+++ /dev/null
-#include "mltaln.h"
-#include "dp.h"
-
-#define DEBUG 1
-#define XXXXXXX 0
-#define USE_PENALTY_EX 0
-
-#define DPTANNI 100
-
-static void OpeningGapCount( double *ogcp, int clus, char **seq, double *eff )
-{
- int i, j, gc, gb;
- int len = strlen( seq[0] );
- double totaleff = 0.0;
-
- for( i=0; i<len; i++ ) ogcp[i] = 0.0;
- for( j=0; j<clus; j++ )
- {
- gc = 0;
- for( i=0; i<len; i++ )
- {
- gb = gc;
- gc = ( seq[j][i] == '-' );
- {
- if( !gb * gc ) ogcp[i] += eff[j];
- }
- }
- totaleff+= eff[j];
- }
- for( i=0; i<len; i++ )
- ogcp[i] /= totaleff;
-}
-
-static void FinalGapCount( double *fgcp, int clus, char **seq, double *eff )
-{
- int i, j, gc, gb;
- int len = strlen( seq[0] );
- double totaleff = 0.0;
-
- for( i=0; i<len; i++ ) fgcp[i] = 0.0;
- for( j=0; j<clus; j++ )
- {
- gc = ( seq[j][0] == '-' );
- for( i=1; i<len+1; i++ )
- {
- gb = gc;
- gc = ( seq[j][i] == '-' );
- {
- if( gb * !gc ) fgcp[i-1] += eff[j];
- }
- }
- totaleff += eff[j];
- }
- for( i=0; i<len; i++ )
- fgcp[i] /= totaleff;
-}
-
-static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
-{
- int j, k, l;
- float scarr[26];
- float **cpmxpd = floatwork;
- int **cpmxpdn = intwork;
- int count = 0;
-
- if( initialize )
- {
- for( j=0; j<lgth2; j++ )
- {
- count = 0;
- for( l=0; l<26; l++ )
- {
- if( cpmx2[j][l] )
- {
- cpmxpd[j][count] = cpmx2[j][l];
- cpmxpdn[j][count] = l;
- count++;
- }
- }
- cpmxpdn[j][count] = -1;
- }
- }
-
- for( l=0; l<26; l++ )
- {
- scarr[l] = 0.0;
- for( k=0; k<26; k++ )
- {
- scarr[l] += n_dis[k][l] * cpmx1[i1][k];
- }
- }
-#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
- {
- float *fpt, **fptpt, *fpt2;
- int *ipt, **iptpt;
- fpt2 = match;
- iptpt = cpmxpdn;
- fptpt = cpmxpd;
- while( lgth2-- )
- {
- *fpt2 = 0.0;
- ipt=*iptpt,fpt=*fptpt;
- while( *ipt > -1 )
- *fpt2 += scarr[*ipt++] * *fpt++;
- fpt2++,iptpt++,fptpt++;
- }
- }
-#else
- for( j=0; j<lgth2; j++ )
- {
- match[j] = 0.0;
- for( k=0; cpmxpdn[j][k]>-1; k++ )
- match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
- }
-#endif
-}
-
-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 ist, int ien, int jst, int jen )
-{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
- char gap[] = "-";
- float wm;
- lgth1 = ien-ist+1;
- lgth2 = jen-jst+1;
-
-#if 1
- 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 );
- }
-
- 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;
- klim = lgth1+lgth2;
- for( k=0; k<=klim; 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][ist+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][jst+jfi+l];
- k++;
- }
- if( iin <= 0 || jin <= 0 ) break;
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = seq1[i][ist+ifi];
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = seq2[j][jst+jfi];
- k++;
- iin = ifi; jin = jfi;
-
- fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
- }
- fprintf( stderr, "in Atracking (owari), mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
- return( 0.0 );
-}
-
-static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2 )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- register int i, j;
- int ll1, ll2;
- int lasti, lastj;
- int resultlen;
- float wm; /* int ?????? */
- float g;
- float *currentw, *previousw;
- float fpenalty = (float)penalty;
- float fpenalty_ex = (float)penalty_ex;
-#if 1
- float *wtmp;
- short *ijppt;
- float *mjpt, *prept, *curpt;
- int *mpjpt;
-#endif
- float mi, *m;
- short **ijp;
- int mpi, *mp;
- float *w1, *w2;
- float *match;
- float *initverticalw; /* kufuu sureba iranai */
- float *lastverticalw; /* kufuu sureba iranai */
- int **intwork;
- float **floatwork;
- short **shortmtx;
- float **WMMTX;
- float dumfl;
- int lgth1, lgth2;
- static char **aseq1 = NULL;
- static char **aseq2 = NULL;
- static char **aseq1bk, **aseq2bk;
-
- if( !aseq1 )
- {
- aseq1 = AllocateCharMtx( icyc, 0 );
- aseq2 = AllocateCharMtx( jcyc, 0 );
- }
-
- lgth1 = ien-ist+1;
- lgth2 = jen-jst+1;
-
- fprintf( stderr, "seq1[0]+ist = %s\n", seq1[0]+ist );
- fprintf( stderr, "seq2[0]+jst = %s\n", seq2[0]+jst );
-
- fprintf( stderr, "ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
- fprintf( stderr, "jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
-
-
- ll1 = ( (int)(1.3*lgth1) ) + 100;
- ll2 = ( (int)(1.3*lgth2) ) + 100;
-
- aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
- aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
- for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
- for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
-
- 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 );
-
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
-
-
- shortmtx = AllocateShortMtx( ll1, ll2 );
- WMMTX = AllocateFloatMtx( ll1, ll2 );
-
- ijp = shortmtx;
-
- currentw = w1;
- previousw = w2;
-
- fprintf( stderr, "calling match_calc\n" );
- match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
-
- match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
-
- WMMTX[0][0] = initverticalw[0];
- for( i=1; i<lgth1+1; i++ )
- {
- initverticalw[i] += fpenalty;
- WMMTX[i][0] = initverticalw[i];
- }
- for( j=1; j<lgth2+1; j++ )
- {
- currentw[j] += fpenalty;
- WMMTX[0][j] = currentw[j];
- }
-
- for( j=1; j<lgth2+1; ++j )
- {
- m[j] = currentw[j-1];
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- fprintf( stderr, "entering to loop\n" );
-
- lasti = lgth1+1;
- for( i=1; i<lasti; i++ )
- {
-
- fprintf( stderr, "i=%d\n", i );
- wtmp = previousw;
- previousw = currentw;
- currentw = wtmp;
-
- previousw[0] = initverticalw[i-1];
-
- fprintf( stderr, "calling match_calc, ist=%d, lgth2=%d\n", ist, lgth2 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
- fprintf( stderr, "done\n" );
- currentw[0] = initverticalw[i];
-
- mi = previousw[0]; mpi = 0;
-
- ijppt = ijp[i] + 1;
- mjpt = m + 1;
- prept = previousw;
- curpt = currentw + 1;
- mpjpt = mp + 1;
- lastj = lgth2+1;
- for( j=1; j<lastj; j++ )
- {
- fprintf( stderr, "j=%d\n", 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;
-
- ijppt++;
- mjpt++;
- prept++;
- mpjpt++;
- curpt++;
- fprintf( stderr, "j=%d end\n", j );
- }
- lastverticalw[i] = currentw[lgth2-1];
- fprintf( stderr, "i=%d end\n", i );
- }
-
-#if 1
- for( i=0; i<lgth1; i++ )
- {
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
- }
- fprintf( stderr, "\n" );
- }
- fprintf( stderr, "\n" );
-#endif
-
- Atracking( currentw, lastverticalw, seq1, seq2, aseq1, aseq2, cpmx1+ist, cpmx2+jst, ijp, icyc, jcyc, ist, ien, jst, jen );
-
- for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
-
- fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
- fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
-
- FreeFloatVec( w1 );
- FreeFloatVec( w2 );
- FreeFloatVec( match );
- FreeFloatVec( initverticalw );
- FreeFloatVec( lastverticalw );
-
- FreeFloatVec( m );
- FreeIntVec( mp );
-
-
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
-
- FreeShortMtx( shortmtx );
- FreeFloatMtx( WMMTX );
-
- FreeCharMtx( aseq1bk );
- FreeCharMtx( aseq2bk );
-
- return( wm );
-}
-
-static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- register int i, j;
- char **aseq1, **aseq2;
- int ll1, ll2;
- int lasti, lastj, imid, jmid;
- int resultlen;
- float wm; /* int ?????? */
- float g;
- float *currentw, *previousw;
- float fpenalty = (float)penalty;
- float fpenalty_ex = (float)penalty_ex;
-#if 1
- float *wtmp;
- short *ijppt;
- float *mjpt, *prept, *curpt;
- int *mpjpt;
-#endif
- float mi, *m;
- short **ijp;
- int mpi, *mp;
- float *w1, *w2;
- float *match;
- float *initverticalw; /* kufuu sureba iranai */
- float *lastverticalw; /* kufuu sureba iranai */
- int **intwork;
- float **floatwork;
- short **shortmtx;
- float **WMMTX;
- float dumfl;
- int lgth1, lgth2;
- float maxwm;
-
- depth++;
-
- lgth1 = ien-ist+1;
- lgth2 = jen-jst+1;
-
- fprintf( stderr, "==== MSalign (%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, ist, ien, jst, jen );
- if( lgth2 <= 0 )
- {
- fprintf( stderr, "==== Jimei\n" );
- for( i=0; i<icyc; i++ )
- {
- strncpy( mseq1[i], seq1[i]+ist, lgth1 );
- mseq1[i][lgth1] = 0;
- }
- for( i=0; i<jcyc; i++ )
- {
- mseq2[i][0] = 0;
- for( j=0; j<lgth1; j++ )
- strcat( mseq2[i], "-" );
- }
-
- fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
- fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
-
- return( (float)offset * lgth1 );
- }
-
-
- aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
- aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
-
- if( lgth1 < DPTANNI )
- {
- fprintf( stderr, "==== Going to _tanni\n" );
- wm = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2 );
-
-
- for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
-
- fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
- fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
-
- fprintf( stderr, "freeing aseq\n" );
- FreeCharMtx( aseq1 );
- FreeCharMtx( aseq2 );
-
- return( wm );
- }
- fprintf( stderr, "Trying to divide the mtx\n" );
-
-
- ll1 = ( (int)(1.3*lgth1) ) + 100;
- ll2 = ( (int)(1.3*lgth2) ) + 100;
-
- fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
-
- 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 );
-
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n" );
-#endif
-
-
-#if DEBUG
- fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
-#endif
-
- shortmtx = AllocateShortMtx( ll1, ll2 );
- WMMTX = AllocateFloatMtx( ll1, ll2 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n\n" );
-#endif
-
- ijp = shortmtx;
-
- currentw = w1;
- previousw = w2;
-
- match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
-
- match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
-
- WMMTX[0][0] = initverticalw[0];
- for( i=1; i<lgth1+1; i++ )
- {
- initverticalw[i] += fpenalty;
- WMMTX[i][0] = initverticalw[i];
- }
- for( j=1; j<lgth2+1; j++ )
- {
- currentw[j] += fpenalty;
- WMMTX[0][j] = currentw[j];
- }
-
- for( j=1; j<lgth2+1; ++j )
- {
- m[j] = currentw[j-1];
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- imid = lgth1 / 2;
-
- lasti = lgth1+1;
-// for( i=1; i<lasti; i++ )
- for( i=1; i<=imid; i++ )
- {
- wtmp = previousw;
- previousw = currentw;
- currentw = wtmp;
-
- previousw[0] = initverticalw[i-1];
-
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
- currentw[0] = initverticalw[i];
-
- mi = previousw[0]; mpi = 0;
-
- 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;
-
- ijppt++;
- mjpt++;
- prept++;
- mpjpt++;
- curpt++;
- }
- lastverticalw[i] = currentw[lgth2-1];
- }
-
-#if 0
- for( i=0; i<lgth1; i++ )
- {
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
- }
- fprintf( stderr, "\n" );
- }
- fprintf( stderr, "\n" );
-#endif
-
-// gyakudp
-
- match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
-
- 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;
- }
-
- for( j=lgth2-1; j>0; --j )
- {
- m[j-1] = currentw[j];
- }
-
-// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
- // m[lgth2-1] ha irunoka?
-
- for( i=lgth1-2; i>=imid; i-- )
-// 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 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
-
- currentw[lgth2-1] = initverticalw[i];
-
- mi = previousw[lgth2-1];
-
- mjpt = m + lgth2 - 2;
- prept = previousw + lgth2 - 1;
- curpt = currentw + lgth2 - 2;
- mpjpt = mp + lgth2 - 2;
-
- for( j=lgth2-2; j>-1; j-- )
- {
- wm = *prept;
- g = mi + fpenalty;
- if( g > wm ) wm = g;
-
- g = *prept;
- if( g >= mi ) mi = g;
-
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
- g = *mjpt + fpenalty;
- if( g > wm ) wm = g;
-
- g = *prept;
- if( g >= *mjpt ) *mjpt = g;
-
-#if USE_PENALTY_EX
- m[j] += fpenalty_ex;
-#endif
-
- WMMTX[i][j] += wm;
- *curpt += wm;
-
- mjpt--;
- prept--;
- mpjpt--;
- curpt--;
- }
- }
-
-#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
-
-// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
-
-#if 0 // irukamo
- 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" );
- }
-#endif
-
-
- maxwm = -999999999.9;
- jmid = -100;
- for( j=0; j<lgth2; j++ )
- {
- wm = WMMTX[imid][j];
- if( wm > maxwm )
- {
- jmid = j;
- maxwm = wm;
- }
- }
- // gap no tochu de kirrareru kanousei ari.
-
- fprintf( stderr, "wm = %f\n", wm );
- fprintf( stderr, "imid = %d\n", imid );
- fprintf( stderr, "jmid = %d\n", jmid );
-
- FreeFloatVec( w1 );
- FreeFloatVec( w2 );
- FreeFloatVec( match );
- FreeFloatVec( initverticalw );
- FreeFloatVec( lastverticalw );
-
- FreeFloatVec( m );
- FreeIntVec( mp );
-
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
-
- FreeShortMtx( shortmtx );
- FreeFloatMtx( WMMTX );
-
-
- fprintf( stderr, "==== calling myself (first)\n" );
- MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+imid, jst, jst+jmid, alloclen, aseq1, aseq2, depth );
- for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
-
- fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
- fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
-
-
- fprintf( stderr, "==== calling myself (second)\n" );
- MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid+1, ien, jst+jmid+1, jen, alloclen, aseq1, aseq2, depth );
-
- for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
-
- fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
- fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
-
- fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
- fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
-
- FreeCharMtx( aseq1 );
- FreeCharMtx( aseq2 );
-
- return( wm );
-}
-
-
-
-float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- int i, j;
- int ll1, ll2;
- int lgth1, lgth2;
- float wm; /* int ?????? */
- static char **mseq1 = NULL;
- static char **mseq2 = NULL;
- char **mseq;
- double *ogcp1;
- double *ogcp2;
- double *fgcp1;
- double *fgcp2;
- float **cpmx1;
- float **cpmx2;
-
-#if 1
- fprintf( stderr, "eff in SA+++align\n" );
- for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
-#endif
- if( mseq1 == NULL )
- {
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- }
-
-
-
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-
- ll1 = ( (int)(1.3*lgth1) ) + 100;
- ll2 = ( (int)(1.3*lgth2) ) + 100;
-
- mseq = AllocateCharMtx( njob, ll1+ll2 );
-
- ogcp1 = AllocateDoubleVec( ll1+2 );
- ogcp2 = AllocateDoubleVec( ll2+2 );
- fgcp1 = AllocateDoubleVec( ll1+2 );
- fgcp2 = AllocateDoubleVec( ll2+2 );
-
- cpmx1 = AllocateFloatMtx( ll1+2, 26 );
- cpmx2 = AllocateFloatMtx( ll2+2, 26 );
-
- for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
- for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
-
-
- MScpmx_calc_new( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
- MScpmx_calc_new( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
-
-#if 0
- OpeningGapCount( ogcp1, icyc, seq1, eff1 );
- OpeningGapCount( ogcp2, jcyc, seq2, eff2 );
- FinalGapCount( fgcp1, icyc, seq1, eff1 );
- FinalGapCount( fgcp2, jcyc, seq2, eff2 );
-
- for( i=0; i<lgth1; i++ )
- {
- ogcp1[i] = 1.0 - ogcp1[i];
- fgcp1[i] = 1.0 - fgcp1[i];
- }
- for( i=0; i<lgth2; i++ )
- {
- ogcp2[i] = 1.0 - ogcp2[i];
- fgcp2[i] = 1.0 - fgcp2[i];
- }
-#endif
-
- wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0 );
-
- for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
-
-
- FreeDoubleVec( ogcp1 );
- FreeDoubleVec( ogcp2 );
- FreeDoubleVec( fgcp1 );
- FreeFloatMtx( cpmx1 );
- FreeFloatMtx( cpmx2 );
- FreeDoubleVec( fgcp2 );
-
- FreeCharMtx( mseq );
-
- return( wm );
-}
git://source.jalview.org / jabaws.git / blobdiff