+++ /dev/null
-#include "mltaln.h"
-#include "dp.h"
-
-#define MEMSAVE 1
-
-#define DEBUG 0
-#define USE_PENALTY_EX 0
-#define STOREWM 0
-
-#define DPTANNI 100
-
-
-static TLS int reccycle = 0;
-
-
-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;
- float *matchpt;
- float **cpmxpdpt;
- int **cpmxpdnpt;
- int cpkd;
-
- 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++;
- }
- }
- 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];
- }
-#else
- matchpt = match;
- cpmxpdnpt = cpmxpdn;
- cpmxpdpt = cpmxpd;
- while( lgth2-- )
- {
- *matchpt = 0.0;
- for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
- *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
- matchpt++;
- cpmxpdnpt++;
- cpmxpdpt++;
- }
-#endif
-}
-
-static float Atracking( float *lasthorizontalw, float *lastverticalw,
- char **seq1, char **seq2,
- char **mseq1, char **mseq2,
- int **ijp, int icyc, int jcyc,
- int ist, int ien, int jst, int jen,
- int fulllen1, int fulllen2, int tailgp )
-{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
- char *gaptable1, *gt1bk;
- char *gaptable2, *gt2bk;
- float wm;
- lgth1 = ien-ist+1;
- lgth2 = jen-jst+1;
-
- gt1bk = AllocateCharVec( lgth1+lgth2+1 );
- gt2bk = AllocateCharVec( lgth1+lgth2+1 );
-
-#if 0
- for( i=0; i<lgth1; i++ )
- {
- fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
- }
-#endif
-
-
-// fprintf( stderr, "in Atracking, tailgp=%d, ien=%d, fulllen1=%d, jen=%d, fulllen2=%d\n", tailgp, ien, fulllen1, jen, fulllen2 );
-
- if( tailgp == 1 )
- ;
- else if( ien == fulllen1-1 || jen == fulllen2-1 )
- {
-// fprintf( stderr, "searching lasthorizontalw and lasthorizontalw\n" );
- 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 );
- }
- }
- }
-#if 0
- else if( jen == fulllen2-1 )
- {
- fprintf( stderr, "searching lastverticalw\n" );
- 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 );
- }
- }
- }
- else if( ien == fulllen1-1 )
- {
- fprintf( stderr, "searching lasthorizontalw\n" );
- wm = lasthorizontalw[0];
- for( j=0; j<lgth2; j++ )
- {
- if( lasthorizontalw[j] >= wm )
- {
- wm = lasthorizontalw[j];
- iin = lgth1-1; jin = j;
- ijp[lgth1][lgth2] = -( lgth2 - j );
- }
- }
- }
-#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 );
- }
-
-
- gaptable1 = gt1bk + lgth1+lgth2;
- *gaptable1 = 0;
- gaptable2 = gt2bk + lgth1+lgth2;
- *gaptable2 = 0;
-
-// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[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 )
- {
- *--gaptable1 = 'o';
- *--gaptable2 = '-';
- k++;
- }
- l= jin - jfi;
- while( --l )
- {
- *--gaptable1 = '-';
- *--gaptable2 = 'o';
- k++;
- }
- if( iin <= 0 || jin <= 0 ) break;
- *--gaptable1 = 'o';
- *--gaptable2 = 'o';
- k++;
- iin = ifi; jin = jfi;
-
- }
-
- for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
- for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
-
- free( gt1bk );
- free( gt2bk );
-
-// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
-// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", 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, int fulllen1, int fulllen2, char **mseq1, char **mseq2, float **gapinfo, int headgp, int tailgp )
-/* 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;
- float wm = 0.0; /* int ?????? */
- float g;
- float *currentw, *previousw;
-#if USE_PENALTY_EX
- float fpenalty_ex = (float)penalty_ex;
-#endif
-#if 1
- float *wtmp;
- int *ijppt;
- float *mjpt, *prept, *curpt;
- int *mpjpt;
-#endif
- float mi, *m;
- int **ijp;
- int mpi, *mp;
- float *w1, *w2;
- float *initverticalw; /* kufuu sureba iranai */
- float *lastverticalw; /* kufuu sureba iranai */
- int **intwork;
- float **floatwork;
- int **intmtx;
- int lgth1, lgth2;
- float *ogcp1;
- float *fgcp1;
- float *ogcp2;
- float *fgcp2;
-// char **aseq1;
-// char **aseq2;
-// char **aseq1bk, **aseq2bk;
-
-
- ogcp1 = gapinfo[0] + ist;
- fgcp1 = gapinfo[1] + ist;
- ogcp2 = gapinfo[2] + jst;
- fgcp2 = gapinfo[3] + jst;
-
-#if STOREWM
- char ttt1[10000], ttt2[10000];
-#endif
-
-
- lgth1 = ien-ist+1;
- lgth2 = jen-jst+1;
-
-#if STOREWM
- strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
- strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
-
- fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
- fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
- fprintf( stderr, "ttt1 = %s\n", ttt1 );
- fprintf( stderr, "ttt2 = %s\n", ttt2 );
-#endif
-
-#if 0
- fprintf( stderr, "in _tanni ist,ien = %d,%d, fulllen1=%d\n", ist, ien, fulllen1 );
- fprintf( stderr, "in _tanni jst,jen = %d,%d, fulllen2=%d\n", jst, jen, fulllen2 );
- fprintf( stderr, "in _tanni seq1[0] = %-*.*s\n", ien-ist+1, ien-ist+1, seq1[0]+ist );
- fprintf( stderr, "in _tanni seq2[0] = %-*.*s\n", jen-jst+1, jen-jst+1, seq2[0]+jst );
-#endif
-
-
- ll1 = ( (int)(lgth1) ) + 100;
- ll2 = ( (int)(lgth2) ) + 100;
-
-// aseq1 = AllocateCharMtx( icyc, 0 );
-// aseq2 = AllocateCharMtx( jcyc, 0 );
-// 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 );
-
- initverticalw = AllocateFloatVec( ll1+2 );
- lastverticalw = AllocateFloatVec( ll1+2 );
-
- m = AllocateFloatVec( ll2+2 );
- mp = AllocateIntVec( ll2+2 );
-
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
-
-
- intmtx = AllocateIntMtx( ll1+1, ll2+1 );
-
- ijp = intmtx;
-
- 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 );
-
- if( headgp || ist != 0 )
- {
- for( i=1; i<lgth1+1; i++ )
- {
- initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
- }
- }
- if( headgp || jst != 0 )
- {
- for( j=1; j<lgth2+1; j++ )
- {
- currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
- }
- }
-
- for( j=1; j<lgth2+1; ++j )
- {
- m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;;
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
-
-
- if( tailgp || jen != fulllen2-1 ) lasti = lgth1+1; else lasti = lgth1;
-// if( 1 ) lasti = lgth1+1; else lasti = lgth1;
- for( i=1; i<lasti; 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] + ogcp2[1];
- mpi = 0;
-
- ijppt = ijp[i] + 1;
- mjpt = m + 1;
- prept = previousw;
- curpt = currentw + 1;
- mpjpt = mp + 1;
-// if( tailgp && jen != fulllen2-1 ) lastj = lgth2+1; else lastj = lgth2;
- lastj = lgth2+1;
- for( j=1; j<lastj; j++ )
- {
- wm = *prept;
- *ijppt = 0;
-
-#if 0
- fprintf( stderr, "%5.0f->", wm );
-#endif
- g = mi + fgcp2[j-1];
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
- *ijppt = -( j - mpi );
- }
- g = *prept + ogcp2[j];
- if( g >= mi )
- {
- mi = g;
- mpi = j-1;
- }
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
- g = *mjpt + fgcp1[i-1];
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
- *ijppt = +( i - *mpjpt );
- }
- g = *prept + ogcp1[i];
- 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;
-
-
- ijppt++;
- mjpt++;
- prept++;
- mpjpt++;
- curpt++;
- }
- lastverticalw[i] = currentw[lgth2-1];
- }
-
-// fprintf( stderr, "wm = %f\n", wm );
-
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, ist, ien, jst, jen, fulllen1, fulllen2, tailgp );
-#if 0
- fprintf( stderr, "res in _tanni mseq1[0] = %s\n", mseq1[0] );
- fprintf( stderr, "res in _tanni mseq2[0] = %s\n", mseq2[0] );
-#endif
-
-// 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( initverticalw );
- FreeFloatVec( lastverticalw );
-
- FreeFloatVec( m );
- FreeIntVec( mp );
-
-
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
-
- FreeIntMtx( intmtx );
-
-
-// FreeCharMtx( aseq1bk );
-// FreeCharMtx( aseq2bk );
-
-// free( aseq1 );
-// free( aseq2 );
-
- return( wm );
-
-}
-
-static void freearrays_rec1(
- float *w1, float *w2, float *initverticalw, float *lastverticalw,
- float *midw, float *midm, float *midn,
- int *jumpbacki, int *jumpbackj, int *jumpforwi, int *jumpforwj, int *jumpdummi, int *jumpdummj,
- float *m, int *mp,
- float **floatwork, int **intwork
-#if STOREWM
- , float **WMMTX, float **WMMTX2
-#endif
-)
-{
-
- FreeFloatVec( w1 );
- FreeFloatVec( w2 );
- FreeFloatVec( initverticalw );
- FreeFloatVec( lastverticalw );
- FreeFloatVec( midw );
- FreeFloatVec( midm );
- FreeFloatVec( midn );
-
- FreeIntVec( jumpbacki );
- FreeIntVec( jumpbackj );
- FreeIntVec( jumpforwi );
- FreeIntVec( jumpforwj );
- FreeIntVec( jumpdummi );
- FreeIntVec( jumpdummj );
-
- FreeFloatVec( m );
- FreeIntVec( mp );
-
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
-
-#if STOREWM
- FreeFloatMtx( WMMTX );
- FreeFloatMtx( WMMTX2 );
-#endif
-}
-
-static void freearrays_rec2( char *gaps, char **aseq1, char **aseq2 )
-{
- free( gaps );
-#if MEMSAVE
- free( aseq1 );
- free( aseq2 );
-#else
- FreeCharMtx( aseq1 );
- FreeCharMtx( aseq2 );
-#endif
-}
-
-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, int fulllen1, int fulllen2, char **mseq1, char **mseq2, int depth, float **gapinfo, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- int alnlen;
- float value = 0.0;
- register int i, j;
- char **aseq1, **aseq2;
- int ll1, ll2, l, len;
- int lasti, lastj, imid;
- int jmid = 0; // by D.Mathog, a guess
- float wm = 0.0; /* int ?????? */
- float g;
- float *currentw, *previousw;
-#if USE_PENALTY_EX
- float fpenalty_ex = (float)penalty_ex;
-#endif
- float *wtmp;
-// short *ijppt;
- int *mpjpt;
-// short **ijp;
- int *mp;
- int mpi;
- float *mjpt, *prept, *curpt;
- float mi;
- float *m;
- float *w1, *w2;
-// float *match;
- float *initverticalw; /* kufuu sureba iranai */
- float *lastverticalw; /* kufuu sureba iranai */
- int **intwork;
- float **floatwork;
-// short **shortmtx;
-#if STOREWM
- float **WMMTX;
- float **WMMTX2;
-#endif
- float *midw;
- float *midm;
- float *midn;
- int lgth1, lgth2;
- float maxwm;
- int *jumpforwi;
- int *jumpforwj;
- int *jumpbacki;
- int *jumpbackj;
- int *jumpdummi; //muda
- int *jumpdummj = NULL; // by D.Mathog, a guess
- int jumpi, jumpj = 0; // by D.Mathog, a guess
- char *gaps;
- int ijpi, ijpj;
- float *ogcp1;
- float *fgcp1;
- float *ogcp2;
- float *fgcp2;
- float firstm;
- int firstmp;
-#if STOREWM
- static TLS char ttt1[50000];
- static TLS char ttt2[50000];
-#endif
-
-#if 0
- int nglen1, nglen2;
- nglen1 = seqlen( seq1[0] );
- nglen2 = seqlen( seq2[0] );
-#endif
-
-// fprintf( stderr, "fulllen1 = %d, fulllen2 = %d, headgp = %d, tailgp = %d\n", fulllen1, fulllen2, headgp, tailgp );
-
- ogcp1 = gapinfo[0] + ist;
- fgcp1 = gapinfo[1] + ist;
- ogcp2 = gapinfo[2] + jst;
- fgcp2 = gapinfo[3] + jst;
-
- depth++;
- reccycle++;
-
- lgth1 = ien-ist+1;
- lgth2 = jen-jst+1;
-
-// if( lgth1 < 5 )
-// fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
-// if( lgth2 < 5 )
-// fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
-//
-
-
-#if STOREWM
- fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
- strncpy( ttt1, seq1[0]+ist, lgth1 );
- strncpy( ttt2, seq2[0]+jst, lgth2 );
- ttt1[lgth1] = 0;
- ttt2[lgth2] = 0;
- fprintf( stderr, "seq1 = %s\n", ttt1 );
- fprintf( stderr, "seq2 = %s\n", ttt2 );
-#endif
- if( lgth2 <= 0 ) // lgth1 <= 0 ha?
- {
-// fprintf( stderr, "\n\n==== jimei\n\n" );
-// exit( 1 );
- 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( 0.0 );
- }
-
-#if MEMSAVE
- aseq1 = AllocateCharMtx( icyc, 0 );
- aseq2 = AllocateCharMtx( jcyc, 0 );
- for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
- for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
-#else
- aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
- aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
-#endif
-
-// fprintf( stderr, "####(s) seq1[0] (%d) = \n%-*.*s\n (a%d-a%d)\n", depth, ien-ist+1, ien-ist+1, seq1[0]+ist, ist, ien );
-// fprintf( stderr, "####(s) seq2[0] (%d) = \n%-*.*s\n (b%d-b%d)\n", depth, jen-jst+1, jen-jst+1, seq2[0]+jst, jst, jen );
-
-// if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
-// if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
- if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
- {
-// fprintf( stderr, "==== Going to _tanni\n" );
-
- value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, gapinfo, headgp, tailgp );
-
-
-#if MEMSAVE
- free( aseq1 );
- free( aseq2 );
-#else
- for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
-
- FreeCharMtx( aseq1 );
- FreeCharMtx( aseq2 );
-#endif
-
-// fprintf( stderr, "value = %f\n", value );
-
- return( value );
- }
-// fprintf( stderr, "Trying to divide the mtx\n" );
-
- ll1 = ( (int)(lgth1) ) + 100;
- ll2 = ( (int)(lgth2) ) + 100;
-
-// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
-
- w1 = AllocateFloatVec( ll2+2 );
- w2 = AllocateFloatVec( ll2+2 );
-// match = AllocateFloatVec( ll2+2 );
- midw = AllocateFloatVec( ll2+2 );
- midn = AllocateFloatVec( ll2+2 );
- midm = AllocateFloatVec( ll2+2 );
- jumpbacki = AllocateIntVec( ll2+2 );
- jumpbackj = AllocateIntVec( ll2+2 );
- jumpforwi = AllocateIntVec( ll2+2 );
- jumpforwj = AllocateIntVec( ll2+2 );
- jumpdummi = AllocateIntVec( ll2+2 );
- jumpdummj = AllocateIntVec( ll2+2 );
-
- initverticalw = AllocateFloatVec( ll1+2 );
- lastverticalw = AllocateFloatVec( ll1+2 );
-
- m = AllocateFloatVec( ll2+2 );
- mp = AllocateIntVec( ll2+2 );
- gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
-
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n" );
-#endif
-
-#if STOREWM
- WMMTX = AllocateFloatMtx( ll1, ll2 );
- WMMTX2 = AllocateFloatMtx( ll1, ll2 );
-#endif
-#if 0
- shortmtx = AllocateShortMtx( ll1, ll2 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n\n" );
-#endif
-
- ijp = shortmtx;
-#endif
-
- 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 );
-
- for( i=1; i<lgth1+1; i++ )
- {
- initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
- }
- for( j=1; j<lgth2+1; j++ )
- {
- currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
- }
-
-#if STOREWM
- WMMTX[0][0] = initverticalw[0];
- for( i=1; i<lgth1+1; i++ )
- {
- WMMTX[i][0] = initverticalw[i];
- }
- for( j=1; j<lgth2+1; j++ )
- {
- WMMTX[0][j] = currentw[j];
- }
-#endif
-
-
- for( j=1; j<lgth2+1; ++j )
- {
- m[j] = currentw[j-1] + ogcp1[1];
-// m[j] = currentw[j-1];
- mp[j] = 0;
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- imid = lgth1 * 0.5;
-
- jumpi = 0; // atode kawaru.
- lasti = lgth1+1;
-#if STOREWM
- for( i=1; i<lasti; i++ )
-#else
- for( i=1; i<=imid; i++ )
-#endif
- {
-#ifdef enablemultithread
-// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
- if( chudanpt && *chudanpt != chudanref )
- {
-// fprintf( stderr, "\n\n## CHUUDAN!!! zenhan\n" );
- *chudanres = 1;
- freearrays_rec1
- (
- w1, w2, initverticalw, lastverticalw, midw, midm, midn,
- jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
- m, mp,
- floatwork, intwork
-#if STOREWM
- , WMMTX, WMMTX2
-#endif
- );
- freearrays_rec2( gaps, aseq1, aseq2 );
- return( -1.0 );
- }
-#endif
- 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];
-
- m[0] = ogcp1[i];
-#if STOREM
- WMMTX2[i][0] = m[0];
-#endif
- if( i == imid ) midm[0] = m[0];
-
- mi = previousw[0] + ogcp2[1];
-// 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;
-
-#if 0
- fprintf( stderr, "%5.0f->", wm );
-#endif
- g = mi + fgcp2[j-1];
-// g = mi + fpenalty;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
-// *ijppt = -( j - mpi );
- }
- g = *prept + ogcp2[j];
-// g = *prept;
- if( g >= mi )
- {
- mi = g;
- mpi = j-1;
- }
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
- g = *mjpt + fgcp1[i-1];
-// g = *mjpt + fpenalty;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
- {
- wm = g;
-// *ijppt = +( i - *mpjpt );
- }
-
-
- g = *prept + ogcp1[i];
-// 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;
-
-#if STOREWM
- WMMTX[i][j] = *curpt;
- WMMTX2[i][j] = *mjpt;
-#endif
-
- if( i == imid ) //muda
- {
- jumpbackj[j] = *mpjpt; // muda atode matomeru
- jumpbacki[j] = mpi; // muda atode matomeru
-// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
-// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
- midw[j] = *curpt;
- midm[j] = *mjpt;
- midn[j] = mi;
- }
-
-// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
- mjpt++;
- prept++;
- mpjpt++;
- curpt++;
-
- }
- lastverticalw[i] = currentw[lgth2-1];
-
-#if STOREWM
- WMMTX2[i][lgth2] = m[lgth2-1];
-#endif
-
-#if 0 // ue
- if( i == imid )
- {
- for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
- for( j=0; j<lgth2; j++ ) midm[j] = m[j];
- }
-#endif
- }
-// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
-// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
-
-#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" );
- fprintf( stderr, "WMMTX2 = \n" );
- for( i=0; i<lgth1; i++ )
- {
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 10.2f ", WMMTX2[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] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
-// initverticalw[i] += fpenalty;
- }
- for( j=0; j<lgth2-1; j++ )
- {
- currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
-// currentw[j] += fpenalty;
- }
-
-#if STOREWM
- for( i=0; i<lgth1-1; i++ )
- {
- WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
- fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
- }
- for( j=0; j<lgth2-1; j++ )
- {
- WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
- fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
- }
-#endif
-
-
-
-
-
-
- for( j=lgth2-1; j>0; --j )
- {
- m[j-1] = currentw[j] + fgcp2[lgth2-2];
-// m[j-1] = currentw[j];
- mp[j] = lgth1-1;
- }
-
-// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
- // m[lgth2-1] ha irunoka?
-
-
-// for( i=lgth1-2; i>=imid; i-- )
- firstm = -9999999.9;
-// firstmp = lgth1-1;
- firstmp = lgth1;
- for( i=lgth1-2; i>-1; i-- )
- {
-#ifdef enablemultithread
-// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
- if( chudanpt && *chudanpt != chudanref )
- {
-// fprintf( stderr, "\n\n## CHUUDAN!!! kouhan\n" );
- *chudanres = 1;
- freearrays_rec1
- (
- w1, w2, initverticalw, lastverticalw, midw, midm, midn,
- jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
- m, mp,
- floatwork, intwork
-#if STOREWM
- , WMMTX, WMMTX2
-#endif
- );
- freearrays_rec2( gaps, aseq1, aseq2 );
- return( -1.0 );
- }
-#endif
- 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];
-
-// m[lgth2] = fgcp1[i];
-// WMMTX2[i][lgth2] += m[lgth2];
-// fprintf( stderr, "m[] = %f\n", m[lgth2] );
-
- mi = previousw[lgth2-1] + fgcp2[lgth2-2];
-// mi = previousw[lgth2-1];
- mpi = 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;
- ijpi = i+1;
- ijpj = j+1;
-
- g = mi + ogcp2[j+1];
-// g = mi + fpenalty;
- if( g > wm )
- {
- wm = g;
- ijpj = mpi;
- ijpi = i+1;
- }
-
- g = *prept + fgcp2[j];
-// g = *prept;
- if( g >= mi )
- {
-// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
- mi = g;
- mpi = j + 1;
- }
-
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
-// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
- g = *mjpt + ogcp1[i+1];
-// g = *mjpt + fpenalty;
- if( g > wm )
- {
- wm = g;
- ijpi = *mpjpt;
- ijpj = j+1;
- }
-
-// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
- g = *prept + fgcp1[i];
-// g = *prept;
- if( g >= *mjpt )
- {
- *mjpt = g;
- *mpjpt = i + 1;
- }
-
-#if USE_PENALTY_EX
- m[j] += fpenalty_ex;
-#endif
-
- if( i == jumpi || i == imid - 1 )
- {
- jumpforwi[j] = ijpi; //muda
- jumpforwj[j] = ijpj; //muda
-// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
-// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
- }
- if( i == imid ) // muda
- {
- midw[j] += wm;
-// midm[j+1] += *mjpt + fpenalty; //??????
- midm[j+1] += *mjpt; //??????
- }
- if( i == imid - 1 )
- {
-// midn[j] += mi + fpenalty; //????
- midn[j] += mi; //????
- }
-#if STOREWM
- WMMTX[i][j] += wm;
-// WMMTX2[i][j+1] += *mjpt + fpenalty;
- WMMTX2[i][j+1] += *mjpt;
-#endif
- *curpt += wm;
-
- mjpt--;
- prept--;
- mpjpt--;
- curpt--;
- }
-// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
- g = *prept + fgcp1[i];
- if( firstm < g )
- {
- firstm = g;
- firstmp = i + 1;
- }
-#if STOREWM
- WMMTX2[i][j+1] += firstm;
-#endif
- if( i == imid ) midm[j+1] += firstm;
-
-
- if( i == imid - 1 )
- {
- maxwm = midw[1];
- jmid = 0;
-// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
- for( j=2; j<lgth2-1; j++ )
- {
- wm = midw[j];
- if( wm > maxwm )
- {
- jmid = j;
- maxwm = wm;
- }
-// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
- }
- for( j=0; j<lgth2+1; j++ )
- {
- wm = midm[j];
- if( wm > maxwm )
- {
- jmid = j;
- maxwm = wm;
- }
-// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
- }
-
-// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
-
-
-// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
- wm = midw[jmid];
- jumpi = imid-1;
- jumpj = jmid-1;
- if( jmid > 0 && midn[jmid-1] > wm ) //060413
- {
- jumpi = imid-1;
- jumpj = jumpbacki[jmid];
- wm = midn[jmid-1];
-// fprintf( stderr, "rejump (n)\n" );
- }
- if( midm[jmid] > wm )
- {
- jumpi = jumpbackj[jmid];
- jumpj = jmid-1;
- wm = midm[jmid];
-// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
- }
-
-
-// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
-// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
-#if STOREWM
- fprintf( stderr, "imid = %d\n", imid );
- fprintf( stderr, "midn = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7.1f ", midn[j] );
- }
- fprintf( stderr, "\n" );
- fprintf( stderr, "midw = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7.1f ", midw[j] );
- }
- fprintf( stderr, "\n" );
- fprintf( stderr, "midm = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7.1f ", midm[j] );
- }
- fprintf( stderr, "\n" );
-#endif
-// fprintf( stderr, "maxwm = %f\n", maxwm );
- }
- if( i == jumpi ) //saki?
- {
-// fprintf( stderr, "#### FIRST i=%d, jumpi<imid=%d<%d, ist=%d, ien=%d, firstmp=%d, lgth1=%d\n", i, jumpi, imid, ist, ien, firstmp, lgth1 );
-// fprintf( stderr, "#### mark 1\n" );
-// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
-// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
-
- if( jmid == 0 )
- {
-// fprintf( stderr, "#### CHUI2!\n" );
- jumpj = 0; jmid = 1;
-#if 0 // v6.823 made
- jumpi = firstmp-1;
- imid = firstmp;
-#endif
-#if 0
- jumpi = 0;
- imid = 1;
-#else
-// if( 1 || firstmp > 100 ) // naze 100
- if( imid < firstmp-1 ) // naze 100
- {
- jumpi = firstmp;
- imid = firstmp+1;
- }
-#if 0
- else
- {
- jumpi = 0;
- imid = 1;
- }
-#endif
-#endif
- }
-
-#if 0
- else if( jmid == lgth2 )
- {
- fprintf( stderr, "CHUI1!\n" );
- jumpi=0; jumpj=0;
- imid=jumpforwi[0]; jmid=lgth2-1;
- }
-#else // 060414
- else if( jmid >= lgth2 )
- {
-// fprintf( stderr, "CHUI1!\n" );
- jumpi=imid-1; jmid=lgth2;
- jumpj = lgth2-1;
- }
-#endif
- else
- {
-// fprintf( stderr, "#### CHUI3!\n" );
- imid = jumpforwi[jumpj];
- jmid = jumpforwj[jumpj];
- if( imid == jumpi ) jumpi = imid-1;
- }
-#if 0
- fprintf( stderr, "jumpi -> %d\n", jumpi );
- fprintf( stderr, "jumpj -> %d\n", jumpj );
- fprintf( stderr, "imid -> %d\n", imid );
- fprintf( stderr, "jmid -> %d\n", jmid );
-#endif
-// fprintf( stderr, "#### FINAL i=%d, jumpi<imid=%d<%d, ist=%d, ien=%d, firstmp=%d\n", i, jumpi, imid, ist, ien, firstmp );
-
-#if STOREWM
- break;
-#else
- break;
-#endif
- }
- }
-
-// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
-// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
-
-// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
-// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
-// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
-// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
-
-
-#if STOREWM
- fprintf( stderr, "WMMTX = \n" );
- for( i=0; i<lgth1; i++ )
- {
- fprintf( stderr, "%d ", i );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-// fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
- for( i=0; i<lgth1; i++ )
- {
- fprintf( stderr, "%d ", i );
- for( j=0; j<lgth2+1; j++ )
- {
- fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-
- fprintf( stderr, "jumpbacki = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7d ", jumpbacki[j] );
- }
- fprintf( stderr, "\n" );
- fprintf( stderr, "jumpbackj = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7d ", jumpbackj[j] );
- }
- fprintf( stderr, "\n" );
- fprintf( stderr, "jumpforwi = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7d ", jumpforwi[j] );
- }
- fprintf( stderr, "\n" );
- fprintf( stderr, "jumpforwj = \n" );
- for( j=0; j<lgth2; j++ )
- {
- fprintf( stderr, "% 7d ", jumpforwj[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
-
-
-
-#if 0
- fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
- fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
-
- fprintf( stderr, "imid = %d\n", imid );
- fprintf( stderr, "jmid = %d\n", jmid );
-#endif
-
- freearrays_rec1
- (
- w1, w2, initverticalw, lastverticalw, midw, midm, midn,
- jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
- m, mp,
- floatwork, intwork
-#if STOREWM
- , WMMTX, WMMTX2
-#endif
- );
-
-
-// fprintf( stderr, "==== calling myself (first)\n" );
-
- value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp ); // chudan mada
-#if 0
- fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
- fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
-#endif
-#if MEMSAVE
-#else
- for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
-#endif
-
-// 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 );
-
- len = strlen( mseq1[0] );
-// fprintf( stderr, "len = %d\n", len );
- l = jmid - jumpj - 1;
-// fprintf( stderr, "l=%d\n", l );
- if( l > 0 )
- {
- for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
- for( i=0; i<icyc; i++ )
- {
- strcat( mseq1[i], gaps );
- mseq1[i][len+l] = 0;
- }
- for( j=0; j<jcyc; j++ )
- {
- strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
- mseq2[j][len+l] = 0;
- }
-// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
- value += ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
-// value += fpenalty;
- }
- len = strlen( mseq1[0] );
- l = imid - jumpi - 1;
-// fprintf( stderr, "l=%d\n", l );
- if( l > 0 )
- {
- for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
- for( i=0; i<icyc; i++ )
- {
- strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
- mseq1[i][len+l] = 0;
- }
- for( j=0; j<jcyc; j++ )
- {
- strcat( mseq2[j], gaps );
- mseq2[j][len+l] = 0;
- }
-
-// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
-// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
-
-
-// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
- value += ( ogcp1[jumpi+1] + fgcp1[imid-1] );
-// value += fpenalty;
- }
-#if 0
- for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
- for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
-#endif
-
-// fprintf( stderr, "==== calling myself (second)\n" );
-
-#if MEMSAVE
- alnlen = strlen( aseq1[0] );
- for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
- for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
-#endif
-
- value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp ); // chudan mada
-#if 0
- fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
- fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
-#endif
-
-
-
-#if DEBUG
- if( value - maxwm > 1 || maxwm - value > 1 )
- {
- fprintf( stderr, "WARNING value = %f, but maxwm = %f\n", value, maxwm );
- for( i=0; i<icyc; i++ )
- {
- fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
- fprintf( stderr, "%s\n", aseq1[i] );
- }
- for( i=0; i<jcyc; i++ )
- {
- fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
- fprintf( stderr, "%s\n", aseq2[i] );
- }
-
-// exit( 1 );
- }
- else
- {
- fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
- }
-#endif
-
-#if MEMSAVE
-#else
- for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
- for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
-#endif
-
-// fprintf( stderr, "====(s) aseq1[0] (%d) = \n%s\n (a%d-a%d)\n", depth, mseq1[0], ist, ien );
-// fprintf( stderr, "====(s) aseq2[0] (%d) = \n%s\n (b%d-b%d)\n", depth, mseq2[0], jst, jen );
-
- freearrays_rec2( gaps, aseq1, aseq2 );
-
-#if 0
- if( seqlen( seq1[0] ) != nglen1 )
- {
- fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
- fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
- exit( 1 );
- }
- else
- fprintf( stderr, "nglen1 is ok in _rec\n" );
- if( seqlen( seq2[0] ) != nglen2 )
- {
- fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
- exit( 1 );
- }
- else
- fprintf( stderr, "nglen2 is ok in _rec\n" );
-#endif
-
- return( value );
-}
-
-static void freearrays(
- float *ogcp1,
- float *ogcp2,
- float *fgcp1,
- float *fgcp2,
- float **cpmx1,
- float **cpmx2,
- float **gapinfo,
- char **mseq1,
- char **mseq2
-)
-{
- FreeFloatVec( ogcp1 );
- FreeFloatVec( ogcp2 );
- FreeFloatVec( fgcp1 );
- FreeFloatVec( fgcp2 );
- FreeFloatMtx( cpmx1 );
- FreeFloatMtx( cpmx2 );
- free( (void *)gapinfo );
-
- FreeCharMtx( mseq1 );
- FreeCharMtx( mseq2 );
-}
-
-float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
-/* 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 = 0.0; /* int ?????? */
- char **mseq1;
- char **mseq2;
- float *ogcp1;
- float *ogcp2;
- float *fgcp1;
- float *fgcp2;
- float **cpmx1;
- float **cpmx2;
- float **gapinfo;
- float fpenalty = (float)penalty;
- int nglen1, nglen2;
-
-#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
-
- nglen1 = seqlen( seq1[0] );
- nglen2 = seqlen( seq2[0] );
-
-#if 0
- fprintf( stderr, "\n" );
- for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[%d] at root = %s\n", i, seq1[i] );
- for( j=0; j<jcyc; j++ ) fprintf( stderr, "seq2[%d] at root = %s\n", j, seq2[j] );
- fprintf( stderr, "\n" );
-#endif
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-
- ll1 = ( (int)(lgth1) ) + 100;
- ll2 = ( (int)(lgth2) ) + 100;
-
- mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
- mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
-
- gapinfo = AllocateFloatMtx( 4, 0 );
- ogcp1 = AllocateFloatVec( ll1+2 );
- ogcp2 = AllocateFloatVec( ll2+2 );
- fgcp1 = AllocateFloatVec( ll1+2 );
- fgcp2 = AllocateFloatVec( ll2+2 );
-
-
- cpmx1 = AllocateFloatMtx( ll1+2, 27 );
- cpmx2 = AllocateFloatMtx( ll2+2, 27 );
-
- for( i=0; i<icyc; i++ )
- {
- if( strlen( seq1[i] ) != lgth1 )
- {
- fprintf( stderr, "i = %d / %d\n", i, icyc );
- fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
- exit( 1 );
- }
- }
- for( j=0; j<jcyc; j++ )
- {
- if( strlen( seq2[j] ) != lgth2 )
- {
- fprintf( stderr, "j = %d / %d\n", j, jcyc );
- fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
- exit( 1 );
- }
- }
-
- MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
- MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
-
-
-#if 1
-
- if( sgap1 )
- {
- new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
- new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
- new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
- new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
- }
- else
- {
- st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
- st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
- st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
- st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
- }
-
-#if 1
- for( i=0; i<lgth1; i++ )
- {
- ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
- fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
-// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
- }
- for( i=0; i<lgth2; i++ )
- {
- ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
- fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
-// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
- }
-#else
- for( i=0; i<lgth1; i++ )
- {
- ogcp1[i] = 0.5 * fpenalty;
- fgcp1[i] = 0.5 * fpenalty;
- }
- for( i=0; i<lgth2; i++ )
- {
- ogcp2[i] = 0.5 * fpenalty;
- fgcp2[i] = 0.5 * fpenalty;
- }
-#endif
-
- gapinfo[0] = ogcp1;
- gapinfo[1] = fgcp1;
- gapinfo[2] = ogcp2;
- gapinfo[3] = fgcp2;
-#endif
-
-#if 0
- fprintf( stdout, "in MSalignmm.c\n" );
- for( i=0; i<icyc; i++ )
- {
- fprintf( stdout, ">%d of GROUP1\n", i );
- fprintf( stdout, "%s\n", seq1[i] );
- }
- for( i=0; i<jcyc; i++ )
- {
- fprintf( stdout, ">%d of GROUP2\n", i );
- fprintf( stdout, "%s\n", seq2[i] );
- }
- fflush( stdout );
-#endif
-
- wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, lgth1, lgth2, mseq1, mseq2, 0, gapinfo, chudanpt, chudanref, chudanres, headgp, tailgp );
-#ifdef enablemultithread
- if( chudanres && *chudanres )
- {
-// fprintf( stderr, "\n\n## CHUUDAN!!! relay\n" );
- *chudanres = 1;
- freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapinfo, mseq1, mseq2 );
- return( -1.0 );
- }
-#endif
-
-#if DEBUG
- fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
- fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
- fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
- fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
-#endif
-
-// fprintf( stderr, "wm = %f\n", wm );
-
-
- for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
- for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
-
- if( seqlen( seq1[0] ) != nglen1 )
- {
- fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
- fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
- exit( 1 );
- }
- if( seqlen( seq2[0] ) != nglen2 )
- {
- fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
- exit( 1 );
- }
-
-
- freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapinfo, mseq1, mseq2 );
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
- for( i=0; i<icyc; i++ )
- {
- if( strlen( seq1[i] ) != lgth1 )
- {
- fprintf( stderr, "i = %d / %d\n", i, icyc );
- fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
- exit( 1 );
- }
- }
- for( j=0; j<jcyc; j++ )
- {
- if( strlen( seq2[j] ) != lgth2 )
- {
- fprintf( stderr, "j = %d / %d\n", j, jcyc );
- fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
- exit( 1 );
- }
- }
-
- return( wm );
-}
git://source.jalview.org / jabaws.git / blobdiff