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

suboptalign11.c

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

#define DEBUG 0
#define DEBUG2 0
#define XXXXXXX    0
#define USE_PENALTY_EX  1

typedef struct _shuryoten
{
      int i;
      int j;
      float wm;
      struct _shuryoten *next;
      struct _shuryoten *prev;
} Shuryoten;


static short localstop;

static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
{
      Shuryoten *s1 = (Shuryoten *)s1_arg; // by Camilla Ip
      Shuryoten *s2 = (Shuryoten *)s2_arg;

      if      ( s1->wm > s2->wm ) return( -1 );
      else if ( s1->wm < s2->wm ) return( 1 );
      else                        return( 0 );
}

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]];
}

static float gentracking( short **used,
                                    char **seq1, char **seq2, 
                        char **mseq1, char **mseq2, 
                        float **cpmx1, float **cpmx2, 
                        short **ijpi, short **ijpj, int *off1pt, int *off2pt, int endi, int endj )
{
      int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
      char gap[] = "-";
      float wm;
      static char *res1 = NULL, *res2 = NULL;
      char *mspt1, *mspt2;
      if( res1 == NULL )
      {
            res1 = (char *)calloc( N, sizeof( char ) );
            res2 = (char *)calloc( N, sizeof( char ) );
      }

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

      mspt1 = res1 + lgth1+lgth2;
      *mspt1 = 0;
      mspt2 = res2 + lgth1+lgth2;
      *mspt2 = 0;
      iin = endi; jin = endj;

      limk = lgth1+lgth2;
      if( used[iin][jin] ) return( -1.0 );
      for( k=0; k<=limk; k++ ) 
      {
            ifi = ( ijpi[iin][jin] );
            jfi = ( ijpj[iin][jin] );

            if( used[ifi][jfi] ) return( -1.0 );

            l = iin - ifi;
            while( --l ) 
            {
                  *--mspt1 = seq1[0][ifi+l];
                  *--mspt2 = *gap;
                  k++;
            }
            l= jin - jfi;
            while( --l )
            {
                  *--mspt1 = *gap;
                  *--mspt2 = seq2[0][jfi+l];
                  k++;
            }

            if( iin <= 0 || jin <= 0 ) break;
            *--mspt1 = seq1[0][ifi];
            *--mspt2 = seq2[0][jfi];
            if( ijpi[ifi][jfi] == localstop ) break;
            if( ijpj[ifi][jfi] == localstop ) break; /*いらない*/
            k++;
            iin = ifi; jin = jfi;
      }
      if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
      if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;

//    fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );

      iin = endi; jin = endj;
      limk = lgth1+lgth2;
      for( k=0; k<=limk; k++ ) 
      {
            ifi = ( ijpi[iin][jin] );
            jfi = ( ijpj[iin][jin] );

            used[ifi][jfi] = 1;
            if( iin <= 0 || jin <= 0 ) break;
            if( ijpi[ifi][jfi] == localstop ) break;
            if( ijpj[ifi][jfi] == localstop ) break; /*いらない*/

            k++;
            iin = ifi; jin = jfi;
      }


      strcpy( mseq1[0], mspt1 );
      strcpy( mseq2[0], mspt2 );

      fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );

      return( 0.0 );
}


float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
      int k;
      static short **used;
      register int i, j;
      int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
      int lgth1, lgth2;
      int resultlen;
      float wm;   /* int ?????? */
      float g;
      float *currentw, *previousw;
#if 1
      float *wtmp;
      short *ijpipt;
      short *ijpjpt;
      float *mjpt, *Mjpt, *prept, *curpt;
      int *mpjpt, *Mpjpt;
#endif
      static float mi, *m;
      static float Mi, *largeM;
      static short **ijpi;
      static short **ijpj;
      static int mpi, *mp;
      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 float **cpmx1;
      static float **cpmx2;
      static int **intwork;
      static float **floatwork;
      static int orlgth1 = 0, orlgth2 = 0;
      float maxwm;
      float tbk;
      int tbki, tbkj;
      int endali, endalj;
//    float localthr = 0.0;
//    float localthr2 = 0.0;
      float fpenalty = (float)penalty;
      float fpenalty_OP = (float)penalty_OP;
      float fpenalty_ex = (float)penalty_ex;
      float fpenalty_EX = (float)penalty_EX;
      float foffset = (float)offset;
      float localthr = -foffset;
      float localthr2 = -foffset;
      static Shuryoten *shuryo = NULL;
      int numshuryo;
      float minshuryowm;
      int minshuryopos;
      float resf;


//    fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );

      fprintf( stderr, "in suboptalign11\n" );
      if( !shuryo )
      {
            shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
      }
      for( i=0; i<100; i++ )
      {
            shuryo[i].i = -1;
            shuryo[i].j = -1;
            shuryo[i].wm = 0.0;
      }
      numshuryo = 0;

      if( orlgth1 == 0 )
      {
      }


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

      fprintf( stderr, "in suboptalign11 step 1\n" );

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

      fprintf( stderr, "in suboptalign11 step 1.3\n" );
            if( orlgth1 > 0 && orlgth2 > 0 )
            {
      fprintf( stderr, "in suboptalign11 step 1.4\n" );
                  FreeFloatVec( w1 );
                  FreeFloatVec( w2 );
//                FreeFloatVec( match );
                  FreeFloatVec( initverticalw );
                  FreeFloatVec( lastverticalw );
      fprintf( stderr, "in suboptalign11 step 1.5\n" );

                  FreeFloatVec( m );
                  FreeIntVec( mp );
                  FreeFloatVec( largeM );
                  FreeIntVec( Mp );
      fprintf( stderr, "in suboptalign11 step 1.6\n" );


                  FreeFloatMtx( cpmx1 );
                  FreeFloatMtx( cpmx2 );

      fprintf( stderr, "in suboptalign11 step 1.7\n" );
                  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 );
            largeM = AllocateFloatVec( ll2+2 );
            Mp = AllocateIntVec( ll2+2 );

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

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

            mseq1 = AllocateCharMtx( njob, ll1+ll2 );
            mseq2 = AllocateCharMtx( njob, ll1+ll2 );

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

            orlgth1 = ll1 - 100;
            orlgth2 = ll2 - 100;
      }
      fprintf( stderr, "in suboptalign11 step 1.6\n" );



      fprintf( stderr, "in suboptalign11 step 2\n" );

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

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

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

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

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

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

            commonAlloc1 = ll1;
            commonAlloc2 = ll2;
      }
      ijpi = commonIP;
      ijpj = commonJP;


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

      fprintf( stderr, "in suboptalign11 step 3\n" );
      currentw = w1;
      previousw = w2;

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

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


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

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


#if 0
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
#if DEBUG2
      fprintf( stderr, "\n" );
      fprintf( stderr, "       " );
      for( j=0; j<lgth2+1; j++ )
            fprintf( stderr, "%c     ", seq2[0][j] );
      fprintf( stderr, "\n" );
#endif

      localstop = lgth1+lgth2+1;
      maxwm = -999.9;
      endali = endalj = 0;
#if DEBUG2
      fprintf( stderr, "\n" );
      fprintf( stderr, "%c   ", seq1[0][0] );

      for( j=0; j<lgth2+1; j++ )
            fprintf( stderr, "%5.0f ", currentw[j] );
      fprintf( stderr, "\n" );
#endif

      lasti = lgth1+1;
      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 DEBUG2
            fprintf( stderr, "%c   ", seq1[0][i] );
            fprintf( stderr, "%5.0f ", currentw[0] );
#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
#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;
            Mi = previousw[0]; Mpi = 0;

#if 0
            if( mi < localthr ) mi = localthr2;
#endif

            ijpipt = ijpi[i] + 1;
            ijpjpt = ijpj[i] + 1;
            mjpt = m + 1;
            Mjpt = largeM + 1;
            prept = previousw;
            curpt = currentw + 1;
            mpjpt = mp + 1;
            Mpjpt = Mp + 1;
            tbk = -999999.9;
            tbki = 0;
            tbkj = 0;
            lastj = lgth2+1;
            for( j=1; j<lastj; j++ )
            {
                  wm = *prept;
                  *ijpipt = i-1;
                  *ijpjpt = j-1;


//                fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
//                fprintf( stderr, "wm=%f\n", wm );
#if 0
                  fprintf( stderr, "%5.0f->", wm );
#endif
                  g = mi + fpenalty;
#if 0
                  fprintf( stderr, "%5.0f?", g );
#endif
                  if( g > wm )
                  {
                        wm = g;
//                      *ijpipt = i - 1; /*いらない*/
                        *ijpjpt = mpi;
                  }
                  g = *prept;
                  if( g > mi )
                  {
                        mi = g;
                        mpi = j-1;
                  }

#if USE_PENALTY_EX
                  mi += fpenalty_ex;
#endif

#if 0
                  fprintf( stderr, "%5.0f->", wm );
#endif
                  g = *mjpt + fpenalty;
#if 0
                  fprintf( stderr, "m%5.0f?", g );
#endif
                  if( g > wm )
                  {
                        wm = g;
                        *ijpipt = *mpjpt;
//                      *ijpjpt = j - 1; /*いらない*/
                  }
                  g = *prept;
                  if( g > *mjpt )
                  {
                        *mjpt = g;
                        *mpjpt = i-1;
                  }
#if USE_PENALTY_EX
                  *mjpt += fpenalty_ex;
#endif


                  g =  tbk + fpenalty_OP; /*別の方がいいかも*/
//                g =  tbk; /*別の方がいいかも*/
                  if( g > wm )
                  {
                        wm = g;
                        *ijpipt = tbki;
                        *ijpjpt = tbkj;
//                      fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
                  }
                  g = Mi;
                  if( g > tbk )
                  {
                        tbk = g;
                        tbki = i-1;
                        tbkj = Mpi;
                  }
                  g = *Mjpt;
                  if( g > tbk )
                  {
                        tbk = g;
                        tbki = *Mpjpt;
                        tbkj = j-1;
                  }
//                tbk += fpenalty_EX;// + foffset;

                  g = *prept;
                  if( g > *Mjpt )
                  {
                        *Mjpt = g;
                        *Mpjpt = i-1;
                  }
//                *Mjpt += fpenalty_EX;// + foffset;

                  g = *prept;
                  if( g > Mi )
                  {
                        Mi = g;
                        Mpi = j-1;
                  }
//                Mi += fpenalty_EX;// + foffset;


//                fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
//                fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );


                  if( maxwm < wm )
                  {
                        maxwm = wm;
                        endali = i;
                        endalj = j;
                  }

#if 1
                  if( numshuryo < 100 )
                  {
                        shuryo[numshuryo].i = i;
                        shuryo[numshuryo].j = j;
                        shuryo[numshuryo].wm = wm;

                        if( minshuryowm > wm )
                        {
                               minshuryowm = wm;
                               minshuryopos = numshuryo;
                        }
                        numshuryo++;
                  }
                  else
                  {
                        if( wm > minshuryowm )
                        {
                              shuryo[minshuryopos].i = i;
                              shuryo[minshuryopos].j = j;
                              shuryo[minshuryopos].wm = wm;
                              minshuryowm = wm;
                              for( k=0; k<100; k++ )    // muda
                              {
                                    if( shuryo[k].wm < minshuryowm )
                                    {
                                          minshuryowm = shuryo[k].wm;
                                          minshuryopos = k;
                                          break;
                                    }
                              }
                        }
                  }
#endif
#if 1
                  if( wm < localthr )
                  {
//                      fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
                        *ijpipt = localstop;
//                      *ijpjpt = localstop; /*いらない*/
                        wm = localthr2;
                  }
#endif
#if 0
                  fprintf( stderr, "%5.0f ", *curpt );
#endif
#if DEBUG2
                  fprintf( stderr, "%5.0f ", wm );
//                fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
#endif

                  *curpt += wm;
                  ijpipt++;
                  ijpjpt++;
                  mjpt++;
                  Mjpt++;
                  prept++;
                  mpjpt++;
                  Mpjpt++;
                  curpt++;
            }
#if DEBUG2
            fprintf( stderr, "\n" );
#endif

            lastverticalw[i] = currentw[lgth2-1];
      }

      for( k=0; k<100; k++ )
      {
            fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
      }


#if 1
      fprintf( stderr, "maxwm = %f\n", maxwm );
      fprintf( stderr, "endali = %d\n", endali );
      fprintf( stderr, "endalj = %d\n", endalj );
#endif

      qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
      for( k=0; k<100; k++ )
      {
            fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
      }

            
      lasti = lgth1+1;
    for( i=0; i<lasti; i++ ) 
    {
        ijpi[i][0] = localstop;
        ijpj[i][0] = localstop;
    }
      lastj = lgth2+1;
    for( j=0; j<lastj; j++ ) 
    {
        ijpi[0][j] = localstop;
        ijpj[0][j] = localstop;
    }

      for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;

      for( k=0; k<numshuryo; k++ )
      {
            if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
            fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
            resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
            if( resf == -1.0 ) continue;
            putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
#if 0
            fprintf( stderr, "\n" );
            fprintf( stderr, ">\n%s\n", mseq1[0] );
            fprintf( stderr, ">\n%s\n", mseq2[0] );
#endif
      }
      for( i=0; i<20; i++ )
      {
            for( j=0; j<20; j++ )
            {
                  fprintf( stderr, "%2d ", used[i][j] );
            }
            fprintf( stderr, "\n" );
      }


//    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" );
      }





      return( wm );
}


Generated by  Doxygen 1.6.0   Back to index