--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+
+
+static TLS float **impmtx = NULL;
+static TLS int impalloclen = 0;
+#if 1 // tditeration to naiveQscore_imp de tsukawareru.
+float imp_match_out_scQ( int i1, int j1 )
+{
+// fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
+// fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+}
+#endif
+
+static void imp_match_out_veadQ_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ int *gapmappt = gapmap2;
+ while( lgth2-- )
+ *imp++ += pt[*gapmappt++];
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[gapmap2[j]];
+#endif
+}
+
+
+static void imp_match_out_vead_tateQ_gapmap( float *imp, int j1, int lgth1, int *gapmap1 )
+{
+#if FASTMATCHCALC
+ int *gapmappt = gapmap1;
+ while( lgth1-- )
+ *imp++ += impmtx[*gapmappt++][j1];
+#else
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[gapmap1[i]][j1];
+#endif
+}
+
+
+static void imp_match_out_veadQ( float *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ while( lgth2-- )
+ *imp++ += *pt++;
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tateQ( float *imp, int j1, int lgth1 )
+{
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[i][j1];
+}
+
+void imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
+{
+ foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair );
+}
+
+#if 1 // tbfast.c kara yobareru.
+void imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ float effij;
+ double effijx;
+ char *pt, *pt1, *pt2;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
+ LocalHom *tmpptr;
+
+ if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = (float)( eff1[i] * eff2[j] * effijx );
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = pt - seq1[i] - 0;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = pt - seq2[j] - 0;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+#if 1
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+// fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+// fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+#else
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
+ if( !nocount1[k1] && !nocount2[k2] )
+ {
+ impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
+ fprintf( stderr, "marked\n" );
+ }
+ else
+ fprintf( stderr, "no count\n" );
+ k1++; k2++;
+ }
+#endif
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+#if 0
+ if( clus1 == 1 && clus2 == 6 )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d ", k1 );
+ for( k2=0; k2<3; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+ }
+#endif
+}
+#endif
+
+
+static void clearvec( float *match, int lgth )
+{
+ while( lgth-- ) *match++ = 0.0;
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+ scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+// scarr[l] *= consweight_multi;
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+// scarr[l] *= consweight_multi;
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom_gapmap( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+// char gap[] = "-";
+ char *gap;
+ float wm;
+ 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
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ 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 );
+ }
+ }
+ }
+
+ 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;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; 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][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][jfi+l];
+ k++;
+ }
+ if( iin != lgth1 && jin != lgth2 ) // ??
+ {
+ *impwmpt += imp_match_out_scQ( gapmap1[iin], gapmap2[jin] );
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+}
+
+#if 0
+static void Atracking_localhom_gapmap_bk( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ 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
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ 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 );
+ }
+ }
+ }
+
+ 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;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; 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 == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_scQ( gapmap1[iin], gapmap2[jin] );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = '-';
+ *--gaptable2 = '-';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+
+
+ free( gt1bk );
+ free( gt2bk );
+}
+
+#endif
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ 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
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ 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 );
+ }
+ }
+ }
+
+ 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;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; 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 == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_scQ( iin, jin );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ 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], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+}
+
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ 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
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ 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 );
+ }
+ }
+ }
+
+ 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;
+
+ iin = lgth1; jin = lgth2;
+ for( k=0; k<=lgth1+lgth2; 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], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+ return( 0.0 );
+}
+
+float Q__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ 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;
+ fprintf( stderr, "fpenalty_ex = %f\n", fpenalty_ex );
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *digf1;
+ static TLS float *digf2;
+ static TLS float *diaf1;
+ static TLS float *diaf2;
+ static TLS float *gapz1;
+ static TLS float *gapz2;
+ static TLS float *gapf1;
+ static TLS float *gapf2;
+ static TLS float *ogcp1g;
+ static TLS float *ogcp2g;
+ static TLS float *fgcp1g;
+ static TLS float *fgcp2g;
+ static TLS float *og_h_dg_n1_p;
+ static TLS float *og_h_dg_n2_p;
+ static TLS float *fg_h_dg_n1_p;
+ static TLS float *fg_h_dg_n2_p;
+ static TLS float *og_t_fg_h_dg_n1_p;
+ static TLS float *og_t_fg_h_dg_n2_p;
+ static TLS float *fg_t_og_h_dg_n1_p;
+ static TLS float *fg_t_og_h_dg_n2_p;
+ static TLS float *gapz_n1;
+ static TLS float *gapz_n2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float tmppenal;
+ float *fg_t_og_h_dg_n2_p_pt;
+ float *og_t_fg_h_dg_n2_p_pt;
+ float *og_h_dg_n2_p_pt;
+ float *fg_h_dg_n2_p_pt;
+ float *gapz_n2_pt0;
+ float *gapz_n2_pt1;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fg_t_og_h_dg_n1_p_va;
+ float og_t_fg_h_dg_n1_p_va;
+ float og_h_dg_n1_p_va;
+ float fg_h_dg_n1_p_va;
+ float gapz_n1_va0;
+ float gapz_n1_va1;
+ float fgcp1va;
+ float ogcp1va;
+ float kyokaipenal;
+#if 1
+ float fpenalty = (float)penalty;
+#else
+ float fpenalty;
+ if( RNAscoremtx != 'r' ) fpenalty = (float)penalty;
+ else fpenalty = (float)penalty * 10;
+#endif
+
+#if 0
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+#endif
+
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+ FreeFloatVec( og_h_dg_n1_p );
+ FreeFloatVec( og_h_dg_n2_p );
+ FreeFloatVec( fg_h_dg_n1_p );
+ FreeFloatVec( fg_h_dg_n2_p );
+ FreeFloatVec( og_t_fg_h_dg_n1_p );
+ FreeFloatVec( og_t_fg_h_dg_n2_p );
+ FreeFloatVec( fg_t_og_h_dg_n1_p );
+ FreeFloatVec( fg_t_og_h_dg_n2_p );
+ FreeFloatVec( gapz_n1 );
+ FreeFloatVec( gapz_n2 );
+
+ 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 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+ og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ gapz_n1 = AllocateFloatVec( ll1+2 );
+ gapz_n2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ 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 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
+ getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ lastj = lgth2+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ gapz_n2[i] = (1.0-gapz2[i]);
+ }
+ lastj = lgth1+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ gapz_n1[i] = (1.0-gapz1[i]);
+ }
+#endif
+
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ if( RNAscoremtx != 'r' )
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ else
+ clearvec( initverticalw, lgth1 );
+ if( localhom )
+ imp_match_out_vead_tateQ( initverticalw, 0, lgth1 ); // 060306
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ else
+ clearvec( currentw, lgth2 );
+ if( localhom )
+ imp_match_out_veadQ( currentw, 0, lgth2 ); // 060306
+
+
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+
+
+ kyokaipenal = 0.0;
+ if( outgap == 1 )
+ {
+ g = 0.0;
+
+ g += ogcp1g[0] * og_h_dg_n2_p[0];
+// g += ogcp1g[0] * ( 1.0-ogcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += ogcp2g[0] * og_h_dg_n1_p[0];
+// g += ogcp2g[0] * ( 1.0-ogcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += fgcp1g[0] * fg_h_dg_n2_p[0];
+// g += fgcp1g[0] * ( 1.0-fgcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ g += fgcp2g[0] * fg_h_dg_n1_p[0];
+// g += fgcp2g[0] * ( 1.0-fgcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ kyokaipenal = g;
+ initverticalw[0] += g;
+ currentw[0] += g;
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
+// tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
+// tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+
+ tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+ mp[j] = 0;
+ m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+ else
+ clearvec( currentw, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_veadQ( currentw, i, lgth2 );
+#else
+ imp_match_out_veadQ( currentw, i, lgth2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mpi = 0;
+ mi = previousw[0] + 10000 * fpenalty;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
+ og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
+ og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
+ fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
+ gapz_n2_pt0 = gapz_n2 + 1;
+ gapz_n2_pt1 = gapz_n2 + 2;
+ fgcp2pt = fgcp2g + 1;
+ ogcp2pt = ogcp2g + 1;
+
+ fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
+ og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
+ og_h_dg_n1_p_va = og_h_dg_n1_p[i];
+ fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
+ gapz_n1_va0 = gapz_n1[i];
+ gapz_n1_va1 = gapz_n1[i+1];
+ fgcp1va = fgcp1g[i];
+ ogcp1va = ogcp1g[i];
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ g = ogcp1va * *og_h_dg_n2_p_pt;
+// g = ogcp1g[i] * og_h_dg_n2_p[j];
+// g = ogcp1g[i] * ( 1.0-ogcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *ogcp2pt * og_h_dg_n1_p_va;
+// g = ogcp2g[j] * og_h_dg_n1_p[i];
+// g = ogcp2g[j] * ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = fgcp1va * *fg_h_dg_n2_p_pt;
+// g = fgcp1g[i] * fg_h_dg_n2_p[j];
+// g = fgcp1g[i] * ( 1.0-fgcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *fgcp2pt * fg_h_dg_n1_p_va;
+// g = fgcp2g[j] * fg_h_dg_n1_p[i];
+// g = fgcp2g[j] * ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i+1] * fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=mi+tmppenal) > wm )
+ {
+// fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i] * og_t_fg_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= mi )
+ {
+// fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j+1] * fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j] * og_t_fg_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+
+
+
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fg_t_og_h_dg_n2_p_pt++;
+ og_t_fg_h_dg_n2_p_pt++;
+ og_h_dg_n2_p_pt++;
+ fg_h_dg_n2_p_pt++;
+ gapz_n2_pt0++;
+ gapz_n2_pt1++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ return( wm );
+}
+
+float Q__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *gapmap1, int *gapmap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ 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;
+ fprintf( stderr, "fpenalty_ex = %f\n", fpenalty_ex );
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *digf1;
+ static TLS float *digf2;
+ static TLS float *diaf1;
+ static TLS float *diaf2;
+ static TLS float *gapz1;
+ static TLS float *gapz2;
+ static TLS float *gapf1;
+ static TLS float *gapf2;
+ static TLS float *ogcp1g;
+ static TLS float *ogcp2g;
+ static TLS float *fgcp1g;
+ static TLS float *fgcp2g;
+ static TLS float *og_h_dg_n1_p;
+ static TLS float *og_h_dg_n2_p;
+ static TLS float *fg_h_dg_n1_p;
+ static TLS float *fg_h_dg_n2_p;
+ static TLS float *og_t_fg_h_dg_n1_p;
+ static TLS float *og_t_fg_h_dg_n2_p;
+ static TLS float *fg_t_og_h_dg_n1_p;
+ static TLS float *fg_t_og_h_dg_n2_p;
+ static TLS float *gapz_n1;
+ static TLS float *gapz_n2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float tmppenal;
+ float *fg_t_og_h_dg_n2_p_pt;
+ float *og_t_fg_h_dg_n2_p_pt;
+ float *og_h_dg_n2_p_pt;
+ float *fg_h_dg_n2_p_pt;
+ float *gapz_n2_pt0;
+ float *gapz_n2_pt1;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fg_t_og_h_dg_n1_p_va;
+ float og_t_fg_h_dg_n1_p_va;
+ float og_h_dg_n1_p_va;
+ float fg_h_dg_n1_p_va;
+ float gapz_n1_va0;
+ float gapz_n1_va1;
+ float fgcp1va;
+ float ogcp1va;
+ float kyokaipenal;
+ float fpenalty = (float)penalty;
+
+#if 0
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+#endif
+
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+ FreeFloatVec( og_h_dg_n1_p );
+ FreeFloatVec( og_h_dg_n2_p );
+ FreeFloatVec( fg_h_dg_n1_p );
+ FreeFloatVec( fg_h_dg_n2_p );
+ FreeFloatVec( og_t_fg_h_dg_n1_p );
+ FreeFloatVec( og_t_fg_h_dg_n2_p );
+ FreeFloatVec( fg_t_og_h_dg_n1_p );
+ FreeFloatVec( fg_t_og_h_dg_n2_p );
+ FreeFloatVec( gapz_n1 );
+ FreeFloatVec( gapz_n2 );
+
+ 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 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+ og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ gapz_n1 = AllocateFloatVec( ll1+2 );
+ gapz_n2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ 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 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
+ getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ lastj = lgth2+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ gapz_n2[i] = (1.0-gapz2[i]);
+ }
+ lastj = lgth1+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ gapz_n1[i] = (1.0-gapz1[i]);
+ }
+#endif
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ if( RNAscoremtx != 'r' )
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ else
+ clearvec( initverticalw, lgth1 );
+ if( localhom )
+ imp_match_out_vead_tateQ_gapmap( initverticalw, gapmap2[0], lgth1, gapmap1 ); // 060306
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ else
+ clearvec( currentw, lgth2 );
+ if( localhom )
+ imp_match_out_veadQ_gapmap( currentw, gapmap1[0], lgth2, gapmap2 ); // 060306
+
+
+
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+
+
+ kyokaipenal = 0.0;
+ if( outgap == 1 )
+ {
+ g = 0.0;
+
+ g += ogcp1g[0] * og_h_dg_n2_p[0];
+// g += ogcp1g[0] * ( 1.0-ogcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += ogcp2g[0] * og_h_dg_n1_p[0];
+// g += ogcp2g[0] * ( 1.0-ogcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += fgcp1g[0] * fg_h_dg_n2_p[0];
+// g += fgcp1g[0] * ( 1.0-fgcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ g += fgcp2g[0] * fg_h_dg_n1_p[0];
+// g += fgcp2g[0] * ( 1.0-fgcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ kyokaipenal = g;
+ initverticalw[0] += g;
+ currentw[0] += g;
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
+// tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
+// tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+
+ tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+ mp[j] = 0;
+ m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+ else
+ clearvec( currentw, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_veadQ( currentw, i, lgth2 );
+#else
+ imp_match_out_veadQ_gapmap( currentw, gapmap1[i], lgth2, gapmap2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mpi = 0;
+ mi = previousw[0] + 10000 * fpenalty;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
+ og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
+ og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
+ fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
+ gapz_n2_pt0 = gapz_n2 + 1;
+ gapz_n2_pt1 = gapz_n2 + 2;
+ fgcp2pt = fgcp2g + 1;
+ ogcp2pt = ogcp2g + 1;
+
+ fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
+ og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
+ og_h_dg_n1_p_va = og_h_dg_n1_p[i];
+ fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
+ gapz_n1_va0 = gapz_n1[i];
+ gapz_n1_va1 = gapz_n1[i+1];
+ fgcp1va = fgcp1g[i];
+ ogcp1va = ogcp1g[i];
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ g = ogcp1va * *og_h_dg_n2_p_pt;
+// g = ogcp1g[i] * og_h_dg_n2_p[j];
+// g = ogcp1g[i] * ( 1.0-ogcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *ogcp2pt * og_h_dg_n1_p_va;
+// g = ogcp2g[j] * og_h_dg_n1_p[i];
+// g = ogcp2g[j] * ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = fgcp1va * *fg_h_dg_n2_p_pt;
+// g = fgcp1g[i] * fg_h_dg_n2_p[j];
+// g = fgcp1g[i] * ( 1.0-fgcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *fgcp2pt * fg_h_dg_n1_p_va;
+// g = fgcp2g[j] * fg_h_dg_n1_p[i];
+// g = fgcp2g[j] * ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i+1] * fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=mi+tmppenal) > wm )
+ {
+// fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i] * og_t_fg_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= mi )
+ {
+// fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j+1] * fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j] * og_t_fg_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+
+
+
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fg_t_og_h_dg_n2_p_pt++;
+ og_t_fg_h_dg_n2_p_pt++;
+ og_h_dg_n2_p_pt++;
+ fg_h_dg_n2_p_pt++;
+ gapz_n2_pt0++;
+ gapz_n2_pt1++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ return( wm );
+}
+
git://source.jalview.org / jabaws.git / blobdiff