalignmm.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 int impalloclen = 0;
static float **impmtx = NULL;
float part_imp_match_out_scQ( int i1, int j1 )
{
//    fprintf( stderr, "impalloclen = %d\n", impalloclen );
//    fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
      return( impmtx[i1][j1] );
#if 0
      if( i1 == l1 || j1 == l2 ) return( 0.0 );
      return( impmtx[i1+start1][j1+start2] );
#endif
}
static void part_imp_match_out_vead_gapmapQ( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
{
#if FASTMACHCALC
      float *pt = imp;
      int *gapmappt = gapmap2;
      while( lgth2-- )
            *pt++ += impmtx[i1][start2+*gapmappt++];
#else
      int j;
      for( j=0; j<lgth2; j++ )
      {
            imp[j] += impmtx[i1][start2+gapmap2[j]];
      }
#endif
}

static void part_imp_match_out_vead_tate_gapmapQ( float *imp, int j1, int lgth1, int start1, int *gapmap1 )
{
#if FASTMACHCALC
      float *pt = imp;
      int *gapmappt = gapmap1;
      while( lgth1-- )
            *pt++ = impmtx[start1+*gapmappt++][j1];
#else
      int i;
      for( i=0; i<lgth1; i++ )
      {
            imp[i] += impmtx[start1+gapmap1[i]][j1];
      }
#endif
}

void part_imp_match_init_strictQ( 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;
      double effij, effijx; 
      char *pt, *pt1, *pt2;
      LocalHom *tmpptr;

      if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
      {
            if( impmtx ) FreeFloatMtx( impmtx );
            impalloclen = MAX( lgth1, lgth2 ) + 2;
            impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
      }


#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 = 1.0 * fastathreshold;
      for( i=0; i<clus1; i++ )
      {
            for( j=0; j<clus2; j++ )
            {
                  effij = 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 = (int)( pt - seq1[i] ) - 1;
      
                        if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
                        else
                        {
#if MACHIGAI
                              while( *pt != 0 )
                              {
                                    if( tmpint == tmpptr->end1 ) break;
                                    if( *pt++ != '-' ) tmpint++;
                              }
                              end1 = (int)( pt - seq1[i] ) - 1;
#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 = (int)( pt - seq1[i] ) - 1;
#endif
                        }
      
                        pt = seq2[j];
                        tmpint = -1;
                        while( *pt != 0 )
                        {
                              if( *pt++ != '-' ) tmpint++;
                              if( tmpint == tmpptr->start2 ) break;
                        }
                        start2 = (int)( 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 = (int)( pt - seq2[j] ) - 1;
#else
                              while( *pt != 0 )
                              {
                                    if( *pt++ != '-' ) tmpint++;
                                    if( tmpint == tmpptr->end2 ) break;
                              }
                              end2 = (int)( 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 );
                        }

                        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, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
//                                  fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                    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;
                        }
                        tmpptr = tmpptr->next;
                  }
            }
      }
#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, "%2.1f ", impmtx[k1][k2] );
            fprintf( stderr, "\n" );
      }
      exit( 1 );
#endif
}

void part_imp_match_initQ( 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;
      static char *nocount1 = NULL;
      static char *nocount2 = NULL;

      if( impalloclen < lgth1 || impalloclen < lgth2 )
      {
            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 );
            impalloclen -= 2;
      }

      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] = 0.0;
      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 1
      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" );
      }
      exit( 1 );
#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 start1, int end1, int start2, int end2,
                                    int *gapmap1, int *gapmap2 )
{
      int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
      char gap[] = "-";
      float wm;
      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
 
      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;
      *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 ) 
            {
                  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 != lgth1 && jin != lgth2 ) // ??
            {
                  *impwmpt += part_imp_match_out_scQ( gapmap1[iin]+start1, gapmap2[jin]+start2 );
//                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;
            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;
      }
}
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, lastk;
      char gap[] = "-";
      float wm = 0.0;
      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
 
      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;
      lastk = lgth1+lgth2;
      for( k=0; k<=lastk; 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 partQ__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, 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;
#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 *digf1; 
      static float *digf2; 
      static float *diaf1; 
      static float *diaf2; 
      static float *gapz1; 
      static float *gapz2; 
      static float *gapf1; 
      static float *gapf2; 
      static float *ogcp1g;
      static float *ogcp2g;
      static float *fgcp1g;
      static float *fgcp2g;
      static float *og_h_dg_n1_p;
      static float *og_h_dg_n2_p;
      static float *fg_h_dg_n1_p;
      static float *fg_h_dg_n2_p;
      static float *og_t_fg_h_dg_n1_p;
      static float *og_t_fg_h_dg_n2_p;
      static float *fg_t_og_h_dg_n1_p;
      static float *fg_t_og_h_dg_n2_p;
      static float *gapz_n1;
      static float *gapz_n2;
      static float **cpmx1;
      static float **cpmx2;
      static int **intwork;
      static float **floatwork;
      static int orlgth1 = 0, orlgth2 = 0;
      float fpenalty = (float)penalty;
#if USE_PENALTY_EX
      float fpenalty_ex = (float)penalty_ex;
#endif
      float tmppenal;
      float *fg_t_og_h_dg_n2_p_pt;
      float *og_t_fg_h_dg_n2_p_pt;
      float *og_h_dg_n2_p_pt;
      float *fg_h_dg_n2_p_pt;
      float *gapz_n2_pt0;
      float *gapz_n2_pt1;
      float *fgcp2pt;
      float *ogcp2pt;
      float fg_t_og_h_dg_n1_p_va;
      float og_t_fg_h_dg_n1_p_va;
      float og_h_dg_n1_p_va;
      float fg_h_dg_n1_p_va;
      float gapz_n1_va0;
      float gapz_n1_va1;
      float fgcp1va;
      float ogcp1va;



#if 0
      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, 0 );
            mseq2 = AllocateCharMtx( njob, 0 );
      }


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

      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( digf1 );
                  FreeFloatVec( digf2 );
                  FreeFloatVec( diaf1 );
                  FreeFloatVec( diaf2 );
                  FreeFloatVec( gapz1 );
                  FreeFloatVec( gapz2 );
                  FreeFloatVec( gapf1 );
                  FreeFloatVec( gapf2 );
                  FreeFloatVec( ogcp1g );
                  FreeFloatVec( ogcp2g );
                  FreeFloatVec( fgcp1g );
                  FreeFloatVec( fgcp2g );
                  FreeFloatVec( og_h_dg_n1_p );
                  FreeFloatVec( og_h_dg_n2_p );
                  FreeFloatVec( fg_h_dg_n1_p );
                  FreeFloatVec( fg_h_dg_n2_p );
                  FreeFloatVec( og_t_fg_h_dg_n1_p );
                  FreeFloatVec( og_t_fg_h_dg_n2_p );
                  FreeFloatVec( fg_t_og_h_dg_n1_p );
                  FreeFloatVec( fg_t_og_h_dg_n2_p );
                  FreeFloatVec( gapz_n1 );
                  FreeFloatVec( gapz_n2 );

                  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 );

            digf1 = AllocateFloatVec( ll1+2 );
            digf2 = AllocateFloatVec( ll2+2 );
            diaf1 = AllocateFloatVec( ll1+2 );
            diaf2 = AllocateFloatVec( ll2+2 );
            gapz1 = AllocateFloatVec( ll1+2 );
            gapz2 = AllocateFloatVec( ll2+2 );
            gapf1 = AllocateFloatVec( ll1+2 );
            gapf2 = AllocateFloatVec( ll2+2 );
            ogcp1g = AllocateFloatVec( ll1+2 );
            ogcp2g = AllocateFloatVec( ll2+2 );
            fgcp1g = AllocateFloatVec( ll1+2 );
            fgcp2g = AllocateFloatVec( ll2+2 );
            og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
            og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
            fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
            fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
            og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
            og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
            fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
            fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
            gapz_n1 = AllocateFloatVec( ll1+2 );
            gapz_n2 = AllocateFloatVec( 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, 26 ); 
#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];
      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 );

#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;

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

      if( sgap1 )
      {
            new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
            new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
            new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
            new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
            getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
            getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
            getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
            getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
            getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
            getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
            getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
            getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
      }
      else
      {
            st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
            st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
            st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
            st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
            getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
            getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
            getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
            getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
            getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
            getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
            getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
            getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
      }

#if 1
      lastj = lgth2+2;
      for( i=0; i<lastj; i++ )
      {
            og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
            fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
            og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
            fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
            gapz_n2[i] = (1.0-gapz2[i]);
      }
      lastj = lgth1+2;
      for( i=0; i<lastj; i++ )
      {
            og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
            fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
            og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
            fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
            gapz_n1[i] = (1.0-gapz1[i]);
      }
#endif

      currentw = w1;
      previousw = w2;


      match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
      if( localhom )
            part_imp_match_out_vead_tate_gapmapQ( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );


      match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
      if( localhom )
            part_imp_match_out_vead_gapmapQ( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
#if 0 // -> tbfast.c
      if( localhom )
            imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );

#endif

      if( outgap == 1 )
      {
            g = 0.0;

            g += ogcp1g[0] * og_h_dg_n2_p[0];

            g += ogcp2g[0] * og_h_dg_n1_p[0];

            g += fgcp1g[0] * fg_h_dg_n2_p[0];

            g += fgcp2g[0] * fg_h_dg_n1_p[0];

            initverticalw[0] += g;
            currentw[0] += g;

            for( i=1; i<lgth1+1; i++ )
            {
                  tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
                  initverticalw[i] += tmppenal;

                  tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
                  initverticalw[i] += tmppenal;

            }
            for( j=1; j<lgth2+1; j++ )
            {
                  tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
                  currentw[j] += tmppenal;

                  tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
                  currentw[j] += tmppenal;
            }
      }
#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

      m[0] = 0.0; // iranai
      for( j=1; j<lgth2+1; ++j ) 
      {
            mp[j] = 0;
            m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
      }
      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;
      lastj = lgth2+1;

#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 );
//                imp_match_out_vead( currentw, i, lgth2 );
                  part_imp_match_out_vead_gapmapQ( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
            }
#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];

            mpi = 0;
            mi = previousw[0] + 10000 * fpenalty;

            ijppt = ijp[i] + 1;
            mjpt = m + 1;
            prept = previousw;
            curpt = currentw + 1;
            mpjpt = mp + 1;
            fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
            og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
            og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
            fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
            gapz_n2_pt0 = gapz_n2 + 1;
            gapz_n2_pt1 = gapz_n2 + 2;
            fgcp2pt = fgcp2g + 1;
            ogcp2pt = ogcp2g + 1;

            fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
            og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
            og_h_dg_n1_p_va = og_h_dg_n1_p[i];
            fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
            gapz_n1_va0 = gapz_n1[i];
            gapz_n1_va1 = gapz_n1[i+1];
            fgcp1va = fgcp1g[i];
            ogcp1va = ogcp1g[i];

            for( j=1; j<lastj; j++ )
            {
                  wm = *prept;

                  g = ogcp1va * *og_h_dg_n2_p_pt;
                  wm += g;

                  g = *ogcp2pt * og_h_dg_n1_p_va;
                  wm += g;

                  g = fgcp1va * *fg_h_dg_n2_p_pt;
                  wm += g;

                  g = *fgcp2pt * fg_h_dg_n1_p_va;
                  wm += g;

                  *ijppt = 0;


#if 0
                  fprintf( stderr, "%5.0f->", wm );
#endif
                  tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
#if 0
                  fprintf( stderr, "%5.0f?", g );
#endif
                  if( (g=mi+tmppenal) > wm )
                  {
                        wm = g;
                        *ijppt = -( j - mpi );
                  }

                  tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
                  if( (g=*prept+tmppenal) >= mi )
                  {
                        mi = g;
                        mpi = j-1;
                  }
#if USE_PENALTY_EX
                  mi += fpenalty_ex;
#endif

                  tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
#if 0 
                  fprintf( stderr, "%5.0f?", g );
#endif
                  if( (g=*mjpt+tmppenal) > wm )
                  {
                        wm = g;
                        *ijppt = +( i - *mpjpt );
                  }

                  tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
                  if( (g=*prept+tmppenal) >= *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++;
                  fg_t_og_h_dg_n2_p_pt++;
                  og_t_fg_h_dg_n2_p_pt++;
                  og_h_dg_n2_p_pt++;
                  fg_h_dg_n2_p_pt++;
                  gapz_n2_pt0++;
                  gapz_n2_pt1++;
                  fgcp2pt++;
                  ogcp2pt++;
            }
            lastverticalw[i] = currentw[lgth2-1];
      }

#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, start1, end1, start2, end2, gapmap1, gapmap2 );
      }
      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] );
      */


      return( wm );
}


Generated by  Doxygen 1.6.0   Back to index