+++ /dev/null
-#include "mltaln.h"
-#include "dp.h"
-
-#define DEBUG 0
-#define XXXXXXX 0
-#define USE_PENALTY_EX 0
-
-static void extendmseq( char **mseq1, char **mseq2, char **seq1, char **seq2, int i, int j, int prevhiti, int prevhitj )
-{
-// char gap[] = "-";
- char *gap;
- gap = newgapstr;
- int l;
-
- fprintf( stderr, "i=%d, prevhiti=%d\n", i, prevhiti );
- fprintf( stderr, "j=%d, prevhitj=%d\n", j, prevhitj );
- l = prevhiti - i - 1;
- fprintf( stderr, "l=%d\n", l );
- while( l>0 )
- {
- *--mseq1[0] = seq1[0][i+l--];
- *--mseq2[0] = *gap;
- }
- l= prevhitj - j - 1;
- fprintf( stderr, "l=%d\n", l );
- while( l>0 )
- {
- *--mseq1[0] = *gap;
- *--mseq2[0] = seq2[0][j+l--];
- }
- if( i < 0 || j < 0 ) return;
- *--mseq1[0] = seq1[0][i];
- *--mseq2[0] = seq2[0][j];
- fprintf( stderr, "added %c to mseq1, mseq1 = %s \n", seq1[0][i], mseq1[0] );
- fprintf( stderr, "added %c to mseq2, mseq2 = %s \n", seq2[0][j], mseq2[0] );
-}
-
-static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
-{
- char tmpc = s1[0][i1];
- char *seq2 = s2[0];
-
- while( lgth2-- )
- *match++ = amino_dis[(int)tmpc][(int)*seq2++];
-}
-
-static float Atracking( float *lasthorizontalw, float *lastverticalw,
- char **seq1, char **seq2,
- char **mseq1, char **mseq2,
- float **cpmx1, float **cpmx2,
- int **ijp )
-{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
-// char gap[] = "-";
- char *gap;
- gap = newgapstr;
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-
-
-#if 0
- for( i=0; i<lgth1; i++ )
- {
- fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
- }
-#endif
-
- for( i=0; i<lgth1+1; i++ )
- {
- ijp[i][0] = i + 1;
- }
- for( j=0; j<lgth2+1; j++ )
- {
- ijp[0][j] = -( j + 1 );
- }
-
-
- mseq1[0] += lgth1+lgth2;
- *mseq1[0] = 0;
- mseq2[0] += lgth1+lgth2;
- *mseq2[0] = 0;
- iin = lgth1; jin = lgth2;
- limk = lgth1+lgth2 + 1;
- for( k=0; k<limk; k++ )
- {
- if( ijp[iin][jin] < 0 )
- {
- ifi = iin-1; jfi = jin+ijp[iin][jin];
- }
- else if( ijp[iin][jin] > 0 )
- {
- ifi = iin-ijp[iin][jin]; jfi = jin-1;
- }
- else
- {
- ifi = iin-1; jfi = jin-1;
- }
- l = iin - ifi;
- while( --l )
- {
- *--mseq1[0] = seq1[0][ifi+l];
- *--mseq2[0] = *gap;
- k++;
- }
- l= jin - jfi;
- while( --l )
- {
- *--mseq1[0] = *gap;
- *--mseq2[0] = seq2[0][jfi+l];
- k++;
- }
- if( iin <= 0 || jin <= 0 ) break;
- *--mseq1[0] = seq1[0][ifi];
- *--mseq2[0] = seq2[0][jfi];
- k++;
- iin = ifi; jin = jfi;
- }
- return( 0.0 );
-}
-
-void backdp( float **WMMTX, float wmmax, float *maxinw, float *maxinh, int lgth1, int lgth2, int alloclen, float *w1, float *w2, float *initverticalw, float *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 )
-{
- register int i, j;
- int prevhiti, prevhitj;
-// int lasti, lastj;
- float g;
- float fpenalty = (float)penalty;
-#if USE_PENALTY_EX
- float fpenalty_ex = (float)penalty_ex;
-#endif
- float *currentw, *previousw, *wtmp;
- float mi;
- int mpi;
- int *mpjpt;
- float *mjpt, *prept, *curpt;
- float wm = 0.0;
- float forwwm;
-
- currentw = w1;
- previousw = w2;
-
- match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 );
- match_calc( currentw, seq1, seq2, lgth1-1, lgth2 );
-
-
- prevhiti = iin;
- prevhitj = jin;
- fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 );
- fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 );
- extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 );
-
- for( i=0; i<lgth1-1; i++ )
- {
- initverticalw[i] += fpenalty;
- WMMTX[i][lgth2-1] += fpenalty;
- }
- for( j=0; j<lgth2-1; j++ )
- {
- currentw[j] += fpenalty;
- WMMTX[lgth1-1][j] += fpenalty;
- }
-
-
-#if 0
- fprintf( stderr, "initverticalw = \n" );
- for( i=0; i<lgth1; i++ )
- fprintf( stderr, "% 8.2f", initverticalw[i] );
- fprintf( stderr, "\n" );
- fprintf( stderr, "currentw = \n" );
- for( i=0; i<lgth2; i++ )
- fprintf( stderr, "% 8.2f", currentw[i] );
- fprintf( stderr, "\n" );
-#endif
-
- for( j=lgth2-1; j>0; --j )
- {
- m[j-1] = currentw[j];
- mp[j] = 0; // iranai
- }
-
- for( j=0; j<lgth2; j++ ) m[j] = 0.0;
- //m[lgth2-1] ga, irunoka iranainoka irahai.
-
- for( i=lgth1-2; i>-1; i-- )
- {
- wtmp = previousw;
- previousw = currentw;
- currentw = wtmp;
-
- previousw[lgth2-1] = initverticalw[i+1];
-
- match_calc( currentw, seq1, seq2, i, lgth2 );
-
-#if 0
- fprintf( stderr, "i=%d, currentw = \n", i );
- for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] );
- fprintf( stderr, "\n" );
-#endif
-
- currentw[lgth2-1] = initverticalw[i];
-
- mi = previousw[lgth2-1];
- mpi = lgth2-1; //iranai
-
-
- mjpt = m + lgth2 - 2;
- prept = previousw + lgth2 - 1;
- curpt = currentw + lgth2 - 2;
- mpjpt = mp + lgth2 - 2;
-
- for( j=lgth2-2; j>-1; j-- )
- {
-
-// fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] );
- wm = *prept;
- g = mi + fpenalty;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
- }
- g = *prept;
- if( g >= mi )
- {
- mi = g;
- mpi = j+1; //iranai
- }
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
- g = *mjpt + fpenalty;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
- }
- g = *prept;
- if( g >= *mjpt )
- {
- *mjpt = g;
- *mpjpt = i-1; //iranai
- }
-#if USE_PENALTY_EX
- m[j] += fpenalty_ex;
-#endif
-
-#if 0
- fprintf( stderr, "*curpt = %5.0f \n", *curpt );
-#endif
-
-// forwwm = wm + MIN( maxinw[i], maxinh[j] );
- forwwm = wm + MIN( maxinw[i], maxinh[j] );
- WMMTX[i][j] = forwwm;
- if( forwwm == wmmax && i<prevhiti && j<prevhitj )
- {
- fprintf( stderr, "hit!\n" );
- extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj );
- if( forwwm == wmmax )
- {
- *--mseq1[0] = 'u';
- *--mseq2[0] = 'u';
- }
- prevhiti = i;
- prevhitj = j;
- }
- *curpt += wm;
-
- mjpt--;
- prept--;
- mpjpt--;
- curpt--;
- }
- }
- extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj );
-}
-
-
-float MSalign11( char **seq1, char **seq2, int alloclen )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- register int i, j;
- int lasti, lastj;
- int iin = 0, jin = 0; // by Mathog, a guess
- 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
- float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess
- float *maxinh = NULL; // by D.Mathog, guess
-#if 1
- float wmmax;
- float *wtmp;
- int *ijppt;
- float *mjpt, *prept, *curpt;
- int *mpjpt;
-#endif
- static float mi, *m;
- static int **ijp;
- static int mpi, *mp;
- static float *w1, *w2;
- static float *match;
- static float *initverticalw; /* kufuu sureba iranai */
- static float *lastverticalw; /* kufuu sureba iranai */
- static char **mseq1;
- static char **mseq2;
- static char **mseq;
- static float **cpmx1;
- static float **cpmx2;
- static int **intwork;
- static float **WMMTX;
- static float **floatwork;
- static int orlgth1 = 0, orlgth2 = 0;
-
- 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( maxinw );
- FreeFloatVec( maxinh );
-
- FreeFloatVec( m );
- FreeIntVec( mp );
-
- FreeCharMtx( mseq );
-
-
- FreeFloatMtx( cpmx1 );
- FreeFloatMtx( cpmx2 );
-
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
- }
-
- ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
- ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
-
-#if DEBUG
- fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
-#endif
-
- w1 = AllocateFloatVec( ll2+2 );
- w2 = AllocateFloatVec( ll2+2 );
- match = AllocateFloatVec( ll2+2 );
-
- initverticalw = AllocateFloatVec( ll1+2 );
- lastverticalw = AllocateFloatVec( ll1+2 );
- maxinw = AllocateFloatVec( ll1+2 );
-
-
- m = AllocateFloatVec( ll2+2 );
- mp = AllocateIntVec( ll2+2 );
- maxinh = AllocateFloatVec( ll2+2 );
-
- mseq = AllocateCharMtx( njob, ll1+ll2 );
-
- cpmx1 = AllocateFloatMtx( 26, ll1+2 );
- cpmx2 = AllocateFloatMtx( 26, ll2+2 );
-
- floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
- intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n" );
-#endif
-
- orlgth1 = ll1 - 100;
- orlgth2 = ll2 - 100;
- }
-
-
- mseq1[0] = mseq[0];
- mseq2[0] = mseq[1];
-
-
- if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
- {
- int ll1, ll2;
-
- if( commonAlloc1 && commonAlloc2 )
- {
- FreeIntMtx( commonIP );
- FreeFloatMtx( WMMTX );
- }
-
- 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 = AllocateIntMtx( ll1+10, ll2+10 );
- WMMTX = AllocateFloatMtx( ll1+10, ll2+10 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n\n" );
-#endif
-
- commonAlloc1 = ll1;
- commonAlloc2 = ll2;
- }
- ijp = commonIP;
-
-
-#if 0
- for( i=0; i<lgth1; i++ )
- fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
-#endif
-
- currentw = w1;
- previousw = w2;
-
- match_calc( initverticalw, seq2, seq1, 0, lgth1 );
-
-
- match_calc( currentw, seq1, seq2, 0, lgth2 );
-
- WMMTX[0][0] = initverticalw[0];
-
- maxinh[0] = initverticalw[0];
- for( i=1; i<lgth1+1; i++ )
- {
- initverticalw[i] += fpenalty;
- WMMTX[i][0] = initverticalw[i];
- if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
- }
- maxinw[0] = currentw[0];
- for( j=1; j<lgth2+1; j++ )
- {
- currentw[j] += fpenalty;
- WMMTX[0][j] = currentw[j];
- if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
- }
-
- for( j=1; j<lgth2+1; ++j )
- {
- m[j] = currentw[j-1]; mp[j] = 0;
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- 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 );
-
- currentw[0] = initverticalw[i];
-
- mi = previousw[0]; mpi = 0;
-
- maxinwpt = maxinw + i;
- *maxinwpt = currentw[0];
-
- fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
-
- ijppt = ijp[i] + 1;
- mjpt = m + 1;
- prept = previousw;
- curpt = currentw + 1;
- mpjpt = mp + 1;
- lastj = lgth2+1;
-
- for( j=1; j<lastj; j++ )
- {
- wm = *prept;
- *ijppt = 0;
-
-#if 0
- fprintf( stderr, "%5.0f->", wm );
-#endif
- g = mi + fpenalty;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
- *ijppt = -( j - mpi );
- }
- g = *prept;
- if( g >= mi )
- {
- mi = g;
- mpi = j-1;
- }
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
- g = *mjpt + fpenalty;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
- *ijppt = +( i - *mpjpt );
- }
- g = *prept;
- if( g >= *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;
-
- WMMTX[i][j] = *curpt;
-
-
- if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt;
- if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt;
-// fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
-
- ijppt++;
- mjpt++;
- prept++;
- mpjpt++;
- curpt++;
- }
- lastverticalw[i] = currentw[lgth2-1];
- }
-
- wmmax = -999.9;
- for( i=0; i<lgth1; i++ )
- {
- g = lastverticalw[i];
- if( g > wmmax )
- {
- wmmax = g;
- iin = i;
- jin = lgth2-1;
- }
- }
- for( j=0; j<lgth2; j++ )
- {
- g = currentw[j];
- if( g > wmmax )
- {
- wmmax = g;
- iin = lgth1-1;
- jin = j;
- }
- }
-
- for( i=0; i<lgth1; i++ )
- fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
- for( j=0; j<lgth2; j++ )
- fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
-
- fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
- if( iin == lgth1 - 1 && jin == lgth2 - 1 )
- ;
- else
- wmmax += fpenalty;
-
- fprintf( stderr, "wmmax = %f\n", wmmax );
-
-#if 0
- for( i=0; i<lgth1; i++ )
- {
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-#endif
-
- mseq1[0] += lgth1+lgth2;
- *mseq1[0] = 0;
- mseq2[0] += lgth1+lgth2;
- *mseq2[0] = 0;
-
- backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
-
- fprintf( stderr, "\n" );
-#if 1
- fprintf( stderr, "\n" );
- fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
- fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
-#endif
-
-#if 0
- for( i=0; i<lgth1; i++ )
- {
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-#endif
-
- mseq1[0] = mseq[0];
- mseq2[0] = mseq[1];
- mseq1[0] += lgth1+lgth2;
- *mseq1[0] = 0;
- mseq2[0] += lgth1+lgth2;
- *mseq2[0] = 0;
-
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
-
-
- resultlen = strlen( mseq1[0] );
- if( alloclen < resultlen || resultlen > N )
- {
- fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
- ErrorExit( "LENGTH OVER!\n" );
- }
-
-
- strcpy( seq1[0], mseq1[0] );
- strcpy( seq2[0], mseq2[0] );
-#if 1
- fprintf( stderr, "\n" );
- fprintf( stderr, ">\n%s\n", mseq1[0] );
- fprintf( stderr, ">\n%s\n", mseq2[0] );
-#endif
-
-
- return( wm );
-}
-
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