--- /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