+++ /dev/null
-#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 int localstop;
-
-static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
-{
- Shuryoten *s1 = (Shuryoten *)s1_arg;
- 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[(int)(*s1)[i1]][(int)(*s2)[j]];
-}
-
-static float gentracking( int **used,
- char **seq1, char **seq2,
- char **mseq1, char **mseq2,
- float **cpmx1, float **cpmx2,
- int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
-{
- int l, iin, jin, lgth1, lgth2, k, limk;
- int ifi=0, jfi=0;
-// char gap[] = "-";
- char *gap;
- gap = newgapstr;
- 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;
- 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;
-
- 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 int **used;
- register int i, j;
- int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
- int lgth1, lgth2;
- int resultlen;
- float wm = 0.0; // by D.Mathog,
- float g;
- float *currentw, *previousw;
-#if 1
- float *wtmp;
- int *ijpipt;
- int *ijpjpt;
- float *mjpt, *Mjpt, *prept, *curpt;
- int *mpjpt, *Mpjpt;
-#endif
- static float mi, *m;
- static float Mi, *largeM;
- static int **ijpi;
- static int **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 = 0.0; // by D.Mathog
- int minshuryopos = 0; // by D.Mathog
- 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 )
- {
- FreeIntMtx( commonIP );
- FreeIntMtx( commonJP );
- FreeIntMtx( 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 = AllocateIntMtx( ll1+10, ll2+10 );
- commonIP = AllocateIntMtx( ll1+10, ll2+10 );
- commonJP = AllocateIntMtx( 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;
- *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;
- }
- g = *prept;
- if( g > *mjpt )
- {
- *mjpt = g;
- *mpjpt = i-1;
- }
-#if USE_PENALTY_EX
- *mjpt += fpenalty_ex;
-#endif
-
-
- g = tbk + fpenalty_OP;
-// g = tbk;
- 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;
- 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 );
-}
-
git://source.jalview.org / jabaws.git / blobdiff