--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+
+#define WMCHECK 1
+#define ALGZSTRAIGHT 0
+#define ALGZGAP 0
+#define USEGAPLENMTX 0
+#define USEGAPLENHALF 0
+#define FREEFREQUENTLY 1
+
+#define IDATEND 0
+
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+#define SLOW 0
+
+#define zero 0
+#define one 1
+
+#if USEGAPLENHALF
+#define USEGAPLENHALFORMTX 1
+#endif
+#if USEGAPLENMTX
+#define USEGAPLENHALFORMTX 1
+#endif
+
+
+#if WMCHECK
+static int PFACERROR = 0;
+#endif
+
+
+static TLS double **impmtx = NULL;
+static TLS int impalloclen = 0;
+
+double imp_match_out_scD( 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] );
+}
+
+typedef struct _gaplenvec
+{
+ int relend;
+#if USEGAPLENHALFORMTX
+ int idatend;
+#endif
+ int idatnext;
+ int idatprev;
+ int npat;
+ int len; // sukoshi muda.
+ double freq;
+} Gaplen;
+
+#if 0
+static void imp_match_out_vead_gapmap( double *imp, int i1, int lgth2, int *gapmap2 )
+{
+#if FASTMATCHCALC
+ double *pt = impmtx[i1];
+ int *gapmappt = gapmap2;
+ while( lgth2-- )
+ *imp++ += pt[*gapmappt++];
+#else
+ int j;
+ double *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[gapmap2[j]];
+#endif
+}
+
+
+static void imp_match_out_vead_tate_gapmap( double *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
+}
+#endif
+
+static void imp_match_out_vead( double *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC
+ double *pt = impmtx[i1];
+ while( lgth2-- )
+ *imp++ += *pt++;
+#else
+ int j;
+ double *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tate( double *imp, int j1, int lgth1 )
+{
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[i][j1];
+}
+
+void imp_rnaD( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *pair )
+{
+ foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, pair );
+}
+
+
+void imp_match_init_strictD( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, char *swaplist, int forscore, int *orinum1, int *orinum2 )
+{
+// int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+// double effij;
+// double effij_kozo;
+// double effijx;
+// char *pt, *pt1, *pt2;
+// static TLS char *nocount1 = NULL;
+// static TLS char *nocount2 = NULL;
+// LocalHom *tmpptr;
+
+ if( seq1 == NULL )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ impmtx = NULL;
+// if( nocount1 ) free( nocount1 );
+// nocount1 = NULL;
+// if( nocount2 ) free( nocount2 );
+// nocount2 = NULL;
+
+ return;
+ }
+
+ 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 );
+ }
+
+ fillimp( impmtx, imp, clus1, clus2, lgth1, lgth2, seq1, seq2, eff1, eff2, eff1_kozo, eff2_kozo, localhom, swaplist, forscore, orinum1, orinum2 );
+}
+
+
+
+
+
+static void match_calc_del( int **which, double ***matrices, double *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, int mid, int nmask, int *mask1, int *mask2 )
+{
+// osoi!
+ int i, j, k, m;
+ int c1, c2;
+// fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
+// fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
+// fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
+// for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+// {
+// if( flip ) reporterr( "in match_calc_slow, which[%d][%d] = %d\n", j, i, which[j][i] );
+// else reporterr( "in match_calc_slow, which[%d][%d] = %d\n", i, j, which[i][j] );
+// }
+ for( k=0; k<lgth2; k++ )
+ {
+ for( m=0; m<nmask; m++ )
+ {
+ i = mask1[m];
+ j = mask2[m];
+// reporterr( "Deleting %d-%d (c=%d)\n", i, j, mid );
+// if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
+ c1 = amino_n[(unsigned char)seq1[i][i1]];
+ c2 = amino_n[(unsigned char)seq2[j][k]];
+// reporterr( "k=%d, c1=%d, c2=%d, seq1[i][i1]=%c, seq2[%d][%d]=%c\n", k, c1, c2, seq1[i][i1], j, k, seq2[j][k] );
+ if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
+ if( c1 < 0 || c2 < 0 ) continue;
+// fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
+// fprintf( stderr, "match[k] = %f -> ", match[k], mid );
+ match[k] -= matrices[mid][c1][c2] * eff1[i] * eff2[j];
+// fprintf( stderr, "match[k] = %f (mid=%d)\n", match[k], mid );
+ }
+ }
+// fprintf( stderr, "done\n" );
+ return;
+}
+
+#if SLOW
+static void match_calc_slow( int **which, double ***matrices, double *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, double **doublework, int **intwork, int initialize, int flip )
+{
+// osoi!
+ int i, j, k;
+ int c1, c2;
+ int mid;
+// fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
+// fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
+// fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
+// for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+// {
+// if( flip ) reporterr( "in match_calc_slow, which[%d][%d] = %d\n", j, i, which[j][i] );
+// else reporterr( "in match_calc_slow, which[%d][%d] = %d\n", i, j, which[i][j] );
+// }
+ for( k=0; k<lgth2; k++ )
+ {
+ match[k] = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ if( flip ) mid = which[j][i];
+ else mid = which[i][j];
+// if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
+ c1 = amino_n[(unsigned char)seq1[i][i1]];
+ c2 = amino_n[(unsigned char)seq2[j][k]];
+ if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
+ if( c1 < 0 || c2 < 0 ) continue;
+// fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
+ if( flip )
+ match[k] += matrices[mid][c1][c2] * eff1[i] * eff2[j];
+ else
+ match[k] += matrices[mid][c1][c2] * eff1[i] * eff2[j];
+// fprintf( stderr, "match[k] = %f (which=%d)\n", match[k], mid );
+ }
+ }
+// fprintf( stderr, "done\n" );
+ return;
+}
+#endif
+
+static void fillzero( double *s, int l )
+{
+ while( l-- ) *s++ = 0.0;
+}
+
+
+static void match_calc_add( double **scoreingmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+// fprintf( stderr, "\nmatch_calc... %d", i1 );
+ int j, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ double *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<nalphabets; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<nalphabets; j++ )
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+// scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+// *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+ free( scarr );
+// fprintf( stderr, "done\n" );
+#else
+ int j, k, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<nalphabets; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<nalphabets; k++ )
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+ scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1];
+ }
+ 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];
+ }
+ free( scarr );
+#endif
+}
+
+static void match_calc( double **n_dynamicmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+// fprintf( stderr, "\nmatch_calc... %d", i1 );
+ int j, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ double *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<nalphabets; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<nalphabets; j++ )
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+// scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ scarr[l] += n_dynamicmtx[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+ free( scarr );
+// fprintf( stderr, "done\n" );
+#else
+ int j, k, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<nalphabets; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<nalphabets; k++ )
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+ scarr[l] += n_dynamicmtx[k][l] * cpmx1[k][i1];
+ }
+ 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];
+ }
+ free( scarr );
+#endif
+}
+
+static void Atracking_localhom( double *impwmpt, double *lasthorizontalw, double *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp, int icyc, int jcyc,
+ int *warpis, int *warpjs, int warpbase )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+ double 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;
+ limk = lgth1+lgth2 + 1;
+ *impwmpt = 0.0;
+ for( k=0; k<limk; k++ )
+ {
+ if( ijp[iin][jin] >= warpbase )
+ {
+ ifi = warpis[ijp[iin][jin]-warpbase];
+ jfi = warpjs[ijp[iin][jin]-warpbase];
+ }
+ else 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;
+ }
+ if( ifi == -warpbase && jfi == -warpbase )
+ {
+ l = iin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ }
+ break;
+ }
+ else
+ {
+ 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 += (double)imp_match_out_scD( 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 double Atracking( double *lasthorizontalw, double *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp, int icyc, int jcyc,
+ int tailgp,
+ int *warpis, int *warpjs, int warpbase )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+ double 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( tailgp == 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;
+ limk = lgth1+lgth2 + 1;
+ for( k=0; k<limk; k++ )
+ {
+ if( ijp[iin][jin] >= warpbase )
+ {
+ ifi = warpis[ijp[iin][jin]-warpbase];
+ jfi = warpjs[ijp[iin][jin]-warpbase];
+ }
+ else 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;
+ }
+
+ if( ifi == -warpbase && jfi == -warpbase )
+ {
+ l = iin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ }
+ break;
+ }
+ else
+ {
+ 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 );
+}
+
+#if 1
+static void cleargaplens( Gaplen ****gaplens )
+{
+ int i;
+// int j, k;
+ Gaplen ****ptptptpt, ***ptptpt, ***ptptptmv, **ptptmv, **ptpt;
+ for( i=0; i<12; i++ )
+ {
+ ptptptpt = gaplens+i;
+
+ ptptptmv = *ptptptpt;
+ while( *(ptptpt=ptptptmv++) )
+// for( j=0; *(ptptpt=*ptptptpt+j); j++ )
+ {
+ ptptmv = *ptptpt;
+ while( *(ptpt=ptptmv++)!=(Gaplen *)1 )
+// for( k=0; gaplens[i][j][k]!=(Gaplen *)1; k++ )
+// for( k=0; *(ptpt=*ptptpt+k)!=(Gaplen *)1; k++ )
+ {
+// if( gaplens[i][j][k] ) free( gaplens[i][j][k] );
+ if( *ptpt ) free( *ptpt );
+ *ptpt = NULL;
+ }
+// free( gaplens[i][j] );
+ free( *ptptpt );
+// gaplens[i][j] = NULL;
+ *ptptpt = NULL;
+ }
+ }
+}
+#else
+static void cleargaplens( Gaplen ****gaplens )
+{
+ int i, j, k;
+ for( i=0; i<12; i++ )
+ {
+ for( j=0; gaplens[i][j]; j++ )
+ {
+ for( k=0; gaplens[i][j][k]!=(Gaplen *)1; k++ )
+ {
+ if( gaplens[i][j][k] ) free( gaplens[i][j][k] );
+ gaplens[i][j][k] = NULL;
+ }
+ free( gaplens[i][j] );
+ gaplens[i][j] = NULL;
+ }
+ }
+}
+#endif
+
+#if USEGAPLENHALFORMTX
+static void FreeGaplenMtxReport( Gaplen **mtx )
+{
+ int i;
+ if( mtx == NULL ) return;
+
+ for( i=0; ; i++ )
+ {
+ reporterr( "i=%d, mtx[i] = %p\n", i, mtx[i] );
+ if( mtx[i] )
+ {
+ if( mtx[i] == (Gaplen *)1 ) break;
+ free( mtx[i] ); mtx[i] = NULL;
+ }
+ mtx[i] = NULL;
+ }
+ free( mtx );
+ mtx = NULL;
+}
+#endif
+
+static void FreeGaplenMtx( Gaplen **mtx, int inclfreq )
+{
+ int i;
+ if( mtx == NULL ) return;
+
+ for( i=0; ; i++ )
+ {
+ if( mtx[i] )
+ {
+ if( mtx[i] == (Gaplen *)1 ) break;
+
+#if 0
+ if( inclfreq )
+ {
+// reporterr( "inclfreq=%d\n", inclfreq );
+ for( j=0; mtx[i][j].relend==0; j++ )
+ {
+// reporterr( "j=%d\n", j );
+// reporterr( "Free! freq\n" );
+ if( mtx[i][j].freq )
+ {
+ free( mtx[i][j].freq );
+ }
+ mtx[i][j].freq = NULL;
+ }
+ }
+#endif
+
+ free( mtx[i] ); mtx[i] = NULL;
+ }
+ }
+ free( mtx );
+ mtx = NULL;
+}
+
+#if USEGAPLENHALFORMTX
+static void FreeGaplenCubgaplenReport( Gaplen ***cub )
+{
+ int i;
+ if( cub == NULL ) return;
+
+ for( i=0; cub[i]; i++ )
+ {
+ reporterr( "i=%d, cub[i]=%p\n", i, cub[i] );
+ FreeGaplenMtx( cub[i], 0 );
+ cub[i] = NULL;
+ }
+ free( cub );
+ cub = NULL;
+}
+#endif
+
+static void FreeGaplenCub( Gaplen ***cub )
+{
+ int i;
+ if( cub == NULL ) return;
+
+ for( i=0; cub[i]; i++ )
+ {
+ FreeGaplenMtx( cub[i], 0 );
+ cub[i] = NULL;
+ }
+ free( cub );
+ cub = NULL;
+}
+
+static int strralpha( const char *s, const char *first )
+{
+ int v = 0;
+ s--;
+ while( s >= first )
+ {
+ if( *s-- != '-' ) return( v );
+ v++;
+ }
+ if( s == first-1 ) return( v );
+ return( -1 );
+}
+
+static void fillgaplen( Gaplen **mtx, int l )
+{
+ int i, j, n, k, len, pos, idatnext;
+ double freq;
+ for( i=0; i<=l; i++ )
+ {
+// reporterr( "i=%d\n", i );
+ if( mtx[i] == NULL ) continue;
+ for( n=0; (len=mtx[i][n].len)!=-1; n++ )
+ {
+ freq = mtx[i][n].freq;
+ idatnext = n;
+ for( j=0; j<len; j++ )
+ {
+// reporterr( "n=%d, j=%d, i=%d, len=%d\n", n, j, i, len );
+ pos = i-1-j;
+// reporterr( "pos = %d\n", pos );
+ if( mtx[pos] == NULL )
+ {
+ mtx[pos] = calloc( 2, sizeof( Gaplen ) );
+ mtx[pos][0].len = -1;
+#if USEGAPLENHALFORMTX
+ mtx[pos][0].idatend = -1;
+#endif
+ mtx[pos][0].idatnext = -1;
+ mtx[pos][0].idatprev = -1;
+ mtx[pos][0].relend = -1;
+ mtx[pos][0].freq = 0.0;
+ mtx[pos][0].npat = -1;
+ k = 0;
+ }
+ else
+ {
+ k = mtx[pos][0].npat;
+ }
+ mtx[pos] = realloc( mtx[pos], sizeof( Gaplen ) * ( k + 2 ) );
+// mtx[pos][k].len = -100000; // tsukawanai!
+ mtx[pos][k].len = len; // compact no toki tsukau!
+ mtx[pos][k].relend = j+1;
+ mtx[pos][k].freq = freq;// tsukawanai! mtx[i][n].freq;
+ mtx[pos][k].idatnext = idatnext;
+ mtx[pos][k].idatprev =-1;
+ mtx[pos][k].npat = -1;
+ mtx[pos][k+1].len = -1;
+ mtx[pos][k+1].idatnext = -1;
+ mtx[pos][k+1].relend = -1;
+ mtx[pos][k+1].freq = 0.0;
+ mtx[pos][k+1].npat = -1;
+ mtx[pos][0].npat = k+1;
+#if USEGAPLENHALFORMTX
+ mtx[pos][k].idatend = n;
+ mtx[pos][k+1].idatend = -1;
+#endif
+
+ mtx[pos+1][idatnext].idatprev = k; // kanarazu aru?
+
+ idatnext = k;
+ }
+ }
+ }
+}
+
+static int gapvariety( int n, int l, char **seq )
+{
+ int i, j, gl, *known, nknown, val;
+ known = calloc( l+1, sizeof( int ) );
+// for( i=0; i<n; i++ ) reporterr( "seq[%d] = %s\n", i, seq[i] );
+
+ val = 0;
+ for( j=0; j<=l; j++ )
+ {
+ for( i=0; i<j; i++ ) known[i] = 0;
+ nknown = 0;
+ for( i=0; i<n; i++ )
+ {
+ if( seq[i][j] == '-' ) continue;
+
+ gl = strralpha( seq[i]+j, seq[i] );
+// reporterr( "gl = %d\n", gl );
+ if( gl > 0 )
+ {
+ if( known[gl] )
+ {
+ ;
+ }
+ else
+ {
+ nknown++;
+ }
+ }
+ }
+ val += nknown;
+ }
+ free( known );
+
+ return( val );
+}
+
+
+static void gaplencount( int n, int l, Gaplen **mtx, char **seq, double *eff )
+{
+ int i, j, k, gl, *known, nknown;
+ known = calloc( l+1, sizeof( int ) );
+// for( i=0; i<n; i++ ) reporterr( "seq[%d] = %s\n", i, seq[i] );
+
+ for( j=0; j<=l; j++ )
+ {
+ if( mtx[j] )
+ {
+ if( mtx[j] == (Gaplen *)1 ) break;
+ for( k=0; mtx[j][k].relend==0; k++ )
+ {
+#if 0
+// reporterr( "j=%d\n", j );
+// reporterr( "Free! freq\n" );
+ if( mtx[j][k].freq )
+ {
+ free( mtx[j][k].freq );
+ }
+ mtx[j][k].freq = NULL;
+#endif
+ }
+ free( mtx[j] );
+ }
+ mtx[j] = NULL;
+ }
+
+ for( j=0; j<=l; j++ )
+ {
+ for( i=0; i<j; i++ ) known[i] = 0;
+ nknown = 0;
+ for( i=0; i<n; i++ )
+ {
+ if( seq[i][j] == '-' ) continue;
+
+ gl = strralpha( seq[i]+j, seq[i] );
+// reporterr( "gl = %d\n", gl );
+ if( gl > 0 )
+ {
+ if( known[gl] )
+ {
+// reporterr( "gl=%d, Known!\n", gl );
+ for( k=0; mtx[j][k].len!=-1; k++ ) if( mtx[j][k].len == gl ) break;
+ if( mtx[j][k].len == -1 )
+ {
+ reporterr( "Unexpected error!\n" );
+ exit( 1 );
+ }
+ mtx[j][k].freq += eff[i];
+ }
+ else
+ {
+// reporterr( "gl=%d, First!\n", gl );
+ mtx[j] = realloc( mtx[j], sizeof( Gaplen ) * (nknown+2) );
+ mtx[j][nknown].len = gl;
+ mtx[j][nknown].relend = 0;
+ mtx[j][nknown].freq = eff[i];
+ mtx[j][nknown].idatnext = -2;
+ mtx[j][nknown+1].len = -1;
+ mtx[j][nknown+1].idatnext = -1;
+ mtx[j][nknown+1].relend = -1;
+ mtx[j][nknown+1].freq = 0.0;
+ mtx[j][nknown+1].npat = -1;
+#if USEGAPLENHALFORMTX
+ mtx[j][nknown].idatend = nknown;
+ mtx[j][nknown+1].idatend = -1;
+#endif
+ known[gl]++;
+ nknown++;
+ mtx[j][0].npat = nknown;
+ }
+ }
+ }
+ }
+ fillgaplen( mtx, l );
+#if 0
+ reporterr( "Gaplen:\n" );
+ for( i=0; i<=l; i++ )
+ {
+// reporterr( "i=%d, gaplen[i] = %p\n", i, mtx[i] );
+ if( mtx[i] )
+ {
+ for( j=0; mtx[i][j].len!=-1; j++ )
+ reporterr( "i=%d, len = %d, relend = %d, freq = %f\n", i, mtx[i][j].len, mtx[i][j].relend, mtx[i][j].freq );
+ }
+ }
+
+#endif
+
+ free( known );
+}
+
+
+#if DEBUG
+static void showgaplen( Gaplen **mtx, int seqlen )
+{
+ int i, l;
+#if USEGAPLENHALFORMTX
+ int id, pos;
+#endif
+// for( i=0; i<=seqlen; i++ )
+ for( i=0; ; i++ )
+ {
+// reporterr( "chain[%d] = %d\n", i, chain[i] );
+ if( mtx[i] == NULL ) continue;
+ if( mtx[i] == (Gaplen *)1 ) break;
+ for( l=0; mtx[i][l].idatnext!=-1; l++ )
+ {
+#if USEGAPLENHALFORMTX
+ reporterr( "i=%d, l=%d, len=%d, relend=%d, idatend=%d, idatnext=%d, idatprev=%d, freq=%f\n", i, l, mtx[i][l].len, mtx[i][l].relend, mtx[i][l].idatend, mtx[i][l].idatnext, mtx[i][l].idatprev, mtx[i][l].freq );
+ pos = mtx[i][l].relend;
+ id = mtx[i][l].idatend;
+ if( mtx[i+pos] == NULL )
+ {
+// reporterr( "Error in SOURCE\n" );
+ reporterr( ".len and .freq were lost when i=%d!\n", i );
+// exit( 1 );
+ }
+#else
+ reporterr( "i=%d, l=%d, len=%d, relend=%d, idatnext=%d, idatprev=%d, freq=%f\n", i, l, mtx[i][l].len, mtx[i][l].relend, mtx[i][l].idatnext, mtx[i][l].idatprev, mtx[i][l].freq );
+#endif
+ }
+ }
+}
+#endif
+
+#if WMCHECK
+static int pairgapcount( char *s1, char *s2 )
+{
+ char **tmpseq;
+ int i, len, st, k;
+ int v = 0;
+
+ len = strlen( s1 );
+ tmpseq = calloc( sizeof( char * ), 2 );
+ tmpseq[0] = malloc( sizeof( char ) * ( len + 1 ) );
+ tmpseq[1] = malloc( sizeof( char ) * ( len + 1 ) );
+
+ strcpy( tmpseq[0], s1 );
+ strcpy( tmpseq[1], s2 );
+
+ commongappick( 2, tmpseq );
+ len = strlen( tmpseq[0] );
+
+
+ for( k=0; k<2; k++ )
+ {
+ st = 0;
+ for( i=0; i<len; i++ )
+ {
+ if( tmpseq[k][i] == '-' )
+ {
+ if( st == 0 )
+ {
+ v++;
+ st = 1;
+ }
+ }
+ else
+ {
+ st = 0;
+ }
+ }
+ }
+ free( tmpseq[0] );
+ free( tmpseq[1] );
+ free( tmpseq );
+
+ return( v );
+}
+#endif
+
+static double calcpfac_gap_noidatend( Gaplen **gaplen1, Gaplen **gaplen2, int newgaplen, int i, int j, char *seq1, char *seq2, int disp ) // seq1 to seq2 ha debug you
+{
+#if 1
+ double pfac, pfac1, pfac10, pfac2;
+ int k, l, pos1, pos2;
+ Gaplen *gaplen1i, *gaplen2j, *g1, *g2;
+
+#if 0 // .len no shouryaku ni taiou shiteinai
+ int gl;
+ if( disp )
+ {
+ reporterr( "calcpfac_gap_noidatend, %c (%d) - %c (%d)\n", seq1[i], i, seq2[j], j );
+ reporterr( "newgaplen = %d\n", newgaplen );
+ reporterr( "In calcpfac_gap, gaplen1[%d(%c)] = \n", i, seq1[i] );
+ for( k=0; gaplen1[i]&&(id1=gaplen1[i][k].idatnext)!=-1; k++ )
+ {
+ pos1 = gaplen1[i][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen1[i+pos1][id1].len, gaplen1[i][k].relend, gaplen1[i+pos1][id1].freq[0] );
+ }
+ reporterr( "In calcpfac_gap, gaplen2[%d(%c)] = \n", j, seq2[j] );
+ showgaplen( gaplen2, strlen(seq2) );
+ for( k=0; gaplen2[j]&&(id2=gaplen2[j][k].idatnext)!=-1; k++ )
+ {
+ pos2 = gaplen2[j][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen2[j+pos2][id2].len, gaplen2[j][k].relend, gaplen2[j+pos2][id2].freq[0] );
+ }
+ }
+#endif
+ gaplen2j = gaplen2[j];
+ gaplen1i = gaplen1[i];
+
+ pfac = 0.0;
+ pfac1 = 0.0;
+ pfac10 = 0.0;
+ if( gaplen1i ) for( k=0; (g1=gaplen1i+k)->idatnext!=-1; k++ )
+ {
+ pos1 = g1->relend;
+ if( pos1 != 0 )
+ {
+ pfac2 = 0.0;
+ if( gaplen2j ) for( l=0; (g2=gaplen2j+l)->idatnext!=-1; l++ )
+ {
+ pos2 = g2->relend;
+ if( pos2 == 0 && g2->len >g1->len - (pos1) + newgaplen )
+ {
+ pfac2 += g2->freq;
+// reporterr( "hit! pfac2=%f, .freq=%f\n", pfac2, gaplen2[j][l].freq );
+ }
+// else
+// reporterr( "does not hit! pfac2=%f, gaplen1[i][k].len=%d, gaplen[i][k].relend=%d, newgaplen=%d\n", pfac2, gaplen1[i][k].len, gaplen1[i][k].relend, newgaplen );
+ }
+ pfac += pfac2 * g1->freq;
+ pfac1 += g1->freq;
+ }
+ else if( pos1 == 0 )
+ {
+ pfac2 = 1.0;
+ if( gaplen2j ) for( l=0; (g2=gaplen2j+l)->idatnext!=-1; l++ )
+ {
+ pos2 = g2->relend;
+ if( pos2 == 0 && g2->len == g1->len+newgaplen ) pfac2 -= g2->freq;// kokode shuryou suru gap, gaplen1 ha kangaenai.
+ if( pos2 != 0 && g2->len - (pos2-1) > g1->len+newgaplen ) pfac2 -= g2->freq;// keizoku suru gap, gaplen1 ha kangaenai.
+ }
+// reporterr( "pfac2 in line 1056 = %f\n", pfac2 );
+ pfac += pfac2 * g1->freq;
+ pfac10 += g1->freq;
+ }
+ }
+#if DEBUG
+ reporterr( "pfac1 (step2) = %f\n", pfac1 );
+ reporterr( "pfac10 (step2) = %f\n", pfac10 );
+ reporterr( "pfac (step2) = %f\n", pfac );
+#endif
+
+ pfac1 = 1.0 - pfac1 - pfac10;
+ pfac2 = 1.0;
+ if( gaplen2j ) for( l=0; (g2=gaplen2j+l)->idatnext!=-1; l++ )
+ {
+ pos2 = g2->relend;
+ if( pos2 == 0 && g2->len == newgaplen ) pfac2 -= g2->freq;// kokode shuryou suru gap, gaplen1 ha kangaenai.
+ if( pos2 != 0 && g2->len - (pos2-1) > newgaplen ) pfac2 -= g2->freq;// keizoku suru gap, gaplen1 ha kangaenai.
+ }
+#if DEBUG
+ reporterr( "pfac1 (type3) = %f\n", pfac1 );
+ reporterr( "pfac2 (type3) = %f\n", pfac2 );
+ reporterr( "pfac (step3) = %f\n", pfac );
+#endif
+ pfac += pfac1 * pfac2;
+#if DEBUG
+ reporterr( "incomplete pfac = %f, pfac1,pfac2 (%c%d,%c%d) = %f, %f\n", pfac, seq1[i], i, seq2[j], j, pfac1, pfac2 );
+#endif
+
+
+ return( pfac );
+
+#else
+
+ double pfac, pfac1, pfac10, pfac2;
+ int k, l, pos1, pos2, id1, id2;
+ Gaplen *gaplen1i, *gaplen2j;
+
+#if 0 // .len no shouryaku ni taiou shiteinai
+ int gl;
+ if( disp )
+ {
+ reporterr( "calcpfac_gap_noidatend, %c (%d) - %c (%d)\n", seq1[i], i, seq2[j], j );
+ reporterr( "newgaplen = %d\n", newgaplen );
+ reporterr( "In calcpfac_gap, gaplen1[%d(%c)] = \n", i, seq1[i] );
+ for( k=0; gaplen1[i]&&(id1=gaplen1[i][k].idatend)!=-1; k++ )
+ {
+ pos1 = gaplen1[i][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen1[i+pos1][id1].len, gaplen1[i][k].relend, gaplen1[i+pos1][id1].freq[0] );
+ }
+ reporterr( "In calcpfac_gap, gaplen2[%d(%c)] = \n", j, seq2[j] );
+ showgaplen( gaplen2, strlen(seq2) );
+ for( k=0; gaplen2[j]&&(id2=gaplen2[j][k].idatend)!=-1; k++ )
+ {
+ pos2 = gaplen2[j][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen2[j+pos2][id2].len, gaplen2[j][k].relend, gaplen2[j+pos2][id2].freq[0] );
+ }
+ }
+#endif
+ gaplen2j = gaplen2[j];
+ gaplen1i = gaplen1[i];
+
+ pfac = 0.0;
+ pfac1 = 0.0;
+ pfac10 = 0.0;
+ if( gaplen1i ) for( k=0; (gaplen1i[k].idatnext)!=-1; k++ )
+ {
+ pos1 = gaplen1i[k].relend;
+ if( pos1 != 0 )
+ {
+ pfac2 = 0.0;
+ if( gaplen2j ) for( l=0; (gaplen2j[l].idatnext)!=-1; l++ )
+ {
+ pos2 = gaplen2j[l].relend;
+ if( pos2 == 0 && gaplen2j[l].len > gaplen1i[k].len - (pos1) + newgaplen )
+ {
+ pfac2 += gaplen2j[l].freq;
+// reporterr( "hit! pfac2=%f, .freq=%f\n", pfac2, gaplen2[j][l].freq );
+ }
+// else
+// reporterr( "does not hit! pfac2=%f, gaplen1[i][k].len=%d, gaplen[i][k].relend=%d, newgaplen=%d\n", pfac2, gaplen1[i][k].len, gaplen1[i][k].relend, newgaplen );
+ }
+ pfac += pfac2 * gaplen1i[k].freq;
+ pfac1 += gaplen1i[k].freq;
+ }
+ else if( pos1 == 0 )
+ {
+ pfac2 = 1.0;
+ if( gaplen2j ) for( l=0; (gaplen2j[l].idatnext)!=-1; l++ )
+ {
+ pos2 = gaplen2j[l].relend;
+ if( pos2 == 0 && gaplen2j[l].len == gaplen1i[k].len+newgaplen ) pfac2 -= gaplen2j[l].freq;// kokode shuryou suru gap, gaplen1 ha kangaenai.
+ if( pos2 != 0 && gaplen2j[l].len - (pos2-1) > gaplen1i[k].len+newgaplen ) pfac2 -= gaplen2j[l].freq;// keizoku suru gap, gaplen1 ha kangaenai.
+ }
+// reporterr( "pfac2 in line 1056 = %f\n", pfac2 );
+ pfac += pfac2 * gaplen1i[k].freq;
+ pfac10 += gaplen1i[k].freq;
+ }
+ }
+#if DEBUG
+ reporterr( "pfac1 (step2) = %f\n", pfac1 );
+ reporterr( "pfac10 (step2) = %f\n", pfac10 );
+ reporterr( "pfac (step2) = %f\n", pfac );
+#endif
+
+ pfac1 = 1.0 - pfac1 - pfac10;
+ pfac2 = 1.0;
+ if( gaplen2j ) for( l=0; (gaplen2j[l].idatnext)!=-1; l++ )
+ {
+ pos2 = gaplen2j[l].relend;
+ if( pos2 == 0 && gaplen2j[l].len == newgaplen ) pfac2 -= gaplen2j[l].freq;// kokode shuryou suru gap, gaplen1 ha kangaenai.
+ if( pos2 != 0 && gaplen2j[l].len - (pos2-1) > newgaplen ) pfac2 -= gaplen2j[l].freq;// keizoku suru gap, gaplen1 ha kangaenai.
+ }
+#if DEBUG
+ reporterr( "pfac1 (type3) = %f\n", pfac1 );
+ reporterr( "pfac2 (type3) = %f\n", pfac2 );
+ reporterr( "pfac (step3) = %f\n", pfac );
+#endif
+ pfac += pfac1 * pfac2;
+#if DEBUG
+ reporterr( "incomplete pfac = %f, pfac1,pfac2 (%c%d,%c%d) = %f, %f\n", pfac, seq1[i], i, seq2[j], j, pfac1, pfac2 );
+#endif
+
+
+ return( pfac );
+
+#endif
+}
+
+#if USEGAPLENHALFORMTX
+
+static double calcpfac_gap_incomplete( Gaplen **gaplen1, Gaplen **gaplen2, int newgaplen, int i, int j, char *seq1, char *seq2, int disp ) // seq1 to seq2 ha debug you
+{
+ double pfac, pfac1, pfac10, pfac2;
+ int k, l, pos1, pos2, id1, id2;
+ Gaplen *gapend1, *gapend2;
+ Gaplen *gaplen1i, *gaplen2j;
+
+#if 0 // .len no shouryaku ni taiou shiteinai
+ int gl;
+ if( disp )
+ {
+ reporterr( "calcpfac_gap_incomplete, %c (%d) - %c (%d)\n", seq1[i], i, seq2[j], j );
+ reporterr( "newgaplen = %d\n", newgaplen );
+ reporterr( "In calcpfac_gap, gaplen1[%d(%c)] = \n", i, seq1[i] );
+ for( k=0; gaplen1[i]&&(id1=gaplen1[i][k].idatend)!=-1; k++ )
+ {
+ pos1 = gaplen1[i][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen1[i+pos1][id1].len, gaplen1[i][k].relend, gaplen1[i+pos1][id1].freq[0] );
+ }
+ reporterr( "In calcpfac_gap, gaplen2[%d(%c)] = \n", j, seq2[j] );
+ showgaplen( gaplen2, strlen(seq2) );
+ for( k=0; gaplen2[j]&&(id2=gaplen2[j][k].idatend)!=-1; k++ )
+ {
+ pos2 = gaplen2[j][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen2[j+pos2][id2].len, gaplen2[j][k].relend, gaplen2[j+pos2][id2].freq[0] );
+ }
+ }
+#endif
+ gaplen2j = gaplen2[j];
+ gaplen1i = gaplen1[i];
+
+ pfac = 0.0;
+ pfac1 = 0.0;
+ pfac10 = 0.0;
+ if( gaplen1i ) for( k=0; (id1=gaplen1i[k].idatend)!=-1; k++ )
+ {
+ pos1 = gaplen1i[k].relend;
+ gapend1 = gaplen1[i+pos1]+id1;
+ if( pos1 != 0 )
+ {
+ pfac2 = 0.0;
+ if( gaplen2j ) for( l=0; (id2=gaplen2j[l].idatend)!=-1; l++ )
+ {
+ pos2 = gaplen2j[l].relend;
+ gapend2 = gaplen2[j+pos2]+id2;
+// if( pos2 == 0 && gapend2->len + 1 > gapend1->len - (pos1-1) + newgaplen )
+ if( pos2 == 0 && gapend2->len > gapend1->len - (pos1) + newgaplen )
+ {
+ pfac2 += gapend2->freq;
+// reporterr( "hit! pfac2=%f, .freq=%f\n", pfac2, gaplen2[j][l].freq );
+ }
+// else
+// reporterr( "does not hit! pfac2=%f, gaplen1[i][k].len=%d, gaplen[i][k].relend=%d, newgaplen=%d\n", pfac2, gaplen1[i][k].len, gaplen1[i][k].relend, newgaplen );
+ }
+ pfac += pfac2 * gapend1->freq;
+ pfac1 += gapend1->freq;
+ }
+ else if( pos1 == 0 )
+ {
+ pfac2 = 1.0;
+ if( gaplen2j ) for( l=0; (id2=gaplen2j[l].idatend)!=-1; l++ )
+ {
+ pos2 = gaplen2j[l].relend;
+ gapend2 = gaplen2[j+pos2]+id2;
+ if( pos2 == 0 && gapend2->len == gapend1->len+newgaplen ) pfac2 -= gapend2->freq;// kokode shuryou suru gap, gaplen1 ha kangaenai.
+ if( pos2 != 0 && gapend2->len - (pos2-1) > gapend1->len+newgaplen ) pfac2 -= gapend2->freq;// keizoku suru gap, gaplen1 ha kangaenai.
+ }
+// reporterr( "pfac2 in line 1056 = %f\n", pfac2 );
+ pfac += pfac2 * gapend1->freq;
+ pfac10 += gapend1->freq;
+ }
+ }
+#if DEBUG
+ reporterr( "pfac1 (step2) = %f\n", pfac1 );
+ reporterr( "pfac10 (step2) = %f\n", pfac10 );
+ reporterr( "pfac (step2) = %f\n", pfac );
+#endif
+
+ pfac1 = 1.0 - pfac1 - pfac10;
+ pfac2 = 1.0;
+ if( gaplen2j ) for( l=0; (id2=gaplen2j[l].idatend)!=-1; l++ )
+ {
+ pos2 = gaplen2j[l].relend;
+ gapend2 = gaplen2[j+pos2]+id2;
+ if( pos2 == 0 && gapend2->len == newgaplen ) pfac2 -= gapend2->freq;// kokode shuryou suru gap, gaplen1 ha kangaenai.
+ if( pos2 != 0 && gapend2->len - (pos2-1) > newgaplen ) pfac2 -= gapend2->freq;// keizoku suru gap, gaplen1 ha kangaenai.
+ }
+#if DEBUG
+ reporterr( "pfac1 (type3) = %f\n", pfac1 );
+ reporterr( "pfac2 (type3) = %f\n", pfac2 );
+ reporterr( "pfac (step3) = %f\n", pfac );
+#endif
+ pfac += pfac1 * pfac2;
+#if DEBUG
+ reporterr( "incomplete pfac = %f, pfac1,pfac2 (%c%d,%c%d) = %f, %f\n", pfac, seq1[i], i, seq2[j], j, pfac1, pfac2 );
+#endif
+
+
+ return( pfac );
+
+}
+
+static double calcpfac_gapex( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, int newgaplen, char *seq1, char *seq2, int disp )
+{
+ double pfac, pfac1, pfac2, pfac10;
+ int k, l, id1, id2, pos1, pos2;
+ Gaplen *gapend1, *gapend2;
+ Gaplen *gaplen1i, *gaplen2j;
+
+ gaplen1i = gaplen1[i];
+ gaplen2j = gaplen2[j];
+
+ pfac = 0.0;
+ pfac2 = 0.0;
+// for( k=0; gaplen2[j]&&(gl=gaplen2[j][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ if( gaplen2j ) for( k=0; (id2=gaplen2j[k].idatend)!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+#if DEBUG
+ int gl;
+ pos2 = gaplen2j[k].relend;
+ id2 = gaplen2j[k].idatend;
+ gl = gaplen2[j+pos2][id2].len;
+ if( disp ) reporterr( "gaplen2[][].len=%d, .relend=%d, .freq=%f\n", gaplen2[j+pos2][id2].len, gaplen2[j][k].relend, gaplen2[j+pos2][id2].freq );
+ if( disp ) reporterr( "gl = %d, newgaplen=%d\n", gl, newgaplen );
+#endif
+ if( (pos2=gaplen2[j][k].relend) != 0 ) continue;
+
+ gapend2 = gaplen2[j+pos2]+id2;
+ pfac1 = 1.0;
+ pfac10 = 1.0;
+ if( gaplen1i ) for( l=0; (id1=gaplen1i[l].idatend)!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ pos1 = gaplen1i[l].relend;
+ gapend1 = gaplen1[i+pos1]+id1;
+ pfac10 -= gapend1->freq;
+#if DEBUG
+ if( disp ) reporterr( "gaplen1[][].len=%d, .relend=%d, .freq=%f\n", gaplen1[i+pos1][id1].len, gaplen1[i][l].relend, gaplen1[i+pos1][id1].freq );
+#endif
+ if( newgaplen + gapend1->len - (pos1) > gapend2->len - (pos2) ) pfac1 -= gapend1->freq;
+// reporterr( "pfac1 = %f\n", pfac1 );
+ }
+ pfac += pfac1 * gapend2->freq;
+
+
+/* ???? */
+ if( newgaplen >= gapend2->len - (pos2-1) ) // >= or >??
+ {
+ pfac -= pfac10 * gapend2->freq;
+// reporterr( "Hit! pfac1 = %f\n", pfac1 );
+ }
+/* ???? */
+
+
+// if( gaplen2[j][k].relend == -1 ) pfac += gaplen2[j][k].freq;
+ }
+
+ return( pfac );
+}
+
+static double calcpfac( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, char *seq1, char *seq2, int disp ) // seq1 to seq2 ha debug you
+{
+ double pfac, pfac1, pfac2;
+ int k, l, pos1, pos2, id1, id2;
+ Gaplen *gapend1, *gapend2;
+ Gaplen *gaplen1i, *gaplen2j;
+
+ gaplen1i = gaplen1[i];
+ gaplen2j = gaplen2[j];
+
+#if DEBUG
+ if( disp )
+ {
+ reporterr( "seq1[0] = %s\n", seq1 );
+ reporterr( "seq2[0] = %s\n", seq2 );
+ reporterr( "i,j=%d,%d\n", i, j );
+
+ reporterr( "In calcpfac(), gaplen1[%d(%c)] = \n", i, seq1[i] );
+// showgaplen( gaplen1, seqlen( seq1 ) );
+ for( k=0; gaplen1[i]&&(id1=gaplen1[i][k].idatend)!=-1; k++ )
+ {
+ pos1 = gaplen1[i][k].relend;
+ reporterr( "pos1=%d, id1=%d\n", pos1, id1 );
+ reporterr( ".len=%d, .relend=%d, .freq=%f\n", gaplen1[i+pos1][id1].len, gaplen1[i][k].relend, gaplen1[i+pos1][id1].freq );
+ }
+
+ reporterr( "In calcpfac(), gaplen2[%d(%c)] = \n", j, seq2[j] );
+// showgaplen( gaplen2, seqlen( seq2 ) );
+ for( k=0; gaplen2[j]&&(id2=gaplen2[j][k].idatend)!=-1; k++ )
+ {
+ pos2 = gaplen2[j][k].relend;
+ reporterr( "j=%d, k=%d, id2=%d, pos2=%d\n", j, k, id2, pos2 );
+ reporterr( ".len=%d, .relend=%d\n", gaplen2[j+pos2][id2].len, gaplen2[j][k].relend );
+ reporterr( ".freq=%f\n", gaplen2[j+pos2][id2].freq );
+ }
+ }
+#endif
+
+ pfac1 = pfac2 = 0.0;
+ if( gaplen1i ) for( k=0; (id1=gaplen1i[k].idatend)!=-1; k++ )
+ {
+ if( (pos1=gaplen1i[k].relend) == 0 ) pfac1 += gaplen1[i+pos1][id1].freq;
+ }
+
+ if( gaplen2j ) for( l=0; (id2=gaplen2j[l].idatend)!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ if( (pos2=gaplen2j[l].relend) == 0 ) pfac2 += gaplen2[j+pos2][id2].freq;
+ }
+#if DEBUG
+ reporterr( "\n\nInitial pfac1,pfac2 (%c%d,%c%d) = %f, %f\n", seq1[i], i, seq2[j], j, pfac1, pfac2 );
+#endif
+ pfac = pfac1 * pfac2 + pfac1 * (1-pfac2) + pfac2 * (1-pfac1);
+#if DEBUG
+ reporterr( "\n\nInitial pfac (%d,%d) = %f\n", i, j, pfac );
+#endif
+
+#if 1
+// if( pfac ) reporterr( "i,j=%d,%d, Cancel (eq len)? pfac = %f -> ", i, j, pfac );
+ if( gaplen1i ) for( k=0; (id1=gaplen1i[k].idatend)!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+ pos1=gaplen1i[k].relend;
+ gapend1 = gaplen1[i+pos1]+id1;
+ if( gaplen2j ) for( l=0; (id2=gaplen2j[l].idatend)!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ pos2 = gaplen2j[l].relend;
+ gapend2 = gaplen2[j+pos2]+id2;
+ if ( pos1 == 0 && pos2 == 0 && gapend1->len == gapend2->len ) pfac -= gapend1->freq * gapend2->freq;
+ else if( pos1 == 0 && pos2 != 0 && gapend2->len - (pos2-1) > gapend1->len ) pfac -= gapend1->freq * gapend2->freq;
+ else if( pos1 != 0 && pos2 == 0 && gapend1->len - (pos1-1) > gapend2->len ) pfac -= gapend1->freq * gapend2->freq;
+ }
+ }
+
+#if DEBUG
+ reporterr( "\n\nFinal pfac1,pfac2 (%c%d,%c%d, straight) = %f\n\n", seq1[i], i, seq2[j], j, pfac );
+#endif
+#else
+#endif
+ return( pfac );
+}
+#endif
+
+static double calcpfac_gapex_noidatend( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, int newgaplen, char *seq1, char *seq2, int disp )
+{
+#if 1
+ double pfac, pfac1, pfac2, pfac10;
+ int k, l, pos1, pos2;
+ Gaplen *gaplen1i, *gaplen2j, *g1, *g2;
+
+ gaplen1i = gaplen1[i];
+ gaplen2j = gaplen2[j];
+
+ pfac = 0.0;
+ pfac2 = 0.0;
+ if( gaplen2j ) for( k=0; (g2=gaplen2j+k)->idatnext!=-1; k++ )
+ {
+#if DEBUG
+ int gl;
+ pos2 = gaplen2j[k].relend;
+ gl = gaplen2j[k].len;
+ if( disp ) reporterr( "gaplen2[][].len=%d, .relend=%d, .freq=%f\n", gaplen2[j][k].len, gaplen2[j][k].relend, gaplen2[j][k].freq );
+ if( disp ) reporterr( "gl = %d, newgaplen=%d\n", gl, newgaplen );
+#endif
+ if( (pos2=g2->relend) != 0 ) continue;
+
+ pfac1 = 1.0;
+ pfac10 = 1.0;
+ if( gaplen1i ) for( l=0; (g1=gaplen1i+l)->idatnext!=-1; l++ )
+ {
+ pos1 = g1->relend;
+ pfac10 -= g1->freq;
+#if DEBUG
+ if( disp ) reporterr( "gaplen1[][].len=%d, .relend=%d, .freq=%f\n", gaplen1[i][l].len, gaplen1[i][l].relend, gaplen1[i][l].freq );
+#endif
+ if( newgaplen + g1->len - (pos1) > g2->len - (pos2) ) pfac1 -= g1->freq;
+// reporterr( "pfac1 = %f\n", pfac1 );
+ }
+ pfac += pfac1 * g2->freq;
+
+
+/* ???? */
+ if( newgaplen >= g2->len - (pos2-1) ) // >= or >??
+ {
+ pfac -= pfac10 * g2->freq;
+// reporterr( "Hit! pfac1 = %f\n", pfac1 );
+ }
+/* ???? */
+
+
+// if( gaplen2[j][k].relend == -1 ) pfac += gaplen2[j][k].freq;
+ }
+
+ return( pfac );
+#else
+ double pfac, pfac1, pfac2, pfac10;
+ int k, l, id1, id2, pos1, pos2;
+ Gaplen *gaplen1i, *gaplen2j;
+
+ gaplen1i = gaplen1[i];
+ gaplen2j = gaplen2[j];
+
+ pfac = 0.0;
+ pfac2 = 0.0;
+// for( k=0; gaplen2[j]&&(gl=gaplen2[j][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ if( gaplen2j ) for( k=0; (gaplen2j[k].idatnext)!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+#if DEBUG
+ int gl;
+ pos2 = gaplen2j[k].relend;
+ gl = gaplen2j[k].len;
+ if( disp ) reporterr( "gaplen2[][].len=%d, .relend=%d, .freq=%f\n", gaplen2[j][k].len, gaplen2[j][k].relend, gaplen2[j][k].freq );
+ if( disp ) reporterr( "gl = %d, newgaplen=%d\n", gl, newgaplen );
+#endif
+ if( (pos2=gaplen2[j][k].relend) != 0 ) continue;
+
+ pfac1 = 1.0;
+ pfac10 = 1.0;
+ if( gaplen1i ) for( l=0; (gaplen1i[l].idatnext)!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ pos1 = gaplen1i[l].relend;
+ pfac10 -= gaplen1i[l].freq;
+#if DEBUG
+ if( disp ) reporterr( "gaplen1[][].len=%d, .relend=%d, .freq=%f\n", gaplen1[i][l].len, gaplen1[i][l].relend, gaplen1[i][l].freq );
+#endif
+ if( newgaplen + gaplen1i[l].len - (pos1) > gaplen2j[k].len - (pos2) ) pfac1 -= gaplen1i[l].freq;
+// reporterr( "pfac1 = %f\n", pfac1 );
+ }
+ pfac += pfac1 * gaplen2j[k].freq;
+
+
+/* ???? */
+ if( newgaplen >= gaplen2j[k].len - (pos2-1) ) // >= or >??
+ {
+ pfac -= pfac10 * gaplen2j[k].freq;
+// reporterr( "Hit! pfac1 = %f\n", pfac1 );
+ }
+/* ???? */
+
+
+// if( gaplen2[j][k].relend == -1 ) pfac += gaplen2[j][k].freq;
+ }
+
+ return( pfac );
+
+#endif
+}
+
+
+static double calcpfacnoidatend( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, char *seq1, char *seq2, int disp ) // seq1 to seq2 ha debug you
+{
+ double pfac, pfac1, pfac2;
+ int k, l, pos1, pos2;
+ Gaplen *gaplen1i, *gaplen2j, *g1, *g2;
+
+ gaplen1i = gaplen1[i];
+ gaplen2j = gaplen2[j];
+
+#if DEBUG
+ if( disp )
+ {
+ reporterr( "seq1[0] = %s\n", seq1 );
+ reporterr( "seq2[0] = %s\n", seq2 );
+ reporterr( "i,j=%d,%d\n", i, j );
+
+ reporterr( "In calcpfacnoidatend(), gaplen1[%d(%c)] = \n", i, seq1[i] );
+ showgaplen( gaplen1, seqlen( seq1 ) );
+ for( k=0; gaplen1[i]&&gaplen1[i][k].idatnext!=-1; k++ )
+ {
+ pos1 = gaplen1[i][k].relend;
+ reporterr( ".len=%d, .relend=%d, .freq=%f (i=%d)\n", gaplen1[i][k].len, gaplen1[i][k].relend, gaplen1[i][k].freq, i );
+ }
+
+ reporterr( "In calcpfacnoidatend(), gaplen2[%d(%c)] = \n", j, seq2[j] );
+ showgaplen( gaplen2, seqlen( seq2 ) );
+ for( k=0; gaplen2[j]&&gaplen2[j][k].idatnext!=-1; k++ )
+ {
+ pos2 = gaplen2[j][k].relend;
+ reporterr( ".len=%d, .relend=%d (j=%d)\n", gaplen2[j][k].len, gaplen2[j][k].relend, j );
+ reporterr( ".freq=%f\n", gaplen2[j][k].freq );
+ }
+ }
+#endif
+
+#if 1
+ pfac1 = pfac2 = 0.0;
+ if( gaplen1i ) for( k=0; (g1=gaplen1i+k)->idatnext!=-1; k++ )
+ {
+ if( (pos1=g1->relend) == 0 ) pfac1 += g1->freq;
+ }
+
+ if( gaplen2j ) for( l=0; (g2=gaplen2j+l)->idatnext!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ if( (pos2=g2->relend) == 0 ) pfac2 += g2->freq;
+ }
+#if DEBUG
+ reporterr( "\n\nInitial pfac1,pfac2 (%c%d,%c%d) = %f, %f\n", seq1[i], i, seq2[j], j, pfac1, pfac2 );
+#endif
+ pfac = pfac1 * pfac2 + pfac1 * (1-pfac2) + pfac2 * (1-pfac1);
+#if DEBUG
+ reporterr( "\n\nInitial pfac (%d,%d) = %f\n", i, j, pfac );
+#endif
+
+// if( pfac ) reporterr( "i,j=%d,%d, Cancel (eq len)? pfac = %f -> ", i, j, pfac );
+ if( gaplen1i ) for( k=0; (g1=gaplen1i+k)->idatnext!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+ pos1=g1->relend;
+ if( gaplen2j ) for( l=0; (g2=gaplen2j+l)->idatnext!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ pos2 = gaplen2j[l].relend;
+ if ( pos1 == 0 && pos2 == 0 && g1->len == g2->len ) pfac -= g1->freq * g2->freq;
+ else if( pos1 == 0 && pos2 != 0 && g2->len - (pos2-1) > g1->len ) pfac -= g1->freq * g2->freq;
+ else if( pos1 != 0 && pos2 == 0 && g1->len - (pos1-1) > g2->len ) pfac -= g1->freq * g2->freq;
+ }
+ }
+
+#else
+
+ pfac1 = pfac2 = 0.0;
+ if( gaplen1i ) for( k=0; (gaplen1i[k].idatnext)!=-1; k++ )
+ {
+ if( gaplen1i[k].relend == 0 ) pfac1 += gaplen1[i][k].freq;
+ }
+
+ if( gaplen2j ) for( l=0; (gaplen2j[l].idatnext)!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ if( gaplen2j[l].relend == 0 ) pfac2 += gaplen2[j][l].freq;
+ }
+#if DEBUG
+ reporterr( "\n\nInitial pfac1,pfac2 (%c%d,%c%d) = %f, %f\n", seq1[i], i, seq2[j], j, pfac1, pfac2 );
+#endif
+ pfac = pfac1 * pfac2 + pfac1 * (1-pfac2) + pfac2 * (1-pfac1);
+#if DEBUG
+ reporterr( "\n\nInitial pfac (%d,%d) = %f\n", i, j, pfac );
+#endif
+
+#if 1
+// if( pfac ) reporterr( "i,j=%d,%d, Cancel (eq len)? pfac = %f -> ", i, j, pfac );
+ if( gaplen1i ) for( k=0; (gaplen1i[k].idatnext)!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+ pos1=gaplen1i[k].relend;
+ if( gaplen2j ) for( l=0; (gaplen2j[l].idatnext)!=-1; l++ ) // ososugi! hash ni atode henkou
+ {
+ pos2 = gaplen2j[l].relend;
+ if ( pos1 == 0 && pos2 == 0 && gaplen1i[k].len == gaplen2j[l].len ) pfac -= gaplen1i[k].freq * gaplen2j[l].freq;
+ else if( pos1 == 0 && pos2 != 0 && gaplen2j[l].len - (pos2-1) > gaplen1i[k].len ) pfac -= gaplen1i[k].freq * gaplen2j[l].freq;
+ else if( pos1 != 0 && pos2 == 0 && gaplen1i[k].len - (pos1-1) > gaplen2j[l].len ) pfac -= gaplen1i[k].freq * gaplen2j[l].freq;
+ }
+ }
+#endif
+#endif
+
+#if DEBUG
+ reporterr( "\n\nFinal pfac1,pfac2 (%c%d,%c%d, straight) = %f\n\n", seq1[i], i, seq2[j], j, pfac );
+#endif
+ return( pfac );
+}
+
+
+static void extendgaplencompactx( Gaplen **cpy, Gaplen **orig, int start )
+{
+ Gaplen *opt, *cpt;
+ int l, id;
+#if DEBUG
+ Gaplen cpybk;
+#endif
+
+// if( start < 0 ) start = 0;
+
+ if( orig[start] == NULL )
+ {
+ if( cpy[start] )
+ {
+ free( cpy[start] );
+ cpy[start] = NULL;
+ }
+ return;
+ }
+
+
+#if DEBUG
+ reporterr( "At first, cpy -> \n" );
+ showgaplen( cpy, 100 );
+ reporterr( "Look at %d \n", start );
+#endif
+
+ if( cpy[start] == NULL )
+ {
+ l = orig[start][0].npat;
+
+ cpy[start] = realloc( cpy[start], (l+2) * sizeof( Gaplen ) );
+
+#if 0
+ for( l=0; (gl=orig[start][l].idatend)!=-1; l++ )
+ cpy[start][l] = orig[start][l]; // freq ha pointer de copy
+ cpy[start][l] = orig[start][l]; // dekiru?
+#else
+ for( opt = orig[start],cpt = cpy[start]; opt->idatnext!=-1; )
+ *cpt++ = *opt++;
+ *cpt = *opt;
+#endif
+ }
+
+#if DEBUG
+ cpybk = cpy[start][0];
+#endif
+
+#if 0
+ for( l=0; (opt=orig[start]+l)->idatend!=-1; l++ )
+ {
+ if( (pos=opt->relend) == 0 ) continue;
+
+ if( cpy[posplus=start+pos] != NULL )
+ {
+ id = opt->idatend;
+// reporterr( "cpy[%d][%d].len: %d -> %d (relend=%d)\n", start, l, cpy[start][l].len, cpy[posplus][id].len, pos );
+ cpy[start][l].len = cpy[posplus][id].len; // Ato de posplus wo tsukawanaiyouni henkou.
+ continue; // HITSUYOU!!!
+ }
+ else
+ {
+// reporterr( "cpy[%d][%d].len: %d (relend=%d)\n", start, l, cpy[start][l].len, pos );
+ }
+
+#if 0
+ for( k=0; orig[start+pos][k].idatend!=-1; k++ )
+ ;
+#else
+ optplus = orig[posplus];
+ k = optplus->npat;
+#endif
+
+
+ cptplus = cpy[posplus] = realloc( cpy[posplus], (k+2) * sizeof( Gaplen ) );
+// cptplus = realloc( cptplus, (k+2) * sizeof( Gaplen ) );
+
+#if 0
+ for( k=0; optplus[k].idatend!=-1; k++ )
+ {
+ cptplus[k] = optplus[k]; // dekiru?
+ }
+ cptplus[k] = optplus[k]; // dekiru?
+#else
+ while( optplus->idatend!=-1 ) *cptplus++ = *optplus++;
+ *cptplus = *optplus;
+#endif
+ }
+#endif
+
+
+ if( start == 0 ) return;
+ if( cpy[start-1] == NULL ) return;
+
+#if DEBUG
+ reporterr( "cpy -> \n" );
+ showgaplen( cpy, 100 );
+ reporterr( "Look at %d \n", start );
+#endif
+
+ for( l=0; orig[start][l].idatnext!=-1; l++ )
+ {
+ if( (id=orig[start][l].idatprev) == -1 ) continue;
+
+// if( cpy[start][l].relend != 0 ) cpy[start][l].len = cpy[start-1][id].len; // Shinchou ni
+ cpy[start][l].len = cpy[start-1][id].len; // Shinchou ni
+
+// if( cpy[start][l].len != cpy[start-1][id].len )
+#if DEBUG
+ if( 1 || cpy[start][l].len != cpy[start-1][id].len )
+ {
+ reporterr( "Check!! cpy[%d][%d].len=%d, but [start-1][].len=%d, relend=%d\n", start, l, cpy[start][l].len, cpy[start-1][id].len, cpy[start][l].relend );
+ reporterr( "orig[%d][%d].len=%d, relend=%d\n", start, l, orig[start][l].len, orig[start][l].relend );
+ reporterr( "cpybk.len=%d, relend=%d\n", cpybk.len, cpybk.relend );
+
+ }
+ else
+ {
+// reporterr( "OK, cpy[%d][%d].len=%d, relend=%d\n", start, l, cpy[start][l].len, cpy[start][l].relend );
+ }
+#endif
+ }
+
+}
+
+
+#if USEGAPLENHALFORMTX
+static void extendgaplenpartly( Gaplen **cpy, Gaplen **orig, int start, int end )
+{
+ int i, l, gl, extrascope;
+ Gaplen *pt;
+
+ if( start < 0 ) start = 0;
+// for( i=start; i<=end; i++ )
+// {
+// if( cpy[i] == (Gaplen *)1 )
+// {
+// end = i-1;
+// break;
+//// reporterr( "Okashii! i=%d\n", i );
+//// exit( 1 );
+// }
+// if( cpy[i] ) free( cpy[i] );
+// cpy[i] = NULL;
+// }
+
+
+ extrascope = 0;
+#if 0
+ for( i=start; i<=end; i++ ) if( orig[i] )
+ {
+ for( pt=orig[i]; (pt->idatend)!=-1; )
+ {
+ if( (gl=pt++->relend) > extrascope ) extrascope = i+gl-end+1;
+ }
+// extrascope = 10; // Kinji
+
+ }
+#else
+ if( orig[end] )
+ {
+ for( pt=orig[end]; (pt->idatend)!=-1; )
+ {
+ if( (gl=pt++->relend) > extrascope ) extrascope = gl;
+ }
+// extrascope = 10; // Kinji
+
+ }
+#endif
+ end += extrascope;
+
+ for( i=start; i<=end; i++ )
+ {
+ if( cpy[i] != NULL ) continue;
+
+ if( orig[i] == NULL )
+ {
+ if( cpy[i] ) free( cpy[i] ); // muda dakedo
+ cpy[i] = NULL;
+ continue;
+ }
+
+ for( l=0; (gl=orig[i][l].idatend)!=-1; l++ )
+ ;
+
+ cpy[i] = realloc( cpy[i], (l+2) * sizeof( Gaplen ) );
+// cpy[i] = calloc( sizeof( Gaplen ), l+2 );
+
+ for( l=0; (gl=orig[i][l].idatend)!=-1; l++ )
+ {
+#if 1
+ cpy[i][l] = orig[i][l]; // freq ha pointer de copy
+#else
+ cpy[i][l].len = gl;
+ cpy[i][l].relend = orig[i][l].relend;
+ cpy[i][l].freq = orig[i][l].freq;
+ cpy[i][l].gapidatend = orig[i][l].gapidatend;
+#endif
+
+// reporterr( "i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+ cpy[i][l] = orig[i][l]; // dekiru?
+// cpy[i][l].relend = -1;
+// cpy[i][l].len = -1;
+ }
+
+}
+#endif
+
+static void duplicategaplencompactx( Gaplen **cpy, Gaplen **orig, int maxlen, int start, int end )
+{
+ int i, l;
+
+
+ if( start < 0 ) start = 0;
+ for( i=start; i<=end; i++ )
+ {
+// reporterr( "i=%d / %d\n", i, maxlen );
+ if( cpy[i] == (Gaplen *)1 )
+ {
+ end = i-1;
+ break;
+// reporterr( "Okashii! i=%d\n", i );
+// exit( 1 );
+ }
+ if( cpy[i] ) free( cpy[i] );
+ cpy[i] = NULL;
+ }
+
+ for( i=start; i<=end; i++ )
+ {
+ if( orig[i] == NULL )
+ {
+ if( cpy[i] ) free( cpy[i] ); // muda dakedo
+ cpy[i] = NULL;
+ continue;
+ }
+
+#if 0
+ for( l=0; (gl=orig[i][l].idatend)!=-1; l++ )
+ ;
+#else
+ l = orig[i][0].npat;
+#endif
+
+ cpy[i] = realloc( cpy[i], (l+2) * sizeof( Gaplen ) );
+// cpy[i] = calloc( sizeof( Gaplen ), l+2 );
+
+ for( l=0; orig[i][l].idatnext!=-1; l++ )
+ {
+ cpy[i][l] = orig[i][l]; // freq ha pointer de copy
+// reporterr( "i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+ cpy[i][l] = orig[i][l]; // dekiru?
+// cpy[i][l].relend = -1;
+// cpy[i][l].len = -1;
+ }
+
+ return;
+}
+
+
+
+#if USEGAPLENHALFORMTX
+static void duplicategaplenpartly( Gaplen **cpy, Gaplen **orig, int start, int end )
+{
+ int i, l, gl, extrascope;
+ Gaplen *pt;
+
+ if( start < 0 ) start = 0;
+ for( i=start; i<=end; i++ )
+ {
+ if( cpy[i] == (Gaplen *)1 )
+ {
+ end = i-1;
+ break;
+// reporterr( "Okashii! i=%d\n", i );
+// exit( 1 );
+ }
+ if( cpy[i] ) free( cpy[i] );
+ cpy[i] = NULL;
+ }
+
+
+ extrascope = 0;
+#if 0
+ for( i=start; i<=end; i++ ) if( orig[i] )
+ {
+ for( pt=orig[i]; (pt->idatend)!=-1; )
+ {
+ if( (gl=pt++->relend) > extrascope ) extrascope = i+gl-end+1;
+ }
+// extrascope = 10; // Kinji
+
+ }
+#else
+ if( orig[end] )
+ {
+ for( pt=orig[end]; (pt->idatend)!=-1; )
+ {
+ if( (gl=pt++->relend) > extrascope ) extrascope = gl;
+ }
+// extrascope = 10; // Kinji
+
+ }
+#endif
+ end += extrascope;
+
+ for( i=start; i<=end; i++ )
+ {
+ if( orig[i] == NULL )
+ {
+ if( cpy[i] ) free( cpy[i] ); // muda dakedo
+ cpy[i] = NULL;
+ continue;
+ }
+
+ for( l=0; (gl=orig[i][l].idatend)!=-1; l++ )
+ ;
+
+ cpy[i] = realloc( cpy[i], (l+2) * sizeof( Gaplen ) );
+// cpy[i] = calloc( sizeof( Gaplen ), l+2 );
+
+ for( l=0; (gl=orig[i][l].idatend)!=-1; l++ )
+ {
+#if 1
+ cpy[i][l] = orig[i][l]; // freq ha pointer de copy
+#else
+ cpy[i][l].len = gl;
+ cpy[i][l].relend = orig[i][l].relend;
+ cpy[i][l].freq = orig[i][l].freq;
+ cpy[i][l].gapidatend = orig[i][l].gapidatend;
+#endif
+
+// reporterr( "i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+ cpy[i][l] = orig[i][l]; // dekiru?
+// cpy[i][l].relend = -1;
+// cpy[i][l].len = -1;
+ }
+
+}
+#endif
+
+
+static void gaplenextendnoidatend( Gaplen **cpy, int gapstartpos, int insertionlen )
+{
+ int l, id, idn, pos, len;
+
+#if 0
+// reporterr( "inserting %d gaps at position %d\n", insertionlen, gapstartpos );
+ for( l=0; cpy[gapstartpos] && (id=cpy[gapstartpos][l].idatend) !=-1; l++ )
+ {
+ pos = cpy[gapstartpos][l].relend;
+ cpy[gapstartpos+pos][id].len += insertionlen;
+ }
+#endif
+
+#if 1
+ for( l=0; cpy[gapstartpos] && (id=cpy[gapstartpos][l].idatnext) !=-1; l++ )
+ {
+ len = cpy[gapstartpos][l].len + insertionlen;
+// reporterr( "ext\n" );
+ for( pos=gapstartpos, idn=l; cpy[pos] != NULL && cpy[pos][idn].relend != 0; pos++ )
+ {
+// reporterr( "%d, plus %d %d->%d\n", pos, insertionlen, cpy[pos][idn].len, cpy[pos][idn].len+insertionlen );
+ cpy[pos][idn].len = len;
+ idn = cpy[pos][idn].idatnext;
+// if( pos == gapstartpos + 1 ) break;
+ break;
+ }
+// reporterr( "end\n" );
+
+ idn = cpy[gapstartpos][l].idatprev;
+ if( gapstartpos != 0 && idn != -1 && cpy[gapstartpos-1] ) cpy[gapstartpos-1][idn].len = len;
+ }
+#endif
+}
+
+
+#if USEGAPLENHALFORMTX
+
+static void gaplenextend( Gaplen **cpy, int gapstartpos, int insertionlen )
+{
+ int l, id, idn, pos, len;
+
+#if 1
+// reporterr( "inserting %d gaps at position %d\n", insertionlen, gapstartpos );
+ for( l=0; cpy[gapstartpos] && (id=cpy[gapstartpos][l].idatend) !=-1; l++ )
+ {
+ pos = cpy[gapstartpos][l].relend;
+ cpy[gapstartpos+pos][id].len += insertionlen;
+ }
+#endif
+
+#if 1
+ for( l=0; cpy[gapstartpos] && (id=cpy[gapstartpos][l].idatend) !=-1; l++ )
+ {
+ len = cpy[gapstartpos][l].len + insertionlen;
+// reporterr( "ext\n" );
+ for( pos=gapstartpos, idn=l; cpy[pos] != NULL && cpy[pos][idn].relend != 0; pos++ )
+ {
+// reporterr( "%d, plus %d %d->%d\n", pos, insertionlen, cpy[pos][idn].len, cpy[pos][idn].len+insertionlen );
+ cpy[pos][idn].len = len;
+ idn = cpy[pos][idn].idatnext;
+// if( pos == gapstartpos + 1 ) break;
+// break;
+ }
+// reporterr( "end\n" );
+
+ idn = cpy[gapstartpos][l].idatprev;
+ if( gapstartpos != 0 && idn != -1 && cpy[gapstartpos-1] ) cpy[gapstartpos-1][idn].len = len;
+ }
+#endif
+}
+#endif
+
+static void copygaplencompactx( Gaplen **cpy, Gaplen **orig, int seqlen, int gapstartpos, int insertionlen, int posincopy, int posinori )
+{
+ Gaplen *pt, *cpt;
+
+
+
+#if DEBUG
+ reporterr( "At the head of copygaplencompactx, cpy=\n" );
+ showgaplen( cpy+posincopy, 100 );
+ reporterr( "At the head of copygaplencompactx, orig=\n" );
+ showgaplen( orig+posinori, 100 );
+ reporterr( "posinori=%d\n", posinori );
+#endif
+
+ if( orig[posinori] == NULL ) return;
+
+// for( pt=orig[posinori],cpt=cpy[posincopy]; pt->relend==0; ) // zenhan ni relend=0 ga matomatteirukara.
+ for( pt=orig[posinori],cpt=cpy[posincopy]; pt->idatnext!=-1; ) // kouhan mo copy
+ {
+ cpt++->len = pt++->len;
+ }
+
+
+#if 0
+ for( l=0; (id=orig[posinori][l].idatend)!=-1; l++ )
+ {
+ pos = orig[posinori][l].relend;
+ if( pos == 0 ) continue;
+ if( orig[posinori+pos] == NULL )
+ {
+ reporterr( "Okashii\n" );
+ PFACERROR = 1;
+ continue;
+ }
+
+#if 0
+ for( k=0; orig[posinori+pos][k].relend==0; k++ ) // zenhan dake
+ {
+ cpy[posincopy+pos][k].len = orig[posinori+pos][k].len; // dekiru?
+ }
+#else
+ cpy[posincopy+pos][id].len = orig[posinori+pos][id].len; // dekiru?
+#endif
+ }
+#endif
+
+
+ if( gapstartpos == -1 ) gapstartpos = posincopy;
+ gaplenextendnoidatend( cpy, gapstartpos, insertionlen );
+
+#if DEBUG
+ reporterr( "At the end of copygaplencompactx, cpy=\n" );
+ showgaplen( cpy+posincopy, 100 );
+#endif
+}
+
+
+#if USEGAPLENHALF
+static void copygaplenrestricted_zurasu( Gaplen **cpy, Gaplen **orig, int seqlen, int gapstartpos, int insertionlen, int startincopy, int endincopy, int startinori, int endinori )
+{
+ int i, extrascope, gl, j;
+ int zure, newend;
+ Gaplen *pt, *cpt;
+// int ncopied = 0;
+
+#if 0
+// mae houkou nimo renzoku gap de enchou suru hitsuyou ga aru to omou.
+ for( i=startinori-1; 0<=i&&i<=seqlen; i-- )
+ {
+// reporterr( "i=%d\n", i );
+ if( orig[i] == NULL ) break;
+ for( pt=orig[i],cpt=cpy[i]; (gl=pt++->len)!=-1; ) cpt++->len = gl;
+ }
+#endif
+
+ zure = startincopy - startinori; // end ha check shinai
+
+// int ncopied = 0;
+ if( orig[endinori] )
+ {
+ extrascope = 0;
+ for( pt=orig[endinori]; (pt->idatend)!=-1; )
+ {
+ if( (gl=pt++->relend) > extrascope ) extrascope = gl;
+ }
+// extrascope = 10; // Kinji
+
+ newend = endinori + extrascope;
+ }
+ else newend = endinori;
+
+// reporterr( "ncopy = %d\n", newend - startinori );
+//
+#if 0 // extra end wo shizen ni kimereba iranai
+ if( newend > seqlen ) newend = seqlen;
+// if( startinori < 0 ) startinori = 0;
+#endif
+
+ for( i=startinori, j=startincopy; i<=newend; i++, j++ )
+ {
+ if( orig[i] == NULL ) continue;
+
+// ncopied += 1;
+
+#if 0
+ for( pt=orig[i],cpt=cpy[i]; (gl=pt++->len)!=-1; )
+ cpt++->len = gl;
+#else
+ for( pt=orig[i],cpt=cpy[j]; pt->relend==0; ) // zenhan ni relend=0 ga matomatteirukara.
+// int k;
+// for( k=0; orig[i][k].relend==0; k++ ) // zenhan ni relend=0 ga matomatteirukara.
+ {
+ cpt++->len = pt++->len;
+// reporterr( "i=%d, k=%d\n", i, k );
+// cpy[i][k].len = orig[i][k].len;
+ }
+#endif
+ }
+
+
+
+#if 0
+ for( i=0; i<=seqlen; i++ )
+ {
+ for( l=0; cpy[i]&&(gl=cpy[i][l].len)!=-1; l++ )
+ reporterr( "after copy, i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+#endif
+
+ if( gapstartpos < 0 ) return;
+
+ gaplenextend( cpy, gapstartpos, insertionlen );
+
+
+
+// return;
+
+
+// TEST
+// for( i=endinori+1; i<=newend; i++ )
+ for( i=endincopy+1; i<=newend+zure; i++ )
+ {
+ if( cpy[i] == NULL ) continue;
+ for( j=0; cpy[i][j].idatend!=-1; j++ )
+ {
+ if( cpy[i][j].relend == 0 )
+ {
+ break;
+ }
+ }
+ if( cpy[i][j].idatend == -1 )
+ {
+ free( cpy[i] );
+ cpy[i] = NULL;
+ }
+ }
+
+
+
+
+
+
+#if 0
+ reporterr( "\n" );
+ for( i=0; i<=seqlen; i++ )
+ {
+ for( l=0; cpy[i]&&(gl=cpy[i][l].len)!=-1; l++ )
+ reporterr( "after add, i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+#endif
+}
+#endif
+
+#if USEGAPLENHALFORMTX
+static void copygaplenrestricted( Gaplen **cpy, Gaplen **orig, int seqlen, int gapstartpos, int insertionlen, int scopestart, int scopeend )
+{
+ int i, j, extrascope, gl, endinori, newend;
+ Gaplen *pt, *cpt;
+// int ncopied = 0;
+
+#if 0
+// mae houkou nimo renzoku gap de enchou suru hitsuyou ga aru to omou.
+ for( i=scopestart-1; 0<=i&&i<=seqlen; i-- )
+ {
+// reporterr( "i=%d\n", i );
+ if( orig[i] == NULL ) break;
+ for( pt=orig[i],cpt=cpy[i]; (gl=pt++->len)!=-1; ) cpt++->len = gl;
+ }
+#endif
+
+// int ncopied = 0;
+ endinori = scopeend;
+ if( orig[scopeend] )
+ {
+ extrascope = 0;
+ for( pt=orig[scopeend]; (pt->idatend)!=-1; )
+ {
+ if( (gl=pt++->relend) > extrascope ) extrascope = gl;
+ }
+// extrascope = 10; // Kinji
+
+ scopeend += extrascope;
+ }
+ newend = scopeend;
+
+// reporterr( "ncopy = %d\n", scopeend - scopestart );
+//
+#if 0 // extra end wo shizen ni kimereba iranai
+ if( scopeend > seqlen ) scopeend = seqlen;
+// if( scopestart < 0 ) scopestart = 0;
+#endif
+
+ if( scopestart < 0 ) scopestart = 0;
+ for( i=scopestart; i<=scopeend; i++ )
+ {
+ if( orig[i] == NULL ) continue;
+
+// ncopied += 1;
+
+#if 0
+ for( pt=orig[i],cpt=cpy[i]; (gl=pt++->len)!=-1; )
+ cpt++->len = gl;
+#else
+ for( pt=orig[i],cpt=cpy[i]; pt->relend==0; ) // zenhan ni relend=0 ga matomatteirukara.
+// int k;
+// for( k=0; orig[i][k].relend==0; k++ ) // zenhan ni relend=0 ga matomatteirukara.
+ {
+ cpt++->len = pt++->len;
+// reporterr( "i=%d, k=%d\n", i, k );
+// cpy[i][k].len = orig[i][k].len;
+ }
+#endif
+ }
+
+
+
+#if 0
+ for( i=0; i<=seqlen; i++ )
+ {
+ for( l=0; cpy[i]&&(gl=cpy[i][l].len)!=-1; l++ )
+ reporterr( "after copy, i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+#endif
+
+ if( gapstartpos < 0 ) return;
+
+ gaplenextend( cpy, gapstartpos, insertionlen );
+
+ return;
+
+// TEST extra scope de tsukaunoha end dake?
+ for( i=endinori+1; i<=newend; i++ )
+ {
+ if( cpy[i] == NULL ) continue;
+ for( j=0; cpy[i][j].idatend!=-1; j++ )
+ {
+ if( cpy[i][j].relend == 0 ) break;
+ }
+ if( cpy[i][j].idatend == -1 )
+ {
+ free( cpy[i] );
+ cpy[i] = NULL;
+ }
+ }
+
+
+
+#if 0
+ reporterr( "\n" );
+ for( i=0; i<=seqlen; i++ )
+ {
+ for( l=0; cpy[i]&&(gl=cpy[i][l].len)!=-1; l++ )
+ reporterr( "after add, i=%d, l=%d, len=%d, freq=%f, relend=%d\n", i, l, cpy[i][l].len, cpy[i][l].freq, cpy[i][l].relend );
+ }
+#endif
+}
+#endif
+
+#if 1
+static void freegaplenpartly( Gaplen **mtx, int startpos, int endpos )
+{
+ int i;
+ Gaplen **pt;
+ if( startpos < 0 ) startpos = 0;
+
+ for( i=startpos; i<=endpos; i++ )
+ {
+ if( *(pt=mtx+i) == (Gaplen *)1 ) break;
+ if( *pt ) free( *pt );
+ *pt = NULL;
+ }
+}
+#else
+static void freegaplenpartly( Gaplen **mtx, int startpos, int endpos )
+{
+ int i;
+ if( startpos < 0 ) startpos = 0;
+
+ for( i=startpos; i<=endpos; i++ )
+ {
+ if( mtx[i] == (Gaplen *)1 ) break;
+ if( mtx[i] ) free( mtx[i] );
+ mtx[i] = NULL;
+ }
+}
+#endif
+
+
+double D__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, 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;
+ register int i, j;
+
+
+
+
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
+// double fpenalty = (double)penalty;
+#if USE_PENALTY_EX
+ double fpenalty_ex = (double)penalty_ex;
+#endif
+#if 1
+ double *wtmp;
+ int *ijppt;
+ double *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS double mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS double *w1, *w2;
+ static TLS double *match;
+ static TLS double *initverticalw; /* kufuu sureba iranai */
+ static TLS double *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS double **cpmx1;
+ static TLS double **cpmx2;
+ static TLS int **intwork;
+ static TLS double **doublework;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+#if USEGAPLENHALF
+ Gaplen ****gaplen1half = NULL; // NULL ga iru to omou.
+ Gaplen ****gaplen2half = NULL; // NULL ga iru to omou.
+#endif
+#if USEGAPLENMTX
+ Gaplen ****gaplen1mtx = NULL; // NULL ga iru to omou.
+ Gaplen ****gaplen2mtx = NULL; // NULL ga iru to omou.
+#endif
+ static TLS Gaplen **gaplen1 = NULL; // NULL ga iru to omou.
+ static TLS Gaplen **gaplen2 = NULL; // NULL ga iru to omou.
+ static TLS Gaplen ***gaplen1jprev = NULL;
+ static TLS Gaplen ***gaplen2jprev = NULL;
+ static TLS Gaplen ***gaplen1jcurr = NULL;
+ static TLS Gaplen ***gaplen2jcurr = NULL;
+ static TLS Gaplen ***gaplen1icurr = NULL;
+ static TLS Gaplen ***gaplen2icurr = NULL;
+ static TLS Gaplen ***gaplen1jbestkamo = NULL;
+ static TLS Gaplen ***gaplen2jbestkamo = NULL;
+ static TLS Gaplen ***gaplen1ibestkamo = NULL;
+ static TLS Gaplen ***gaplen2ibestkamo = NULL;
+ static TLS Gaplen ***gaplen1jbest = NULL;
+ static TLS Gaplen ***gaplen2jbest = NULL;
+ double fpenalty = (double)penalty;
+ double fpenalty_shift = (double)penalty_shift;
+ static TLS Gaplen ****gaplens = NULL;
+
+ Gaplen ***gaplentmp = NULL;
+ int *warpis = NULL;
+ int *warpjs = NULL;
+ int *warpi = NULL;
+ int *warpj = NULL;
+ int *prevwarpi = NULL;
+ int *prevwarpj = NULL;
+ double *wmrecords = NULL;
+ double *prevwmrecords = NULL;
+ int warpn = 0;
+ int warpbase;
+ double curm = 0.0;
+ double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+ int *warpipt, *warpjpt;
+ int k;
+ double pfac, pfactmp;
+ int newgaplen;
+
+// for( i=0; i<icyc; i++ ) fprintf( stderr, "%s, %f\n", seq1[i], eff1[i] );
+// for( i=0; i<jcyc; i++ ) fprintf( stderr, "%s, %f\n", seq2[i], eff2[i] );
+
+// reporterr( "\nsizeof(gaplen) = %d\n", sizeof( Gaplen ) );
+// reporterr( "\nsizeof(int) = %d\n", sizeof( int ) );
+// reporterr( "\nsizeof(double) = %d\n", sizeof( double ) );
+// reporterr( "\nsizeof(double*) = %d\n", sizeof( double * ) );
+
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 )
+ {
+// fprintf( stderr, "## Freeing local arrays in D__align\n" );
+ orlgth1 = 0;
+ orlgth2 = 0;
+
+ imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
+
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( doublework );
+ FreeIntMtx( intwork );
+
+
+
+ free( gaplens );
+ if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
+ if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
+ if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
+ if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
+
+ if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
+ if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
+ if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
+ if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
+ if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
+ if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
+ if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
+ if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
+ if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
+ if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
+ }
+ else
+ {
+// fprintf( stderr, "## Not allocated\n" );
+ }
+ return( 0.0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+ reporterr( "%d x %d sequences, len=%d, %d\n", icyc, jcyc, lgth1, lgth2 );
+
+
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ {
+ j = lgth2;
+ seq1[i][j] = 0;
+ while( j ) seq1[i][--j] = *newgapstr;
+// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+ }
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ for( i=0; i<jcyc; i++ )
+ {
+ j = lgth1;
+ seq2[i][j] = 0;
+ while( j ) seq2[i][--j] = *newgapstr;
+// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+ }
+ return( 0.0 );
+ }
+
+ warpbase = lgth1 + lgth2;
+ warpis = NULL;
+ warpjs = NULL;
+ warpn = 0;
+
+
+
+ if( trywarp )
+ {
+// reporterr( "Not supported yet!\n" );
+// exit( 1 );
+// fprintf( stderr, "IN D__align, penalty_shift = %d\n", penalty_shift );
+ if( headgp == 0 || tailgp == 0 )
+ {
+ fprintf( stderr, "At present, headgp and tailgp must be 1 to allow shift.\n" );
+ exit( 1 );
+ }
+ wmrecords = AllocateFloatVec( lgth2+1 );
+ warpi = AllocateIntVec( lgth2+1 );
+ warpj = AllocateIntVec( lgth2+1 );
+ prevwmrecords = AllocateFloatVec( lgth2+1 );
+ prevwarpi = AllocateIntVec( lgth2+1 );
+ prevwarpj = AllocateIntVec( lgth2+1 );
+ for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
+ }
+
+
+#if 0
+ fprintf( stderr, "#### eff in SA+++align\n" );
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( doublework );
+ FreeIntMtx( intwork );
+
+
+ free( gaplens );
+
+ if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
+ if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
+ if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
+ if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
+
+ if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
+ if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
+ if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
+ if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
+ if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
+ if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
+ if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
+ if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
+ if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
+ if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
+
+
+ }
+
+ 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 );
+
+ cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
+ cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
+
+#if FASTMATCHCALC
+ doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets+1 );
+#else
+ doublework = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+
+
+// reporterr( "Allocating gaplen1 and gaplen2\n" );
+ gaplen1 = (Gaplen ** )calloc( ll1+2, sizeof( Gaplen * ) );
+ gaplen1[ll1+1] = (Gaplen *)1;
+ gaplen2 = (Gaplen ** )calloc( ll2+2, sizeof( Gaplen * ) );
+ gaplen2[ll2+1] = (Gaplen *)1;
+
+
+// reporterr( "Allocating gaplen*\n" );
+ gaplen1ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen2ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen1icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen2icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen1jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen1jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen1jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen1jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+
+ gaplens = calloc( sizeof( Gaplen ***), 12 );
+ gaplens[0] = gaplen1ibestkamo;
+ gaplens[1] = gaplen2ibestkamo;
+ gaplens[2] = gaplen1icurr;
+ gaplens[3] = gaplen2icurr;
+ gaplens[4] = gaplen1jbestkamo;
+ gaplens[5] = gaplen2jbestkamo;
+ gaplens[6] = gaplen1jbest;
+ gaplens[7] = gaplen2jbest;
+ gaplens[8] = gaplen1jcurr;
+ gaplens[9] = gaplen2jcurr;
+ gaplens[10] = gaplen1jprev;
+ gaplens[11] = gaplen2jprev;
+// reporterr( "Allocation end\n" );
+ }
+
+ {
+ int ll1 = lgth1;
+ int ll2 = lgth2;
+
+// reporterr( "Allocating gaplen*i\n" );
+ for(i=0; i<ll1+1; i++ )
+ {
+ gaplen1ibestkamo[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1-i; k++ ) gaplen1ibestkamo[i][k] = NULL;
+ gaplen1ibestkamo[i][k] = (Gaplen *)1;
+
+ gaplen2ibestkamo[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1; k++ ) gaplen2ibestkamo[i][k] = NULL;
+ gaplen2ibestkamo[i][k] = (Gaplen *)1;
+
+ gaplen1icurr[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1-i; k++ ) gaplen1icurr[i][k] = NULL;
+ gaplen1icurr[i][k] = (Gaplen *)1;
+
+ gaplen2icurr[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1; k++ ) gaplen2icurr[i][k] = NULL;
+ gaplen2icurr[i][k] = (Gaplen *)1;
+ }
+ gaplen1ibestkamo[ll1+1] = NULL;
+ gaplen2ibestkamo[ll1+1] = NULL;
+ gaplen1icurr[ll1+1] = NULL;
+ gaplen2icurr[ll1+1] = NULL;
+
+// reporterr( "Allocating gaplen*j\n" );
+ for(i=0; i<ll2+1; i++ )
+ {
+ gaplen1jbestkamo[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jbestkamo[i][k] = NULL;
+ gaplen1jbestkamo[i][k] = (Gaplen *)1;
+
+ gaplen2jbestkamo[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jbestkamo[i][k] = NULL;
+ gaplen2jbestkamo[i][k] = (Gaplen *)1;
+
+ gaplen1jbest[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jbest[i][k] = NULL;
+ gaplen1jbest[i][k] = (Gaplen *)1;
+
+ gaplen2jbest[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jbest[i][k] = NULL;
+ gaplen2jbest[i][k] = (Gaplen *)1;
+
+ gaplen1jcurr[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jcurr[i][k] = NULL;
+ gaplen1jcurr[i][k] = (Gaplen *)1;
+
+ gaplen2jcurr[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jcurr[i][k] = NULL;
+ gaplen2jcurr[i][k] = (Gaplen *)1;
+
+ gaplen1jprev[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jprev[i][k] = NULL;
+ gaplen1jprev[i][k] = (Gaplen *)1;
+
+ gaplen2jprev[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jprev[i][k] = NULL;
+ gaplen2jprev[i][k] = (Gaplen *)1;
+
+ }
+ gaplen1jbestkamo[ll2+1] = NULL;
+ gaplen2jbestkamo[ll2+1] = NULL;
+ gaplen1jbest[ll2+1] = NULL;
+ gaplen2jbest[ll2+1] = NULL;
+ gaplen1jcurr[ll2+1] = NULL;
+ gaplen2jcurr[ll2+1] = NULL;
+ gaplen1jprev[ll2+1] = NULL;
+ gaplen2jprev[ll2+1] = NULL;
+ }
+
+
+#if USEGAPLENMTX
+/* maikai allocate */
+
+ reporterr( "Allocating gaplenmtx1\n" );
+ gaplen1mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen1mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen1mtx[i][j] = (Gaplen **)calloc( lgth1+2, sizeof( Gaplen * ) );
+ for( k=0; k<lgth1+1; k++ ) gaplen1mtx[i][j][k] = NULL;
+ gaplen1mtx[i][j][k] = (Gaplen *)1;
+ }
+ gaplen1mtx[i][j] = NULL;
+ }
+ gaplen1mtx[i] = NULL;
+
+ reporterr( "Allocating gaplenmtx2\n" );
+ gaplen2mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen2mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen2mtx[i][j] = (Gaplen **)calloc( lgth2+2, sizeof( Gaplen * ) );
+ for( k=0; k<lgth2+1; k++ ) gaplen2mtx[i][j][k] = NULL;
+ gaplen2mtx[i][j][k] = (Gaplen *)1;
+ }
+ gaplen2mtx[i][j] = NULL;
+ }
+ gaplen2mtx[i] = NULL;
+
+#endif
+
+#if USEGAPLENHALF
+ reporterr( "Allocating gaplenhalf1\n" );
+ gaplen1half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen1half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen1half[i][j] = (Gaplen **)calloc( lgth1+2 - i, sizeof( Gaplen * ) );
+ for( k=0; k<lgth1+1-i; k++ ) gaplen1half[i][j][k] = NULL;
+ gaplen1half[i][j][k] = (Gaplen *)1;
+ }
+ gaplen1half[i][j] = NULL;
+ }
+ gaplen1half[i] = NULL;
+
+ reporterr( "Allocating gaplenhalf2\n" );
+ gaplen2half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen2half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen2half[i][j] = (Gaplen **)calloc( lgth2+2 - j, sizeof( Gaplen * ) );
+ for( k=0; k<lgth2+1-j; k++ ) gaplen2half[i][j][k] = NULL;
+ gaplen2half[i][j][k] = (Gaplen *)1;
+ }
+ gaplen2half[i][j] = NULL;
+ }
+ gaplen2half[i] = NULL;
+#endif
+
+
+/* maikai allocate */
+
+
+ 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
+ {
+ double 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 );
+
+
+// reporterr( "Counting gaplen\n" );
+ gaplencount( icyc, lgth1, gaplen1, seq1, eff1 );
+ gaplencount( jcyc, lgth2, gaplen2, seq2, eff2 );
+#if DEBUG
+ reporterr( "group1 = \n" );
+ showgaplen( gaplen1, lgth1 );
+ reporterr( "group2 = \n" );
+ showgaplen( gaplen2, lgth2 );
+#endif
+// reporterr( "done.\n" );
+
+
+ for( i=0; i<lgth1+1; i++ ) for( j=0; j<lgth2+1; j++ )
+ {
+#if USEGAPLENMTX
+// duplicategaplen( gaplen1mtx[i][j], gaplen1, lgth1 );
+// duplicategaplen( gaplen2mtx[i][j], gaplen2, lgth2 );
+
+// duplicategaplenpartly( gaplen2mtx[i][j], gaplen2, j-0, lgth2 ); // anzen
+// duplicategaplenpartly( gaplen1mtx[i][j], gaplen1, i-0, lgth1 ); // anzen
+ duplicategaplenpartly( gaplen1mtx[i][j], gaplen1, i-0, i ); // iranaikamo
+ duplicategaplenpartly( gaplen2mtx[i][j], gaplen2, j-0, j ); // iranaikamo
+#endif
+#if USEGAPLENHALF
+
+// duplicategaplenpartly( gaplen1half[i][j], gaplen1+i, 0, lgth1-i ); // KOKO de setsuyaku dekiru to omou.
+// duplicategaplenpartly( gaplen2half[i][j], gaplen2+j, 0, lgth2-j ); // originally, j-1, lgth2
+ duplicategaplenpartly( gaplen1half[i][j], gaplen1+i, 0, 0 ); // test
+ duplicategaplenpartly( gaplen2half[i][j], gaplen2+j, 0, 0 ); // test
+#endif
+ }
+
+
+#if USEGAPLENMTX
+ reporterr( "Duplicating gaplen*mtx\n" );
+ for( i=0; i<lgth1+1; i++ )
+ {
+// addnewgaplen( gaplen1mtx[i][0], gaplen1, gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2mtx[i][0], gaplen2, gaplen2, lgth2, 0, i );
+// duplicategaplenpartly( gaplen1mtx[i][0], gaplen1, 0, lgth1 );
+// duplicategaplenpartly( gaplen2mtx[i][0], gaplen2, 0, lgth2 );
+ copygaplenrestricted( gaplen2mtx[i][0], gaplen2, lgth2, 0, i, 0, 0 );
+ }
+#endif
+#if USEGAPLENHALF
+ reporterr( "Duplicating gaplen*mtx\n" );
+ for( i=0; i<lgth1+1; i++ )
+ {
+ copygaplenrestricted( gaplen2half[i][0], gaplen2, lgth2, 0, i, 0, 0 );
+ }
+#endif
+
+
+
+ for( i=0; i<1; i++ )
+ {
+// duplicategaplencompactx( gaplen1icurr[i], gaplen1, lgth1, i-0, lgth1 ); //originally, 0, lgth1
+//
+// duplicategaplencompactx( gaplen1icurr[i], gaplen1+i, lgth1-i, 0, lgth1-i ); // half
+ duplicategaplencompactx( gaplen1icurr[i], gaplen1+i, lgth1-i, 0, 1 ); // 0, 1 hitsuyou
+
+
+// duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, lgth2 ); // ichiou zenbu
+ duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, 0 );
+
+
+ copygaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, i, 0, 0 ); // -> zurasu -> error?
+
+
+// duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1, lgth1, 0, 1 );
+// duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1+i, lgth1-i, 0, 1 ); // half
+ duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1+i, lgth1-i, 0, 0 ); // half
+// duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, lgth2 );
+ duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, 0 );
+// copygaplenrestricted( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, 0 ); // -> zurasu -> error?
+// copygaplenrestricted_zurasu( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, lgth2, 0, lgth2 ); // -> zurasu -> error?
+ copygaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, 0 ); // -> zurasu -> error?
+ }
+
+// reporterr( "Duplicating gaplen*j*curr \n" );
+// int nduplicated = 0;
+ for( j=0; j<lgth2+1; j++ )
+// for( j=0; j<1; j++ )
+ {
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[0][j], gaplen1, gaplen1, lgth1, 0, j );
+// addnewgaplen( gaplen2mtx[0][j], gaplen2, gaplen2, lgth2, -1, 0 );
+// duplicategaplenpartly( gaplen1mtx[0][j], gaplen1, 0, lgth1 );
+// duplicategaplenpartly( gaplen2mtx[0][j], gaplen2, 0, lgth2 );
+ copygaplenrestricted( gaplen1mtx[0][j], gaplen1, lgth1, 0, j, 0, 0 );
+#endif
+
+#if USEGAPLENHALF
+ copygaplenrestricted( gaplen1half[0][j], gaplen1, lgth1, 0, j, 0, 0 );
+#endif
+// reporterr( "1jcurr?\n" );
+// duplicategaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, lgth1 ); // test
+ duplicategaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, 0 ); // dame?
+// reporterr( "done\n" );
+// duplicategaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, 0 ); //test
+
+// duplicategaplencompactx( gaplen2jcurr[j], gaplen2, lgth2, j-0, lgth2 ); // full
+// duplicategaplencompactx( gaplen2jcurr[j], gaplen2+j, lgth2-j, 0, lgth2-j ); //half! KOKO????
+//reporterr( "starting suspicious duplication\n" );
+ duplicategaplencompactx( gaplen2jcurr[j], gaplen2+j, lgth2-j, 0, 0 ); //half!
+//reporterr( "starting suspicious copy\n" );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, j, 0, 0 ); // TEST
+//reporterr( "finished\n" );
+
+// reporterr( "Checking gaplen1jcurr[%d]\n", j );
+// checkgaplen( gaplen1jcurr[j], 100 );
+// reporterr( "Checking gaplen2jcurr[%d]\n", j );
+// checkgaplen( gaplen2jcurr[j], 100 );
+ }
+
+// reporterr( "nduplicated (corrected) = %d\n", nduplicated );
+
+// reporterr( "Duplicating gaplen*j*prev \n\n" );
+ for( j=0; j<lgth2+1; j++ ) // allocate nominotame, atode uwagaki
+ {
+// duplicategaplencompactx( gaplen1jprev[j], gaplen1, lgth1, 0, lgth1 );
+ duplicategaplencompactx( gaplen1jprev[j], gaplen1, lgth1, 0, 0 ); // TEST
+// duplicategaplencompactx( gaplen2jprev[j], gaplen2, lgth2, j-0, lgth2 ); // originally, 0,lgth2
+// duplicategaplencompactx( gaplen2jprev[j], gaplen2+j, lgth2-j, 0, lgth2-j ); // half
+ duplicategaplencompactx( gaplen2jprev[j], gaplen2+j, lgth2-j, 0, 0 ); // half
+
+
+ copygaplencompactx( gaplen1jprev[j], gaplen1, lgth1, 0, j, 0, 0 ); // wasuretetakamo
+
+
+ }
+
+
+// reporterr( "Duplicating gaplen*j*best \n\n" );
+
+ for( j=0; j<lgth2+1; j++ )
+// for( j=0; j<1; j++ )
+ {
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, lgth1 ); // KOKO
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 0 ); // test
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 1 );
+ duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 0 );
+
+
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 1 );
+// duplicategaplencompactx( gaplen2jbestkamo[j], gaplen2, lgth2, j-0, j+1 ); // originally, 0, j+1
+ duplicategaplencompactx( gaplen2jbestkamo[j], gaplen2+j, lgth2-j, 0, 1 ); // half!
+ copygaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, j, 0, 0 ); // TEST
+
+// duplicategaplencompactx( gaplen1jbest[j], gaplen1, lgth1, 0, lgth1 ); // KOKO
+ duplicategaplencompactx( gaplen1jbest[j], gaplen1, lgth1, 0, 0 ); // test
+// duplicategaplencompactx( gaplen2jbest[j], gaplen2, lgth2,j-0, j+1 ); // originally, 0,j+1
+ duplicategaplencompactx( gaplen2jbest[j], gaplen2+j, lgth2-j, 0, 1 ); // half!
+ copygaplencompactx( gaplen1jbest[j], gaplen1, lgth1, 0, j, 0, 0 ); // TEST
+
+
+ }
+
+// reporterr( "Duplication end\n" );
+
+
+#if 0
+ reporterr( "Checking gaplen1icurr\n" );
+ checkgaplen( gaplen1icurr[0], 100 );
+ reporterr( "Checking gaplen2icurr\n" );
+ checkgaplen( gaplen2icurr[0], 100 );
+#endif
+
+
+
+
+// showgaplen( gaplen1jcurr[50], lgth2 );
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( n_dynamicmtx, initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
+
+ match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead( currentw, 0, lgth2 ); // 060306
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ for( j=1; j<lgth2+1; j++ )
+ {
+ pfac = calcpfac_gap_noidatend( gaplen1, gaplen2, j, 0, j, seq1[0], seq2[0], 0 );
+// reporterr( "computing initial end gap penalty for %c-%c, i=0, j=%d, pfac=%f\n", seq1[0][0], seq2[0][j], j, pfac );
+// reporterr( "%c-%c, i=0, j=%d, currentw[j]=%f -> ", seq1[0][0], seq2[0][j], j, currentw[j] );
+ currentw[j] += fpenalty * pfac; // tekitou
+// reporterr( " %f\n", currentw[j] );
+ }
+ for( i=1; i<lgth1+1; i++ )
+ {
+ pfac = calcpfac_gap_noidatend( gaplen2, gaplen1, i, 0, i, seq2[0], seq1[0], 0 );
+// reporterr( "computing initial end gap penalty for %c-%c, i=%d, j=0, pfac=%f\n", seq1[0][i], seq2[0][0], i, pfac );
+ initverticalw[i] += fpenalty * pfac; // tekitou
+ }
+
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+
+
+#if ALGZGAP
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
+#else
+ pfac = calcpfac_gapex_noidatend( gaplen2, gaplen1, j, 1, j, seq2[0], seq1[0], 1 );
+#if DEBUG
+ reporterr( "%c-%c, INITIAL jgap extension check, pfac = %f\n\n", seq1[0][j], '=', pfac );
+#endif
+ m[j] = currentw[j-1] + fpenalty * pfac;
+ mp[j] = 0;
+#endif
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
+
+
+ for( i=1; i<lasti; i++ )
+ {
+// reporterr( "i = %d\n", i );
+
+// reporterr( "err1? i=%d/%d\n", i, lgth1 );
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+ cleargaplens( gaplens );
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+#if 1
+ gaplentmp = gaplen1jprev;
+ gaplen1jprev = gaplen1jcurr;
+ gaplen1jcurr = gaplentmp;
+
+ gaplentmp = gaplen2jprev;
+ gaplen2jprev = gaplen2jcurr;
+ gaplen2jcurr = gaplentmp;
+
+#if DEBUG
+ reporterr( "Entering a small j loop, i=%d\n", i );
+ for( j=1; j<lgth2+1; j++ )
+ {
+ reporterr( "before j loop, i=%d, gaplen2jcurr[%d] = \n", i, j );
+ showgaplen( gaplen2jcurr[j], 100 );
+ reporterr( "\n" );
+ reporterr( "before j loop, i=%d, gaplen2prev[%d] = \n", i, j );
+ showgaplen( gaplen2jprev[j], 100 );
+ reporterr( "\n" );
+ }
+#endif
+#else
+
+ reporterr( "Entering a small j loop, i=%\n", i );
+ for( j=1; j<lgth2+1; j++ )
+ {
+// addnewgaplen( gaplen1jprev[j], gaplen1jcurr[j], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jprev[j], gaplen2jcurr[j], gaplen2, lgth2, -1, 0 );
+ reporterr( "err1? j=%d/%d\n", j, lgth2 );
+ copygaplencompactx( gaplen1jprev[j-1], gaplen1jcurr[j-1], lgth1, -1, 0, i-1, i-1 ); // TEST
+ reporterr( "err1? j=%d/%d\n", j, lgth2 );
+ copygaplencompactx( gaplen2jprev[j-1], gaplen2jcurr[j-1], lgth2, -1, 0, j-1, j-1 ); // TETS
+#if DEBUG
+ reporterr( "before j loop, i=%d, gaplen2jcurr[%d] = \n", i, j );
+ showgaplen( gaplen2jcurr[j], 100 );
+ reporterr( "\n" );
+ reporterr( "before j loop, i=%d, gaplen2prev[%d] = \n", i, j );
+ showgaplen( gaplen2jprev[j], 100 );
+ reporterr( "\n" );
+#endif
+ }
+#endif
+
+// reporterr( "err2? i=%d/%d\n", i, lgth1 );
+
+// duplicategaplencompactx( gaplen1icurr[i], gaplen1, lgth1, i, i+1 ); //originally 0, i+1
+// reporterr( "gaplen+0=\n");
+// showgaplen( gaplen1, 10 );
+// reporterr( "i=%d, lgth1=%d, lgth1-i=%d, gaplen+i-1=\n", i, lgth1, lgth1-i );
+// showgaplen( gaplen1+i-1, 100 );
+ duplicategaplencompactx( gaplen1icurr[i], gaplen1+i, lgth1-i, 0, 1 ); // half!!
+// duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, lgth2 ); // KOKO
+ duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, 0 ); // test
+ copygaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, i, 0, 0 ); // IRU? TEST
+
+
+
+// duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1, lgth1, i, i+1 ); //originally 0, i+1
+ duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1+i, lgth1-i, 0, 1 ); //half
+// duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, lgth2 ); // ORIGINALLY, 0, lgth2
+ duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, 0 ); // ORIGINALLY, 0, lgth2
+// copygaplenrestricted( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, lgth2, 0, 0 ); // IRU? // TEST
+ copygaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, 0 ); // IRU? // TEST
+
+ extendgaplencompactx( gaplen1jprev[0], gaplen1, i ); // ???
+
+
+// addnewgaplen( gaplen1jprev[0], gaplen1icurr[i-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jprev[0], gaplen2icurr[i-1], gaplen2, lgth2, -1, 0 );
+// copygaplenrestricted( gaplen1jprev[0], gaplen1icurr[i-1], lgth1, -1, 0, i, i ); // i-1, i da to omou.
+ copygaplencompactx( gaplen1jprev[0], gaplen1icurr[i-1], lgth1-i, -1, 0, i, 1 ); // half? lgth1-i?
+// copygaplenrestricted( gaplen2jprev[0], gaplen2icurr[i-1], lgth2, -1, 0, 0, 0 );
+ copygaplencompactx( gaplen2jprev[0], gaplen2icurr[i-1], lgth2-j, -1, 0, 0, 0 ); // half?? lgth2-j?
+
+
+ match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
+#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_vead( currentw, i, lgth2 );
+#else
+ imp_match_out_vead( 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];
+
+#if 0
+ fprintf( stderr, "%c ", seq1[0][i] );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// mi = previousw[0] + ogcp2[1]; mpi = 0;
+
+
+
+
+
+#if ALGZGAP
+ mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
+#else
+ pfac = calcpfac_gapex_noidatend( gaplen1, gaplen2, i, 1, i, seq1[0], seq2[0], 1 );
+#if DEBUG
+ reporterr( "%c-%c, INITIAL igap extension check, pfac = %f\n\n", '=', seq2[0][j], pfac );
+#endif
+ mi = previousw[0] + fpenalty * pfac;
+ mpi=0;
+#endif
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ if( trywarp )
+ {
+ prevwmrecordspt = prevwmrecords;
+ wmrecordspt = wmrecords+1;
+ wmrecords1pt = wmrecords;
+ warpipt = warpi + 1;
+ warpjpt = warpj + 1;
+ }
+
+
+
+
+// reporterr( "\n\ni=%d, %c\n", i, seq1[0][i] );
+ for( j=1; j<lastj; j++ )
+ {
+
+#if DEBUG
+ reporterr( "***** %c%d-%c%d ******* \n", seq1[0][i], i, seq2[0][j], j );
+ reporterr( "mpi=%d (%c), *mpjpt=%d (%c)\n", mpi, seq2[0][mpi], *mpjpt, seq1[0][*mpjpt] );
+#endif
+
+
+// Hitsuyou na bun dake tsuika
+#if USEGAPLENMTX
+ extendgaplenpartly( gaplen1mtx[i-1][mpi], gaplen1, i, i );
+ extendgaplenpartly( gaplen2mtx[i-1][mpi], gaplen2, j, j );
+ extendgaplenpartly( gaplen1mtx[*mpjpt][j-1], gaplen1, i, i );
+ extendgaplenpartly( gaplen2mtx[*mpjpt][j-1], gaplen2, j, j );
+ extendgaplenpartly( gaplen1mtx[i-1][j-1], gaplen1, i, i );
+ extendgaplenpartly( gaplen2mtx[i-1][j-1], gaplen2, j, j );
+#endif
+#if USEGAPLENHALF
+ extendgaplenpartly( gaplen1half[i-1][mpi], gaplen1+i-1, 1, 1 );
+ extendgaplenpartly( gaplen2half[i-1][mpi], gaplen2+mpi, j-mpi, j-mpi );
+ extendgaplenpartly( gaplen1half[*mpjpt][j-1], gaplen1+*mpjpt, i-*mpjpt, i-*mpjpt );
+ extendgaplenpartly( gaplen2half[*mpjpt][j-1], gaplen2+j-1, 1, 1 );
+ extendgaplenpartly( gaplen1half[i-1][j-1], gaplen1+i-1, 1, 1 );
+ extendgaplenpartly( gaplen2half[i-1][j-1], gaplen2+j-1, 1, 1 );
+
+#endif
+
+// reporterr( "extending gaplen1icurr\n" );
+ extendgaplencompactx( gaplen1icurr[i-1], gaplen1+i-1, 1 ); // iruhazu
+// reporterr( "extending gaplen2icurr\n" );
+ extendgaplencompactx( gaplen2icurr[i-1], gaplen2, j ); // iruhazu
+// reporterr( "extending gaplen1jprev[j-1], j-1=%d\n", j-1 );
+ extendgaplencompactx( gaplen1jprev[j-1], gaplen1, i );
+// reporterr( "extending gaplen1jcurr, j-1=%d\n", j-1 );
+ extendgaplencompactx( gaplen1jcurr[j-1], gaplen1, i );
+// reporterr( "extending gaplen2jprev\n" );
+ extendgaplencompactx( gaplen2jprev[j-1], gaplen2+j-1, 1 );
+// reporterr( "extending gaplen2jcurr\n" );
+ extendgaplencompactx( gaplen2jcurr[j-1], gaplen2+j-1, 1 );
+// reporterr( "extending gaplen1jbest[j-1]\n" );
+ extendgaplencompactx( gaplen1jbest[j-1], gaplen1, i );
+// reporterr( "extending gaplen1jbestkamo[j-1]\n" );
+ extendgaplencompactx( gaplen1jbestkamo[j-1], gaplen1, i );
+// reporterr( "extending gaplen1jprev[mpi], j-1=%d\n", j-1 );
+ extendgaplencompactx( gaplen1jprev[mpi], gaplen1, i ); // full
+// reporterr( "extending gaplen2jprev[mpi]\n" );
+ extendgaplencompactx( gaplen2jprev[mpi], gaplen2+mpi, j-mpi ); // half
+// reporterr( "extending gaplen1ibestkamo[i-1]\n" );
+ extendgaplencompactx( gaplen1ibestkamo[i-1], gaplen1+i-1, 1 );
+// reporterr( "extending gaplen2ibestkamo[i-1]\n" );
+ extendgaplencompactx( gaplen2ibestkamo[i-1], gaplen2, j );
+
+
+#if DEBUG
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jcurr[j]=\n", i, j );
+ showgaplen( gaplen2jcurr[j], 100 );
+
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jcurr[j-1]=\n", i, j );
+ showgaplen( gaplen2jcurr[j-1], 100 );
+
+
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jprev[j]=\n", i, j );
+ showgaplen( gaplen2jprev[j], 100 );
+
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jprev[j-1]=\n", i, j );
+ showgaplen( gaplen2jprev[j-1], 100 );
+#endif
+
+
+#ifdef xxxenablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+ cleargaplens( gaplens );
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+#if USEGAPLENHALF
+// i==248, j==80 wo check
+#if DEBUG80
+ if( j==80 )
+ {
+ reporterr( "When i==%d, j==%d,\n", i, j );
+ reporterr( "gaplen2jprev[j-1=%d]=\n", j-1 );
+ showgaplen( gaplen2jprev[j-1], lgth1 );
+ reporterr( "gaplen2half[i-1=%d][j-1=%d]=\n", i-1, j-1 );
+ showgaplen( gaplen2half[i-1][j-1], lgth1 );
+ }
+ if( j==79 )
+ {
+ reporterr( "When i==%d, j==%d,\n", i, j );
+ reporterr( "gaplen2jprev[j-1=%d]=\n", j-1 );
+ showgaplen( gaplen2jprev[j-1], lgth1 );
+ reporterr( "gaplen2half[i-1=%d][j-1=%d]=\n", i-1, j-1 );
+ showgaplen( gaplen2half[i-1][j-1], lgth1 );
+ }
+#endif
+#endif
+
+
+// pfac = calcpfac( gaplen1jprev[j-1], gaplen2jprev[j-1], i, j, seq1[0], seq2[0] );
+//reporterr( "#### COMPACT, i,j=%d,%d\n", i, j );
+ pfac = calcpfacnoidatend( gaplen1jprev[j-1], gaplen2jprev[j-1], i, 1, seq1[0], seq2[0]+j, one ); // 1j->full, 2j->half
+#if USEGAPLENMTX
+//reporterr( "#### FULL, i,j=%d,%d\n", i, j );
+ pfactmp = calcpfac( gaplen1mtx[i-1][j-1], gaplen2mtx[i-1][j-1], i, j, seq1[0], seq2[0], one );
+#endif
+#if USEGAPLENHALF
+//reporterr( "#### HALF, i,j=%d/%d,%d/%d\n", i, lgth1, j, lgth2 );
+// showgaplen( gaplen2half[i-1][j-1], lgth2-j );
+ pfactmp = calcpfac( gaplen1half[i-1][j-1], gaplen2half[i-1][j-1], 1, 1, seq1[0]+i, seq2[0]+j, zero );
+#endif
+#if USEGAPLENMTX + USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(straight) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+ PFACERROR = 1;
+ exit( 1 );
+ }
+#endif
+//if( i==50 && j==135 ) exit( 1 );
+
+
+// reporterr( "i,j=%d,%d, *prept = %f\n", i, j, *prept );
+
+#if ALGZSTRAIGHT
+ wm = *prept; // Machigai!!
+#else
+ wm = *prept + fpenalty * pfac;
+#endif
+ *ijppt = 0;
+
+
+#if DEBUG
+ if( i == j )
+ {
+ fprintf( stderr, "\n i=%d, j=%d %c, %c ", i, j, seq1[0][i], seq2[0][j] );
+ fprintf( stderr, "%5.0f, pfac for straight =%f\n", wm, pfac );
+ }
+#endif
+ newgaplen = j-mpi-1;
+
+
+//if( i == 53 && j == 93 ) exit( 1 );
+
+
+
+
+// pfac = calcpfac_gap_incomplete( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], newgaplen, i, j, seq1[0], seq2[0], 0 ); // i-1
+ pfac = calcpfac_gap_noidatend( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], newgaplen, 1, j, seq1[0]+i-1, seq2[0], 0 ); // i-1
+#if USEGAPLENMTX
+ pfactmp = calcpfac_gap_incomplete( gaplen1mtx[i-1][mpi], gaplen2mtx[i-1][mpi], newgaplen, i, j, seq1[0], seq2[0], 1 );
+#endif
+#if USEGAPLENHALF
+ pfactmp = calcpfac_gap_incomplete( gaplen1half[i-1][mpi], gaplen2half[i-1][mpi], newgaplen, 1, j-mpi, seq1[0]+i-1, seq2[0]+mpi, 1 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(igap) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+ PFACERROR = 1;
+ }
+#endif
+
+
+#if DEBUG
+ reporterr( "%c-%c pfac for igap end incomplete = %f\n", seq1[0][i], seq2[0][j], pfac );
+ reporterr( "mi when igap end checking = %f\n", mi );
+ reporterr( "wm = %f, mi+fpenalty*pfac=%f\n", wm, mi+fpenalty*pfac );
+#endif
+
+
+#if ALGZGAP
+ if( (g=mi+*fgcp2pt*gf1va) > wm )
+#else
+ if( (g=mi+fpenalty*pfac) > wm )
+#endif
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+#if DEBUG80
+ reporterr( "Selected as igap end! wm = %f, mi = %f\n", wm, mi );
+ fprintf( stderr, "Jump from %d-%d (%c-%c) to %d (%c-%c)!\n", i, j, seq1[0][i], seq2[0][j], mpi, seq1[0][i-1], seq2[0][mpi] );
+#endif
+ }
+
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+// if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
+
+#if 0
+// reporterr( "Checking %c, (current pos = %c)\n", seq2[0][j+1], seq2[0][j] );
+ sfac = 1.0;
+ for( k=0; gaplen2[j+1]&&(gl=gaplen2[j+1][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+// reporterr( ".len = %d, .relend = %d\n", gaplen2[j+1][k].len, gaplen2[j+1][k].relend );
+ if( gl - 1 == gaplen2[j+1][k].relend )
+ {
+ sfac -= gaplen2[j+1][k].freq;
+// reporterr( "Hit! sfac = %f\n", sfac );
+ }
+ }
+ sfac2 = 1.0;
+ for( k=0; gaplen1[i+1]&&(gl=gaplen1[i+1][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ if( gaplen1[i+1][k].relend != -1 ) sfac2 -= gaplen1[i+1][k].freq;
+ sfac *= sfac2;
+#else
+// sfac = 0.0;
+#endif
+
+
+
+#if ALGZGAP
+ if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
+#else
+// if( (g=*prept + fpenalty * sfac ) >= mi )
+ if( (g=*prept ) >= mi )
+#endif
+ {
+// mpibk = mpi;
+// mi = g - fpenalty * sfac;
+ mi = g;
+ mpi = j-1;
+#if DEBUG80
+ reporterr( "Selected as igap start! %c%d-%c%d, mi=%f, g=%f\n", seq1[0][i-1], i-1, seq2[0][mpi], mpi, mi, g );
+#endif
+
+#if FREEFREQUENTLY
+// freegaplenpartly( gaplen1ibestkamo[i-1], 0, i-1 );
+ freegaplenpartly( gaplen2ibestkamo[i-1], j-3, j-2 );
+#endif
+// freegaplenpartly( gaplen1jprev[mpibk], 0, lgth2 ); // full
+// freegaplenpartly( gaplen2jprev[mpibk], 0, lgth2-mpibk ); // half
+// if( gaplen1jprev[mpibk] ) FreeGaplenMtx( gaplen1jprev[mpibk], 0 );
+// gaplen1jprev[mpibk] = NULL;
+// if( gaplen2jprev[mpibk] ) FreeGaplenMtx( gaplen2jprev[mpibk], 0 );
+// gaplen2jprev[mpibk] = NULL;
+
+
+// addnewgaplen( gaplen1ibestkamo[i-1], gaplen1jprev[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2ibestkamo[i-1], gaplen2jprev[j-1], gaplen2, lgth2, -1, 0 );
+// copygaplenrestricted( gaplen1ibestkamo[i-1], gaplen1jprev[j-1], lgth1, -1, 0, i, i ); // i-1, i
+ copygaplencompactx( gaplen1ibestkamo[i-1], gaplen1jprev[j-1], lgth1, -1, 0, 1, i ); // half
+// copygaplenrestricted( gaplen2ibestkamo[i-1], gaplen2jprev[j-1], lgth2, -1, 0, j, j ); // mpi, j
+ copygaplencompactx( gaplen2ibestkamo[i-1], gaplen2jprev[j-1], lgth2, -1, 0, j, 1 ); //half
+
+
+ }
+
+
+
+
+
+
+// reporterr( "g=%f, *prept=%f, mi=%f\n", g, *prept, mi );
+
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if ALGZGAP
+ pfac = 0.0; // CHUUI!
+#else
+
+// pfac = calcpfac_gapex( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], i, j, j-mpi, seq1[0], seq2[0], 1 ); // i-1
+ pfac = calcpfac_gapex_noidatend( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], 1, j, j-mpi, seq1[0]+i, seq2[0], 1 ); // 1ibest->half, 2ibest->full
+#if USEGAPLENMTX
+ pfactmp = calcpfac_gapex( gaplen1mtx[i-1][mpi], gaplen2mtx[i-1][mpi], i, j, j-mpi, seq1[0], seq2[0], 1 );
+#endif
+#if USEGAPLENHALF
+ pfactmp = calcpfac_gapex( gaplen1half[i-1][mpi], gaplen2half[i-1][mpi], 1, j-mpi, j-mpi, seq1[0]+i, seq2[0]+mpi, 1 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(igapex) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+ PFACERROR = 1;
+ }
+#endif
+
+
+
+
+
+
+
+#if DEBUG
+ reporterr( "%c-%c, igap extension check, pfac = %f\n\n", '=', seq2[0][j], pfac );
+#endif
+#endif
+// reporterr( "mi = %f -> ", mi );
+ mi += fpenalty * pfac;
+// reporterr( "mi = %f\n", mi );
+
+
+// reporterr( "using %d-%d, %d, %d\n", *mpjpt, j-1, i, j );
+ newgaplen = i-*mpjpt-1;
+// pfac = calcpfac_gap_incomplete( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], newgaplen, j, i, seq2[0], seq1[0], 0 ); // j-1 deha???
+
+
+ pfac = calcpfac_gap_noidatend( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], newgaplen, 1, i, seq2[0]+j-1, seq1[0], 1 ); // 2jbestkamo->half, 1jbestkamo->full
+#if USEGAPLENMTX
+ pfactmp = calcpfac_gap_incomplete( gaplen2mtx[*mpjpt][j-1], gaplen1mtx[*mpjpt][j-1], newgaplen, j, i, seq2[0], seq1[0], 1 );
+#endif
+#if USEGAPLENHALF
+ pfactmp = calcpfac_gap_incomplete( gaplen2half[*mpjpt][j-1], gaplen1half[*mpjpt][j-1], newgaplen, 1, i-*mpjpt, seq2[0]+j-1, seq1[0]+*mpjpt, 1 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(jgap) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+// exit( 1 );
+ PFACERROR = 1;
+ }
+#endif
+
+#if ALGZGAP
+ if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
+#else
+ if( (g=*mjpt + fpenalty*pfac) > wm )
+#endif
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+
+
+#if FREEFREQUENTLY
+ freegaplenpartly( gaplen1jbest[j-1], i-3, i-2 );
+// freegaplenpartly( gaplen2jbest[j-1], j-3, j-2 );
+#endif
+
+
+#if DEBUG
+ reporterr( "Selected as jgap end!, pfac = %f\n", pfac );
+ fprintf( stderr, "Jump from %d (%c) to %d (%c)!\n", j, seq1[0][j], *mpjpt, seq1[0][*mpjpt] );
+#endif
+// addnewgaplen( gaplen1jbest[j-1], gaplen1jbestkamo[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jbest[j-1], gaplen2jbestkamo[j-1], gaplen2, lgth2, -1, 0 );
+ copygaplencompactx( gaplen1jbest[j-1], gaplen1jbestkamo[j-1], lgth1, -1, 0, i, i );// *mpjpt, i
+// copygaplenrestricted( gaplen2jbest[j-1], gaplen2jbestkamo[j-1], lgth2, -1, 0, j, j ); // j-1, j
+ copygaplencompactx( gaplen2jbest[j-1], gaplen2jbestkamo[j-1], lgth2, -1, 0, 1, 1 ); // half!
+
+
+
+
+ }
+
+
+// extendgaplenpartly( gaplen1jbest[j-1], gaplen1, i, i ); // tmptmptmp
+// extendgaplenpartly( gaplen2jbest[j-1], gaplen2, 0, 0 ); // tmptmptmp
+
+#if 0
+ sfac = 1.0;
+ for( l=0; gaplen1[i+1]&&(gl=gaplen1[i+1][l].len)!=-1; l++ ) // ososugi! hash ni atode henkou
+ if( gl - 1 == gaplen1[i+1][l].relend ) sfac -= gaplen1[i+1][l].freq;
+ sfac2 = 1.0;
+ for( k=0; gaplen2[j+1]&&(gl=gaplen2[j+1][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ if( gaplen2[j+1][k].relend != -1 ) sfac2 -= gaplen2[j+1][k].freq;
+ sfac *= sfac2;
+#else
+// sfac = 0.0;
+#endif
+
+#if DEBUG
+ reporterr( " (jgap start check i=%d) -> *prept=%f, *mjpt=%f\n", i, seq1[0][i], seq2[0][j], *prept, *mjpt );
+#endif
+
+#if ALGZGAP
+ if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
+#else
+// if( (g=*prept + fpenalty * sfac ) >= *mjpt )
+ if( (g=*prept ) >= *mjpt )
+#endif
+ {
+// *mjpt = g - fpenalty * sfac;
+ *mjpt = g;
+ *mpjpt = i-1;
+#if DEBUG
+ reporterr( "Selected as jgap start!\n" );
+#endif
+
+
+#if FREEFREQUENTLY
+ freegaplenpartly( gaplen1jbestkamo[j-1], i-3, i-2 );
+// freegaplenpartly( gaplen2jbestkamo[j-1], j-3, j-2 );
+#endif
+
+
+// addnewgaplen( gaplen1jbestkamo[j-1], gaplen1jprev[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], gaplen2, lgth2, -1, 0 );
+// reporterr( "copying gaplen1jbestkamo[%d-1] from galpen1jprev, j=%d, i=%d\n", j, j, i );
+ copygaplencompactx( gaplen1jbestkamo[j-1], gaplen1jprev[j-1], lgth1, -1, 0, i, i ); // *mpjpt, i
+// copygaplenrestricted( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], lgth2, -1, 0, j, j ); // j-1, j
+// copygaplencompactx( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], lgth2, -1, 0, j, 1 ); // half!
+// reporterr( "copying gaplen2jbestkamo[%d-1] from galpen2jprev\n", j );
+ copygaplencompactx( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], lgth2-j, -1, 0, 1, 1 ); // ryouhou half!
+
+
+// if( j==2 && i==1 ) exit( 1 );
+
+
+
+ }
+
+// extendgaplenpartly( gaplen1ibestkamo[i-1], gaplen1, 0, 0 ); // tmptmptmp
+// extendgaplenpartly( gaplen2ibestkamo[i-1], gaplen2, j, j ); // tmptmptmp
+
+
+// extendgaplenpartly( gaplen1jbestkamo[j-1], gaplen1, i, i ); // tmptmptmp
+// extendgaplenpartly( gaplen2jbestkamo[j-1], gaplen2, 0, 0 ); // tmptmptmp
+
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if ALGZGAP
+ pfac = 0.0;
+#else
+
+// pfactmp = calcpfac_gapex( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], j, i, i-*mpjpt, seq2[0], seq1[0], 0 ); // j-1
+ pfactmp = calcpfac_gapex_noidatend( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], 1, i, i-*mpjpt, seq2[0]+j, seq1[0], 0 ); // 2jbestkamo->half, 1jbestkamo->full
+#if USEGAPLENMTX
+ pfac = calcpfac_gapex( gaplen2mtx[*mpjpt][j-1], gaplen1mtx[*mpjpt][j-1], j, i, i-*mpjpt, seq2[0], seq1[0], 0 );
+#endif
+#if USEGAPLENHALF
+ pfac = calcpfac_gapex( gaplen2half[*mpjpt][j-1], gaplen1half[*mpjpt][j-1], 1, i-*mpjpt, i-*mpjpt, seq2[0]+j, seq1[0]+*mpjpt, 0 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(jgapex) pfac=%f, but pfactmp=%f (i,j=%d,%d) diff=%f\n", pfac, pfactmp, i, j, pfac-pfactmp );
+// exit( 1 );
+ PFACERROR = 1;
+ }
+#endif
+ pfac = pfactmp;
+#if DEBUG
+ reporterr( "%c-%c, jgap extension check (j=%d), pfac = %f\n", seq1[0][i], '=', j, pfac );
+#endif
+#endif
+ m[j] += fpenalty * pfac;
+
+
+
+ if( trywarp )
+ {
+#if USE_PENALTY_EX
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
+#else
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
+#endif
+ {
+// fprintf( stderr, "WARP!!\n" );
+ if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
+ {
+ *ijppt = warpbase + warpn - 1;
+ }
+ else
+ {
+ *ijppt = warpbase + warpn;
+ warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
+ warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
+ warpis[warpn] = prevwarpi[j-1];
+ warpjs[warpn] = prevwarpj[j-1];
+ warpn++;
+ }
+ wm = g;
+ }
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ curm = *curpt + wm;
+
+ if( *wmrecords1pt > *wmrecordspt )
+ {
+ *wmrecordspt = *wmrecords1pt;
+ *warpipt = *(warpipt-1);
+ *warpjpt = *(warpjpt-1);
+ }
+ if( curm > *wmrecordspt )
+ {
+ *wmrecordspt = curm;
+ *warpipt = i;
+ *warpjpt = j;
+ }
+ wmrecordspt++;
+ wmrecords1pt++;
+ warpipt++;
+ warpjpt++;
+ }
+
+#if DEBUG
+ reporterr( "extention-x 1j???, before extention-x, j=%d\n", j );
+ showgaplen( gaplen1jcurr[j], 100 );
+#endif
+ extendgaplencompactx( gaplen1jcurr[j], gaplen1, i );
+
+#if DEBUG
+ reporterr( "after extention-x\n" );
+ showgaplen( gaplen1jcurr[j], 100 );
+ reporterr( "extention-x 2j???\n" );
+#endif
+ extendgaplencompactx( gaplen2jcurr[j], gaplen2+j, 0 );
+
+
+#if 1
+ if( *ijppt < 0 )
+ {
+#if DEBUG
+ reporterr( "Path: %d-%d->%d-%d, i=%d (%c), j=%d (%c), *ijppt=%d\n", i, j, i-1, j+*ijppt, i, seq1[0][i], j, seq2[0][j], *ijppt );
+ reporterr( "Inserting %d gaps to gaplen1 and copying gaplen2 (%c%d-%c%d)\n", -*ijppt-1, seq1[0][i], i, seq2[0][j], j );
+#endif
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[i][j], gaplen1mtx[i-1][j+*ijppt], gaplen1, lgth1, i, -*ijppt-1 );
+// addnewgaplen( gaplen2mtx[i][j], gaplen2mtx[i-1][j+*ijppt], gaplen2, lgth2, -1, 0 );
+ copygaplenrestricted( gaplen1mtx[i][j], gaplen1mtx[i-1][j+*ijppt], lgth1, i, -*ijppt-1, i, i ); // 0, lgth1
+ copygaplenrestricted( gaplen2mtx[i][j], gaplen2mtx[i-1][j+*ijppt], lgth2, -1, 0, j, j ); // 0, lgth2
+#endif
+#if USEGAPLENHALF
+ copygaplenrestricted_zurasu( gaplen1half[i][j], gaplen1half[i-1][j+*ijppt], lgth1, 0, -*ijppt-1, 0, 0, 1, 1 ); // 0, lgth1
+ copygaplenrestricted_zurasu( gaplen2half[i][j], gaplen2half[i-1][j+*ijppt], lgth2, -1, 0, 0, 0, -*ijppt, -*ijppt ); // 0, lgth2
+#endif
+// addnewgaplen( gaplen1jcurr[j], gaplen1jprev[j+*ijppt], gaplen1, lgth1, i, -*ijppt-1 );
+// addnewgaplen( gaplen2jcurr[j], gaplen2jprev[j+*ijppt], gaplen2, lgth2, -1, 0 );
+// reporterr( "copying gaplen1jcurr from gaplen1jbest, with a %d insertion\n", -*ijppt-1 );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1jprev[j+*ijppt], lgth1, i, -*ijppt-1, i, i ); // scope: i+*ijppt+1, i ?
+// reporterr( "copy end\n" );
+// copygaplenrestricted( gaplen2jcurr[j], gaplen2jprev[j+*ijppt], lgth2, -1, 0, j, j );
+ copygaplencompactx( gaplen2jcurr[j], gaplen2jprev[j+*ijppt], lgth2, -1, 0, 0, -*ijppt ); // half! ryouho zureteru
+ }
+ else if( *ijppt > 0 )
+ {
+#if DEBUG
+ reporterr( "Path: %d-%d->%d-%d, i=%d (%c), j=%d (%c), *ijppt=%d\n", i, j, i-*ijppt, j-1, i, seq1[0][i], j, seq2[0][j], *ijppt );
+ reporterr( "Copying gaplen1 inserting %d gaps to gaplen2 (%c%d-%c%d)\n", *ijppt-1, seq1[0][i], i, seq2[0][j], j );
+#endif
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[i][j], gaplen1mtx[i-*ijppt][j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2mtx[i][j], gaplen2mtx[i-*ijppt][j-1], gaplen2, lgth2, j, *ijppt-1 );
+ copygaplenrestricted( gaplen1mtx[i][j], gaplen1mtx[i-*ijppt][j-1], lgth1, -1, 0, i, i ); // 0, lgth1
+ copygaplenrestricted( gaplen2mtx[i][j], gaplen2mtx[i-*ijppt][j-1], lgth2, j, *ijppt-1, j, j ); // 0, lgth2
+#endif
+#if USEGAPLENHALF
+ copygaplenrestricted_zurasu( gaplen1half[i][j], gaplen1half[i-*ijppt][j-1], lgth1, -1, 0, 0, 0, *ijppt, *ijppt ); // 0, lgth1
+ copygaplenrestricted_zurasu( gaplen2half[i][j], gaplen2half[i-*ijppt][j-1], lgth2, 0, *ijppt-1, 0, 0, 1, 1 ); // 0, lgth2
+#endif
+// addnewgaplen( gaplen1jcurr[j], gaplen1jbest[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jcurr[j], gaplen2jbest[j-1], gaplen2, lgth2, j, *ijppt-1 );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1jbest[j-1], lgth1, -1, 0, i, i );
+// copygaplenrestricted( gaplen2jcurr[j], gaplen2jbest[j-1], lgth2, j, *ijppt-1, j, j ); // j-*ijppt+1?
+// copygaplenrestricted_zurasu( gaplen2jcurr[j], gaplen2jbest[j-1], lgth2, 0, *ijppt-1, 0, 0, j, j ); // 2jcurr->half, but 2jbest->full, imanotokoro
+ copygaplencompactx( gaplen2jcurr[j], gaplen2jbest[j-1], lgth2, 0, *ijppt-1, 0, 1 ); //ryouhou half
+
+ }
+ else
+#endif
+ {
+#if DEBUG
+ reporterr( "Path: %d-%d->%d-%d, i=%d (%c), j=%d (%c), *ijppt=%d\n", i, j, i-1, j-1, i, seq1[0][i], j, seq2[0][j], *ijppt );
+ reporterr( "Copying gaplen1 and gaplen2 (%c%d-%c%d)\n", seq1[0][i], i, seq2[0][j], j );
+#endif
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[i][j], gaplen1mtx[i-1][j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2mtx[i][j], gaplen2mtx[i-1][j-1], gaplen2, lgth2, -1, 0 );
+ copygaplenrestricted( gaplen1mtx[i][j], gaplen1mtx[i-1][j-1], lgth1, -1, 0, i, i ); // 0, lgth1
+ copygaplenrestricted( gaplen2mtx[i][j], gaplen2mtx[i-1][j-1], lgth2, -1, 0, j, j ); // 0, lgth2
+#endif
+#if USEGAPLENHALF
+ copygaplenrestricted_zurasu( gaplen1half[i][j], gaplen1half[i-1][j-1], lgth1, -1, 0, 0, 0, 1, 1 ); // 0, lgth1
+ copygaplenrestricted_zurasu( gaplen2half[i][j], gaplen2half[i-1][j-1], lgth2, -1, 0, 0, 0, 1, 1 ); // 0, lgth2
+#endif
+// addnewgaplen( gaplen1jcurr[j], gaplen1jprev[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jcurr[j], gaplen2jprev[j-1], gaplen2, lgth2, -1, 0 );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1jprev[j-1], lgth1, -1, 0, i, i );
+// copygaplenrestricted( gaplen2jcurr[j], gaplen2jprev[j-1], lgth2, -1, 0, j, j );
+ copygaplencompactx( gaplen2jcurr[j], gaplen2jprev[j-1], lgth2, -1, 0, 0, 1 ); // half
+ }
+
+#if DEBUG
+ reporterr( "at the end of j loop, gaplen1jcurr[%d] = \n", j );
+ showgaplen( gaplen1jcurr[j], 100 );
+ reporterr( "at the end of j loop, gaplen1prev[%d] = \n", j );
+ showgaplen( gaplen1jprev[j], 100 );
+#endif
+
+
+
+#if 1
+ freegaplenpartly( gaplen1jcurr[j-1], i-3, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // half!
+ freegaplenpartly( gaplen1jbestkamo[j-1], i-3, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbestkamo[j-1], j-3, j-2 ); // -1 dehanaku -2??
+ freegaplenpartly( gaplen1jbest[j-1], i-3, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbest[j-1], j-3, j-2 ); // -1 dehanaku -2??
+#else
+ freegaplenpartly( gaplen1jprev[j-1], 0, i-2 ); // -1 dehanaku -2??
+ freegaplenpartly( gaplen1jcurr[j-1], 0, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // half!
+ freegaplenpartly( gaplen1jbestkamo[j-1], 0, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbestkamo[j-1], j-3, j-2 ); // -1 dehanaku -2??
+ freegaplenpartly( gaplen1jbest[j-1], 0, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbest[j-1], j-3, j-2 ); // -1 dehanaku -2??
+#endif
+
+
+#if USEGAPLENMTX
+// freegaplenpartly( gaplen1mtx[i-1][j-1], 0, i-2 );
+// freegaplenpartly( gaplen2mtx[i-1][j-1], 0, j-2 );
+#endif
+
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if 1
+// freegaplenpartly( gaplen1icurr[i-1], i-1, i-1 );
+ freegaplenpartly( gaplen1icurr[i-1], 0, lgth1-i );
+ freegaplenpartly( gaplen2icurr[i-1], 0, lgth2 );
+// freegaplenpartly( gaplen1ibestkamo[i-1], i-1, i-1 );
+ freegaplenpartly( gaplen1ibestkamo[i-1], 0, lgth1-i );
+ freegaplenpartly( gaplen2ibestkamo[i-1], 0, lgth2 );
+#endif
+
+ if( trywarp )
+ {
+ fltncpy( prevwmrecords, wmrecords, lastj );
+ intncpy( prevwarpi, warpi, lastj );
+ intncpy( prevwarpj, warpj, lastj );
+ }
+#if 0
+ fprintf( stderr, "i=%d, %15.5f \n", i, wm );
+#endif
+//if( i == 2 ) exit( 1 );
+ }
+
+ if( trywarp )
+ {
+// fprintf( stderr, "wm = %f\n", wm );
+// fprintf( stderr, "warpn = %d\n", warpn );
+ free( wmrecords );
+ free( prevwmrecords );
+ free( warpi );
+ free( warpj );
+ free( prevwarpi );
+ free( prevwarpj );
+ }
+
+
+#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, ijp, icyc, jcyc, warpis, warpjs, warpbase );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase );
+
+ if( warpis ) free( warpis );
+ if( warpjs ) free( warpjs );
+
+// 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] );
+#if 0
+ 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] );
+#endif
+
+// reporterr( "clearing\n" );
+ cleargaplens( gaplens );
+
+#if USEGAPLENMTX
+/* maikai free */
+ reporterr( "Freeing!\n" );
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen1mtx[i][j] ) FreeGaplenMtx( gaplen1mtx[i][j], 0 );
+ gaplen1mtx[i][j] = NULL;
+ }
+ free( gaplen1mtx[i] );
+ gaplen1mtx[i] = NULL;
+ }
+ free( gaplen1mtx );
+ gaplen1mtx = NULL;
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen2mtx[i][j] ) FreeGaplenMtx( gaplen2mtx[i][j], 0 );
+ gaplen2mtx[i][j] = NULL;
+ }
+ free( gaplen2mtx[i] );
+ gaplen2mtx[i] = NULL;
+ }
+ free( gaplen2mtx );
+ gaplen2mtx = NULL;
+#endif
+
+
+#if USEGAPLENHALF
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen1half[i][j] ) FreeGaplenMtx( gaplen1half[i][j], 0 );
+ gaplen1half[i][j] = NULL;
+ }
+ free( gaplen1half[i] );
+ gaplen1half[i] = NULL;
+ }
+ free( gaplen1half );
+ gaplen1half = NULL;
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen2half[i][j] ) FreeGaplenMtx( gaplen2half[i][j], 0 );
+ gaplen2half[i][j] = NULL;
+ }
+ free( gaplen2half[i] );
+ gaplen2half[i] = NULL;
+ }
+ free( gaplen2half );
+ gaplen2half = NULL;
+#endif
+/* maikai free */
+
+
+#if WMCHECK
+ fprintf( stderr, "wm = %f\n", wm - *impmatch);
+ fprintf( stderr, "*impmatch = %f\n", *impmatch);
+
+ int kenzan = 0;
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ kenzan += pairgapcount( mseq1[i], mseq2[j] );
+ }
+
+
+ reporterr( "kenzan = %d -> %f\n", kenzan, (double)kenzan /( icyc*jcyc ) );
+
+ double pairscore, nogappairscore;
+ char **pseq;
+ pseq = AllocateCharMtx( 2, strlen( seq1[0] ) + 1 );
+ pairscore = nogappairscore = 0.0;
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ strcpy( pseq[0], seq1[i] );
+ strcpy( pseq[1], seq2[j] );
+ commongappick( 2, pseq );
+ pairscore += eff1[i] * eff2[j] * naivepairscore11_dynmtx( n_dynamicmtx, pseq[0], pseq[1], penalty );
+ nogappairscore += eff1[i] * eff2[j] * naivepairscore11_dynmtx( n_dynamicmtx, pseq[0], pseq[1], 0 );
+ }
+
+ FreeCharMtx( pseq );
+ reporterr( "pairscore = %f\n", (double)pairscore );
+ reporterr( "pairscore-nogappairscore = %f\n", (double)(pairscore-nogappairscore) );
+ reporterr( "pairscore-nogappairscore / penalty = %f\n", (double)(pairscore-nogappairscore)/(double)(fpenalty) );
+ reporterr( "diff = %f\n\n", (pairscore - wm + *impmatch ) / fpenalty );
+
+#if 1
+ if( ( !trywarp && abs( pairscore - wm +*impmatch ) > 0.01 ) || PFACERROR )
+// if( abs( pairscore - wm +*impmatch ) > 0.01 )
+#else
+ if( abs( pairscore - wm +*impmatch ) > 0.01 )
+#endif
+// if( abs( pairscore - wm +*impmatch ) > 0.01 )
+ {
+ for( i=0; i<icyc; i++ )
+ printf( ">group1\n%s\n", seq1[i] );
+ for( j=0; j<jcyc; j++ )
+ printf( ">group2\n%s\n", seq2[j] );
+ exit( 1 );
+ }
+#else
+ reporterr( "\n" );
+#endif
+
+#if 0
+// if( strlen( seq1[0] ) - lgth1 > 100 && icyc > 1 || strlen( seq2[0] ) - lgth2 > 100 & jcyc > 1 )
+ if( strstr( seq1[0], "LNDDAT" ) && icyc == 1 || strstr( seq2[0], "LNDDAT" ) && jcyc==1)
+ {
+ for( i=0; i<icyc; i++ )
+ printf( ">group1\n%s\n", seq1[i] );
+ for( j=0; j<jcyc; j++ )
+ printf( ">group2\n%s\n", seq2[j] );
+ exit( 1 );
+ }
+#endif
+
+
+ return( wm );
+}
+
+
+double D__align_ls( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+{
+ int v1, v2;
+ double val;
+
+#if 1
+ v1 = gapvariety( icyc, strlen( seq1[0] ), seq1 );
+ v2 = gapvariety( jcyc, strlen( seq2[0] ), seq2 );
+#else
+ v1 = icyc;
+ v2 = jcyc;
+#endif
+
+// reporterr( "\nicyc,jcyc = %d,%d\n", icyc, jcyc );
+ reporterr( " v1,v2 = %d,%d\n", v1, v2 );
+
+ if( v1 >= v2 )
+ {
+ val = D__align( n_dynamicmtx, seq1, seq2, eff1, eff2, icyc, jcyc, alloclen, localhom, impmatch, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+ }
+ else
+ {
+ val = D__align( n_dynamicmtx, seq2, seq1, eff2, eff1, jcyc, icyc, alloclen, localhom, impmatch, sgap2, sgap1, egap2, egap1, chudanpt, chudanref, chudanres, headgp, tailgp );
+ }
+ return val;
+}
+
+
+
+double D__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, int *gapmap1, int *gapmap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+ fprintf( stderr, "Unexpected error. Please contact kazutaka.katoh@aist.go.jp\n" );
+ exit( 1 );
+}
+
+
+double D__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, 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;
+ register int i, j, c;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
+// double fpenalty = (double)penalty;
+#if USE_PENALTY_EX
+ double fpenalty_ex = (double)penalty_ex;
+#endif
+#if 1
+ double *wtmp;
+ int *ijppt;
+ double *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS double mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS double *w1, *w2;
+ static TLS double *match;
+ static TLS double *initverticalw; /* kufuu sureba iranai */
+ static TLS double *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS double ***cpmx1s;
+ static TLS double ***cpmx2s;
+ static TLS int ***intwork;
+ static TLS double ***doublework;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+#if USEGAPLENHALF
+ Gaplen ****gaplen1half = NULL; // NULL ga iru to omou.
+ Gaplen ****gaplen2half = NULL; // NULL ga iru to omou.
+#endif
+#if USEGAPLENMTX
+ Gaplen ****gaplen1mtx = NULL; // NULL ga iru to omou.
+ Gaplen ****gaplen2mtx = NULL; // NULL ga iru to omou.
+#endif
+ static TLS Gaplen **gaplen1 = NULL; // NULL ga iru to omou.
+ static TLS Gaplen **gaplen2 = NULL; // NULL ga iru to omou.
+ static TLS Gaplen ***gaplen1jprev = NULL;
+ static TLS Gaplen ***gaplen2jprev = NULL;
+ static TLS Gaplen ***gaplen1jcurr = NULL;
+ static TLS Gaplen ***gaplen2jcurr = NULL;
+ static TLS Gaplen ***gaplen1icurr = NULL;
+ static TLS Gaplen ***gaplen2icurr = NULL;
+ static TLS Gaplen ***gaplen1jbestkamo = NULL;
+ static TLS Gaplen ***gaplen2jbestkamo = NULL;
+ static TLS Gaplen ***gaplen1ibestkamo = NULL;
+ static TLS Gaplen ***gaplen2ibestkamo = NULL;
+ static TLS Gaplen ***gaplen1jbest = NULL;
+ static TLS Gaplen ***gaplen2jbest = NULL;
+ double fpenalty = (double)penalty;
+ double fpenalty_shift = (double)penalty_shift;
+ static TLS Gaplen ****gaplens = NULL;
+
+ Gaplen ***gaplentmp = NULL;
+ int *warpis = NULL;
+ int *warpjs = NULL;
+ int *warpi = NULL;
+ int *warpj = NULL;
+ int *prevwarpi = NULL;
+ int *prevwarpj = NULL;
+ double *wmrecords = NULL;
+ double *prevwmrecords = NULL;
+ int warpn = 0;
+ int warpbase;
+ double curm = 0.0;
+ double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+ int *warpipt, *warpjpt;
+ int k;
+ double pfac, pfactmp;
+ int newgaplen;
+ int **masklist1 = NULL, **masklist2 = NULL;
+ int *nmask;
+
+// for( i=0; i<icyc; i++ ) fprintf( stderr, "%s, %f\n", seq1[i], eff1[i] );
+// for( i=0; i<jcyc; i++ ) fprintf( stderr, "%s, %f\n", seq2[i], eff2[i] );
+
+// reporterr( "\nsizeof(gaplen) = %d\n", sizeof( Gaplen ) );
+// reporterr( "\nsizeof(int) = %d\n", sizeof( int ) );
+// reporterr( "\nsizeof(double) = %d\n", sizeof( double ) );
+// reporterr( "\nsizeof(double*) = %d\n", sizeof( double * ) );
+
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 )
+ {
+// fprintf( stderr, "## Freeing local arrays in D__align\n" );
+ orlgth1 = 0;
+ orlgth2 = 0;
+
+ imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
+
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatCub( cpmx1s );
+ FreeFloatCub( cpmx2s );
+
+ FreeFloatCub( doublework );
+ FreeIntCub( intwork );
+
+
+
+ free( gaplens );
+ if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
+ if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
+ if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
+ if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
+
+ if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
+ if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
+ if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
+ if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
+ if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
+ if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
+ if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
+ if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
+ if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
+ if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
+
+ }
+ else
+ {
+// fprintf( stderr, "## Not allocated\n" );
+ }
+ return( 0.0 );
+ }
+
+
+#if SLOW
+ nmask = calloc( maxdistclass, sizeof( int ) );
+#else
+ masklist1 = AllocateIntMtx( maxdistclass, 0 );
+ masklist2 = AllocateIntMtx( maxdistclass, 0 );
+ nmask = calloc( maxdistclass, sizeof( int ) );
+
+ for( c=0; c<maxdistclass; c++ )
+ {
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ if( eff1s[c][i] * eff2s[c][j] != 0.0 )
+ {
+// reporterr( "%d-%d, c=%d\n", i, j, c );
+ if( c != which[i][j] )
+ {
+ masklist1[c] = realloc( masklist1[c], sizeof( int ) * nmask[c]+1 );
+ masklist2[c] = realloc( masklist2[c], sizeof( int ) * nmask[c]+1 );
+
+ masklist1[c][nmask[c]] = i;
+ masklist2[c][nmask[c]] = j;
+ nmask[c]++;
+ }
+ }
+ }
+ }
+ for( c=0; c<maxdistclass; c++ ) if( nmask[c] ) break;
+ if( c<maxdistclass ) reporterr( "Found a complex grouping. This step may be a bit slow.\n" );
+#endif
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+ reporterr( "%d x %d sequences, len=%d, %d\n", icyc, jcyc, lgth1, lgth2 );
+
+
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ {
+ j = lgth2;
+ seq1[i][j] = 0;
+ while( j ) seq1[i][--j] = *newgapstr;
+// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+ }
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ for( i=0; i<jcyc; i++ )
+ {
+ j = lgth1;
+ seq2[i][j] = 0;
+ while( j ) seq2[i][--j] = *newgapstr;
+// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+ }
+ return( 0.0 );
+ }
+
+ warpbase = lgth1 + lgth2;
+ warpis = NULL;
+ warpjs = NULL;
+ warpn = 0;
+
+
+
+ if( trywarp )
+ {
+// reporterr( "Not supported yet!\n" );
+// exit( 1 );
+// fprintf( stderr, "IN D__align, penalty_shift = %d\n", penalty_shift );
+ if( headgp == 0 || tailgp == 0 )
+ {
+ fprintf( stderr, "At present, headgp and tailgp must be 1 to allow shift.\n" );
+ exit( 1 );
+ }
+ wmrecords = AllocateFloatVec( lgth2+1 );
+ warpi = AllocateIntVec( lgth2+1 );
+ warpj = AllocateIntVec( lgth2+1 );
+ prevwmrecords = AllocateFloatVec( lgth2+1 );
+ prevwarpi = AllocateIntVec( lgth2+1 );
+ prevwarpj = AllocateIntVec( lgth2+1 );
+ for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
+ }
+
+
+#if 0
+ fprintf( stderr, "#### eff in SA+++align\n" );
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatCub( cpmx1s );
+ FreeFloatCub( cpmx2s );
+
+ FreeFloatCub( doublework );
+ FreeIntCub( intwork );
+
+
+ free( gaplens );
+
+ if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
+ if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
+ if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
+ if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
+
+ if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
+ if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
+ if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
+ if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
+ if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
+ if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
+ if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
+ if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
+ if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
+ if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
+
+ }
+
+ 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 );
+
+ cpmx1s = AllocateFloatCub( maxdistclass, nalphabets, ll1+2 );
+ cpmx2s = AllocateFloatCub( maxdistclass, nalphabets, ll2+2 );
+
+ doublework = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
+ intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets+1 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+
+
+// reporterr( "Allocating gaplen1 and gaplen2\n" );
+ gaplen1 = (Gaplen ** )calloc( ll1+2, sizeof( Gaplen * ) );
+ gaplen1[ll1+1] = (Gaplen *)1;
+ gaplen2 = (Gaplen ** )calloc( ll2+2, sizeof( Gaplen * ) );
+ gaplen2[ll2+1] = (Gaplen *)1;
+
+
+// reporterr( "Allocating gaplen*\n" );
+ gaplen1ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen2ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen1icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen2icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) );
+ gaplen1jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen1jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen1jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen1jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+ gaplen2jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) );
+
+ gaplens = calloc( sizeof( Gaplen ***), 12 );
+ gaplens[0] = gaplen1ibestkamo;
+ gaplens[1] = gaplen2ibestkamo;
+ gaplens[2] = gaplen1icurr;
+ gaplens[3] = gaplen2icurr;
+ gaplens[4] = gaplen1jbestkamo;
+ gaplens[5] = gaplen2jbestkamo;
+ gaplens[6] = gaplen1jbest;
+ gaplens[7] = gaplen2jbest;
+ gaplens[8] = gaplen1jcurr;
+ gaplens[9] = gaplen2jcurr;
+ gaplens[10] = gaplen1jprev;
+ gaplens[11] = gaplen2jprev;
+// reporterr( "Allocation end\n" );
+ }
+
+ {
+ int ll1 = lgth1;
+ int ll2 = lgth2;
+
+// reporterr( "Allocating gaplen*i\n" );
+ for(i=0; i<ll1+1; i++ )
+ {
+ gaplen1ibestkamo[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1-i; k++ ) gaplen1ibestkamo[i][k] = NULL;
+ gaplen1ibestkamo[i][k] = (Gaplen *)1;
+
+ gaplen2ibestkamo[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1; k++ ) gaplen2ibestkamo[i][k] = NULL;
+ gaplen2ibestkamo[i][k] = (Gaplen *)1;
+
+ gaplen1icurr[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1-i; k++ ) gaplen1icurr[i][k] = NULL;
+ gaplen1icurr[i][k] = (Gaplen *)1;
+
+ gaplen2icurr[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1; k++ ) gaplen2icurr[i][k] = NULL;
+ gaplen2icurr[i][k] = (Gaplen *)1;
+ }
+ gaplen1ibestkamo[ll1+1] = NULL;
+ gaplen2ibestkamo[ll1+1] = NULL;
+ gaplen1icurr[ll1+1] = NULL;
+ gaplen2icurr[ll1+1] = NULL;
+
+// reporterr( "Allocating gaplen*j\n" );
+ for(i=0; i<ll2+1; i++ )
+ {
+ gaplen1jbestkamo[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jbestkamo[i][k] = NULL;
+ gaplen1jbestkamo[i][k] = (Gaplen *)1;
+
+ gaplen2jbestkamo[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jbestkamo[i][k] = NULL;
+ gaplen2jbestkamo[i][k] = (Gaplen *)1;
+
+ gaplen1jbest[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jbest[i][k] = NULL;
+ gaplen1jbest[i][k] = (Gaplen *)1;
+
+ gaplen2jbest[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jbest[i][k] = NULL;
+ gaplen2jbest[i][k] = (Gaplen *)1;
+
+ gaplen1jcurr[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jcurr[i][k] = NULL;
+ gaplen1jcurr[i][k] = (Gaplen *)1;
+
+ gaplen2jcurr[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jcurr[i][k] = NULL;
+ gaplen2jcurr[i][k] = (Gaplen *)1;
+
+ gaplen1jprev[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) );
+ for( k=0; k<ll1+1; k++ ) gaplen1jprev[i][k] = NULL;
+ gaplen1jprev[i][k] = (Gaplen *)1;
+
+ gaplen2jprev[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) );
+ for( k=0; k<ll2+1-i; k++ ) gaplen2jprev[i][k] = NULL;
+ gaplen2jprev[i][k] = (Gaplen *)1;
+
+ }
+ gaplen1jbestkamo[ll2+1] = NULL;
+ gaplen2jbestkamo[ll2+1] = NULL;
+ gaplen1jbest[ll2+1] = NULL;
+ gaplen2jbest[ll2+1] = NULL;
+ gaplen1jcurr[ll2+1] = NULL;
+ gaplen2jcurr[ll2+1] = NULL;
+ gaplen1jprev[ll2+1] = NULL;
+ gaplen2jprev[ll2+1] = NULL;
+ }
+
+
+#if USEGAPLENMTX
+/* maikai allocate */
+
+ reporterr( "Allocating gaplenmtx1\n" );
+ gaplen1mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen1mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen1mtx[i][j] = (Gaplen **)calloc( lgth1+2, sizeof( Gaplen * ) );
+ for( k=0; k<lgth1+1; k++ ) gaplen1mtx[i][j][k] = NULL;
+ gaplen1mtx[i][j][k] = (Gaplen *)1;
+ }
+ gaplen1mtx[i][j] = NULL;
+ }
+ gaplen1mtx[i] = NULL;
+
+ reporterr( "Allocating gaplenmtx2\n" );
+ gaplen2mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen2mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen2mtx[i][j] = (Gaplen **)calloc( lgth2+2, sizeof( Gaplen * ) );
+ for( k=0; k<lgth2+1; k++ ) gaplen2mtx[i][j][k] = NULL;
+ gaplen2mtx[i][j][k] = (Gaplen *)1;
+ }
+ gaplen2mtx[i][j] = NULL;
+ }
+ gaplen2mtx[i] = NULL;
+
+#endif
+
+#if USEGAPLENHALF
+ reporterr( "Allocating gaplenhalf1\n" );
+ gaplen1half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen1half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen1half[i][j] = (Gaplen **)calloc( lgth1+2 - i, sizeof( Gaplen * ) );
+ for( k=0; k<lgth1+1-i; k++ ) gaplen1half[i][j][k] = NULL;
+ gaplen1half[i][j][k] = (Gaplen *)1;
+ }
+ gaplen1half[i][j] = NULL;
+ }
+ gaplen1half[i] = NULL;
+
+ reporterr( "Allocating gaplenhalf2\n" );
+ gaplen2half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) );
+ for(i=0; i<lgth1+1; i++ ) gaplen2half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) );
+ for(i=0; i<lgth1+1; i++ )
+ {
+ for(j=0; j<lgth2+1; j++ )
+ {
+ gaplen2half[i][j] = (Gaplen **)calloc( lgth2+2 - j, sizeof( Gaplen * ) );
+ for( k=0; k<lgth2+1-j; k++ ) gaplen2half[i][j][k] = NULL;
+ gaplen2half[i][j][k] = (Gaplen *)1;
+ }
+ gaplen2half[i][j] = NULL;
+ }
+ gaplen2half[i] = NULL;
+#endif
+
+
+/* maikai allocate */
+
+
+ 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
+ {
+ double t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+
+#if SLOW
+#else
+// cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+// cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ cpmx_calc_new( seq1, cpmx1s[c], eff1s[c], lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2s[c], eff2s[c], lgth2, jcyc );
+ }
+#endif
+
+
+// reporterr( "Counting gaplen\n" );
+ gaplencount( icyc, lgth1, gaplen1, seq1, eff1 );
+ gaplencount( jcyc, lgth2, gaplen2, seq2, eff2 );
+#if DEBUG
+ reporterr( "group1 = \n" );
+ showgaplen( gaplen1, lgth1 );
+ reporterr( "group2 = \n" );
+ showgaplen( gaplen2, lgth2 );
+#endif
+// reporterr( "done.\n" );
+
+
+ for( i=0; i<lgth1+1; i++ ) for( j=0; j<lgth2+1; j++ )
+ {
+#if USEGAPLENMTX
+// duplicategaplen( gaplen1mtx[i][j], gaplen1, lgth1 );
+// duplicategaplen( gaplen2mtx[i][j], gaplen2, lgth2 );
+
+// duplicategaplenpartly( gaplen2mtx[i][j], gaplen2, j-0, lgth2 ); // anzen
+// duplicategaplenpartly( gaplen1mtx[i][j], gaplen1, i-0, lgth1 ); // anzen
+ duplicategaplenpartly( gaplen1mtx[i][j], gaplen1, i-0, i ); // iranaikamo
+ duplicategaplenpartly( gaplen2mtx[i][j], gaplen2, j-0, j ); // iranaikamo
+#endif
+#if USEGAPLENHALF
+
+// duplicategaplenpartly( gaplen1half[i][j], gaplen1+i, 0, lgth1-i ); // KOKO de setsuyaku dekiru to omou.
+// duplicategaplenpartly( gaplen2half[i][j], gaplen2+j, 0, lgth2-j ); // originally, j-1, lgth2
+ duplicategaplenpartly( gaplen1half[i][j], gaplen1+i, 0, 0 ); // test
+ duplicategaplenpartly( gaplen2half[i][j], gaplen2+j, 0, 0 ); // test
+#endif
+ }
+
+
+#if USEGAPLENMTX
+ reporterr( "Duplicating gaplen*mtx\n" );
+ for( i=0; i<lgth1+1; i++ )
+ {
+// addnewgaplen( gaplen1mtx[i][0], gaplen1, gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2mtx[i][0], gaplen2, gaplen2, lgth2, 0, i );
+// duplicategaplenpartly( gaplen1mtx[i][0], gaplen1, 0, lgth1 );
+// duplicategaplenpartly( gaplen2mtx[i][0], gaplen2, 0, lgth2 );
+ copygaplenrestricted( gaplen2mtx[i][0], gaplen2, lgth2, 0, i, 0, 0 );
+ }
+#endif
+#if USEGAPLENHALF
+ reporterr( "Duplicating gaplen*mtx\n" );
+ for( i=0; i<lgth1+1; i++ )
+ {
+ copygaplenrestricted( gaplen2half[i][0], gaplen2, lgth2, 0, i, 0, 0 );
+ }
+#endif
+
+
+
+ for( i=0; i<1; i++ )
+ {
+// duplicategaplencompactx( gaplen1icurr[i], gaplen1, lgth1, i-0, lgth1 ); //originally, 0, lgth1
+//
+// duplicategaplencompactx( gaplen1icurr[i], gaplen1+i, lgth1-i, 0, lgth1-i ); // half
+ duplicategaplencompactx( gaplen1icurr[i], gaplen1+i, lgth1-i, 0, 1 ); // 0, 1 hitsuyou
+
+
+// duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, lgth2 ); // ichiou zenbu
+ duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, 0 );
+
+
+ copygaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, i, 0, 0 ); // -> zurasu -> error?
+
+
+// duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1, lgth1, 0, 1 );
+// duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1+i, lgth1-i, 0, 1 ); // half
+ duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1+i, lgth1-i, 0, 0 ); // half
+// duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, lgth2 );
+ duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, 0 );
+// copygaplenrestricted( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, 0 ); // -> zurasu -> error?
+// copygaplenrestricted_zurasu( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, lgth2, 0, lgth2 ); // -> zurasu -> error?
+ copygaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, 0 ); // -> zurasu -> error?
+ }
+
+// reporterr( "Duplicating gaplen*j*curr \n" );
+// int nduplicated = 0;
+ for( j=0; j<lgth2+1; j++ )
+// for( j=0; j<1; j++ )
+ {
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[0][j], gaplen1, gaplen1, lgth1, 0, j );
+// addnewgaplen( gaplen2mtx[0][j], gaplen2, gaplen2, lgth2, -1, 0 );
+// duplicategaplenpartly( gaplen1mtx[0][j], gaplen1, 0, lgth1 );
+// duplicategaplenpartly( gaplen2mtx[0][j], gaplen2, 0, lgth2 );
+ copygaplenrestricted( gaplen1mtx[0][j], gaplen1, lgth1, 0, j, 0, 0 );
+#endif
+
+#if USEGAPLENHALF
+ copygaplenrestricted( gaplen1half[0][j], gaplen1, lgth1, 0, j, 0, 0 );
+#endif
+// reporterr( "1jcurr?\n" );
+// duplicategaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, lgth1 ); // test
+ duplicategaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, 0 ); // dame?
+// reporterr( "done\n" );
+// duplicategaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, 0 ); //test
+
+// duplicategaplencompactx( gaplen2jcurr[j], gaplen2, lgth2, j-0, lgth2 ); // full
+// duplicategaplencompactx( gaplen2jcurr[j], gaplen2+j, lgth2-j, 0, lgth2-j ); //half! KOKO????
+//reporterr( "starting suspicious duplication\n" );
+ duplicategaplencompactx( gaplen2jcurr[j], gaplen2+j, lgth2-j, 0, 0 ); //half!
+//reporterr( "starting suspicious copy\n" );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1, lgth1, 0, j, 0, 0 ); // TEST
+//reporterr( "finished\n" );
+
+// reporterr( "Checking gaplen1jcurr[%d]\n", j );
+// checkgaplen( gaplen1jcurr[j], 100 );
+// reporterr( "Checking gaplen2jcurr[%d]\n", j );
+// checkgaplen( gaplen2jcurr[j], 100 );
+ }
+
+// reporterr( "nduplicated (corrected) = %d\n", nduplicated );
+
+// reporterr( "Duplicating gaplen*j*prev \n\n" );
+ for( j=0; j<lgth2+1; j++ ) // allocate nominotame, atode uwagaki
+ {
+// duplicategaplencompactx( gaplen1jprev[j], gaplen1, lgth1, 0, lgth1 );
+ duplicategaplencompactx( gaplen1jprev[j], gaplen1, lgth1, 0, 0 ); // TEST
+// duplicategaplencompactx( gaplen2jprev[j], gaplen2, lgth2, j-0, lgth2 ); // originally, 0,lgth2
+// duplicategaplencompactx( gaplen2jprev[j], gaplen2+j, lgth2-j, 0, lgth2-j ); // half
+ duplicategaplencompactx( gaplen2jprev[j], gaplen2+j, lgth2-j, 0, 0 ); // half
+
+
+ copygaplencompactx( gaplen1jprev[j], gaplen1, lgth1, 0, j, 0, 0 ); // wasuretetakamo
+
+
+ }
+
+
+// reporterr( "Duplicating gaplen*j*best \n\n" );
+
+ for( j=0; j<lgth2+1; j++ )
+// for( j=0; j<1; j++ )
+ {
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, lgth1 ); // KOKO
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 0 ); // test
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 1 );
+ duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 0 );
+
+
+// duplicategaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, 1 );
+// duplicategaplencompactx( gaplen2jbestkamo[j], gaplen2, lgth2, j-0, j+1 ); // originally, 0, j+1
+ duplicategaplencompactx( gaplen2jbestkamo[j], gaplen2+j, lgth2-j, 0, 1 ); // half!
+ copygaplencompactx( gaplen1jbestkamo[j], gaplen1, lgth1, 0, j, 0, 0 ); // TEST
+
+// duplicategaplencompactx( gaplen1jbest[j], gaplen1, lgth1, 0, lgth1 ); // KOKO
+ duplicategaplencompactx( gaplen1jbest[j], gaplen1, lgth1, 0, 0 ); // test
+// duplicategaplencompactx( gaplen2jbest[j], gaplen2, lgth2,j-0, j+1 ); // originally, 0,j+1
+ duplicategaplencompactx( gaplen2jbest[j], gaplen2+j, lgth2-j, 0, 1 ); // half!
+ copygaplencompactx( gaplen1jbest[j], gaplen1, lgth1, 0, j, 0, 0 ); // TEST
+
+
+ }
+
+// reporterr( "Duplication end\n" );
+
+
+#if 0
+ reporterr( "Checking gaplen1icurr\n" );
+ checkgaplen( gaplen1icurr[0], 100 );
+ reporterr( "Checking gaplen2icurr\n" );
+ checkgaplen( gaplen2icurr[0], 100 );
+#endif
+
+
+
+
+// showgaplen( gaplen1jcurr[50], lgth2 );
+
+ currentw = w1;
+ previousw = w2;
+
+// match_calc( n_dynamicmtx, initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
+#if SLOW
+ match_calc_slow( which, matrices, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, *doublework, *intwork, 1, 1 );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
+#else
+ fillzero( initverticalw, lgth1 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+// fprintf( stderr, "c=%d matrices[c][W][W] = %f\n", c, matrices[c][amino_n['W']][amino_n['W']] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "seq1[i] = %c, cpmx1s[c][3][%d] = %f\n", seq1[0][i], i, cpmx1s[c][3][i] );
+// for( i=0; i<lgth2; i++ ) fprintf( stderr, "seq2[i] = %c, cpmx2s[c][3][%d] = %f\n", seq2[0][i], i, cpmx2s[c][3][i] );
+ match_calc_add( matrices[c], initverticalw, cpmx2s[c], cpmx1s[c], 0, lgth1, doublework[c], intwork[c], 1 );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "c=%d, %d - %f\n", c, i, initverticalw[i] );
+
+ if( nmask[c] ) match_calc_del( which, matrices, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, c, nmask[c], masklist2[c], masklist1[c] );
+ }
+#endif
+// reporterr( "initverticalw = \n" );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
+
+
+ if( localhom )
+ imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
+
+// match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
+#if SLOW
+ match_calc_slow( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, *doublework, *intwork, 1, 0 );
+// for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
+// exit( 1 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], 0, lgth2, doublework[c], intwork[c], 1 );
+ if( nmask[c] ) match_calc_del( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, c, nmask[c], masklist1[c], masklist2[c] );
+ }
+#endif
+// reporterr( "currentw = \n" );
+// for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
+
+
+
+
+
+// exit( 1 );
+
+
+ if( localhom )
+ imp_match_out_vead( currentw, 0, lgth2 ); // 060306
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ for( j=1; j<lgth2+1; j++ )
+ {
+ pfac = calcpfac_gap_noidatend( gaplen1, gaplen2, j, 0, j, seq1[0], seq2[0], 0 );
+// reporterr( "computing initial end gap penalty for %c-%c, i=0, j=%d, pfac=%f\n", seq1[0][0], seq2[0][j], j, pfac );
+// reporterr( "%c-%c, i=0, j=%d, currentw[j]=%f -> ", seq1[0][0], seq2[0][j], j, currentw[j] );
+ currentw[j] += fpenalty * pfac; // tekitou
+// reporterr( " %f\n", currentw[j] );
+ }
+ for( i=1; i<lgth1+1; i++ )
+ {
+ pfac = calcpfac_gap_noidatend( gaplen2, gaplen1, i, 0, i, seq2[0], seq1[0], 0 );
+// reporterr( "computing initial end gap penalty for %c-%c, i=%d, j=0, pfac=%f\n", seq1[0][i], seq2[0][0], i, pfac );
+ initverticalw[i] += fpenalty * pfac; // tekitou
+ }
+
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+
+
+#if ALGZGAP
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
+#else
+ pfac = calcpfac_gapex_noidatend( gaplen2, gaplen1, j, 1, j, seq2[0], seq1[0], 1 );
+#if DEBUG
+ reporterr( "%c-%c, INITIAL jgap extension check, pfac = %f\n\n", seq1[0][j], '=', pfac );
+#endif
+ m[j] = currentw[j-1] + fpenalty * pfac;
+ mp[j] = 0;
+#endif
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
+
+
+ for( i=1; i<lasti; i++ )
+ {
+// reporterr( "i = %d\n", i );
+
+// reporterr( "err1? i=%d/%d\n", i, lgth1 );
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+ cleargaplens( gaplens );
+ if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
+ if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+#if 1
+ gaplentmp = gaplen1jprev;
+ gaplen1jprev = gaplen1jcurr;
+ gaplen1jcurr = gaplentmp;
+
+ gaplentmp = gaplen2jprev;
+ gaplen2jprev = gaplen2jcurr;
+ gaplen2jcurr = gaplentmp;
+
+#if DEBUG
+ reporterr( "Entering a small j loop, i=%d\n", i );
+ for( j=1; j<lgth2+1; j++ )
+ {
+ reporterr( "before j loop, i=%d, gaplen2jcurr[%d] = \n", i, j );
+ showgaplen( gaplen2jcurr[j], 100 );
+ reporterr( "\n" );
+ reporterr( "before j loop, i=%d, gaplen2prev[%d] = \n", i, j );
+ showgaplen( gaplen2jprev[j], 100 );
+ reporterr( "\n" );
+ }
+#endif
+#else
+
+ reporterr( "Entering a small j loop, i=%\n", i );
+ for( j=1; j<lgth2+1; j++ )
+ {
+// addnewgaplen( gaplen1jprev[j], gaplen1jcurr[j], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jprev[j], gaplen2jcurr[j], gaplen2, lgth2, -1, 0 );
+ reporterr( "err1? j=%d/%d\n", j, lgth2 );
+ copygaplencompactx( gaplen1jprev[j-1], gaplen1jcurr[j-1], lgth1, -1, 0, i-1, i-1 ); // TEST
+ reporterr( "err1? j=%d/%d\n", j, lgth2 );
+ copygaplencompactx( gaplen2jprev[j-1], gaplen2jcurr[j-1], lgth2, -1, 0, j-1, j-1 ); // TETS
+#if DEBUG
+ reporterr( "before j loop, i=%d, gaplen2jcurr[%d] = \n", i, j );
+ showgaplen( gaplen2jcurr[j], 100 );
+ reporterr( "\n" );
+ reporterr( "before j loop, i=%d, gaplen2prev[%d] = \n", i, j );
+ showgaplen( gaplen2jprev[j], 100 );
+ reporterr( "\n" );
+#endif
+ }
+#endif
+
+// reporterr( "err2? i=%d/%d\n", i, lgth1 );
+
+// duplicategaplencompactx( gaplen1icurr[i], gaplen1, lgth1, i, i+1 ); //originally 0, i+1
+// reporterr( "gaplen+0=\n");
+// showgaplen( gaplen1, 10 );
+// reporterr( "i=%d, lgth1=%d, lgth1-i=%d, gaplen+i-1=\n", i, lgth1, lgth1-i );
+// showgaplen( gaplen1+i-1, 100 );
+ duplicategaplencompactx( gaplen1icurr[i], gaplen1+i, lgth1-i, 0, 1 ); // half!!
+// duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, lgth2 ); // KOKO
+ duplicategaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, 0 ); // test
+ copygaplencompactx( gaplen2icurr[i], gaplen2, lgth2, 0, i, 0, 0 ); // IRU? TEST
+
+
+
+// duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1, lgth1, i, i+1 ); //originally 0, i+1
+ duplicategaplencompactx( gaplen1ibestkamo[i], gaplen1+i, lgth1-i, 0, 1 ); //half
+// duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, lgth2 ); // ORIGINALLY, 0, lgth2
+ duplicategaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, 0 ); // ORIGINALLY, 0, lgth2
+// copygaplenrestricted( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, lgth2, 0, 0 ); // IRU? // TEST
+ copygaplencompactx( gaplen2ibestkamo[i], gaplen2, lgth2, 0, i, 0, 0 ); // IRU? // TEST
+
+ extendgaplencompactx( gaplen1jprev[0], gaplen1, i ); // ???
+
+
+// addnewgaplen( gaplen1jprev[0], gaplen1icurr[i-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jprev[0], gaplen2icurr[i-1], gaplen2, lgth2, -1, 0 );
+// copygaplenrestricted( gaplen1jprev[0], gaplen1icurr[i-1], lgth1, -1, 0, i, i ); // i-1, i da to omou.
+ copygaplencompactx( gaplen1jprev[0], gaplen1icurr[i-1], lgth1-i, -1, 0, i, 1 ); // half? lgth1-i?
+// copygaplenrestricted( gaplen2jprev[0], gaplen2icurr[i-1], lgth2, -1, 0, 0, 0 );
+ copygaplencompactx( gaplen2jprev[0], gaplen2icurr[i-1], lgth2-j, -1, 0, 0, 0 ); // half?? lgth2-j?
+
+
+// match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
+#if SLOW
+ match_calc_slow( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, *doublework, *intwork, 0, 0 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], i, lgth2, doublework[c], intwork[c], 0 );
+ if( nmask[c] ) match_calc_del( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, c, nmask[c], masklist1[c], masklist2[c] );
+ }
+#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
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_vead( currentw, i, lgth2 );
+#else
+ imp_match_out_vead( 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];
+
+#if 0
+ fprintf( stderr, "%c ", seq1[0][i] );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// mi = previousw[0] + ogcp2[1]; mpi = 0;
+
+
+
+
+
+#if ALGZGAP
+ mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
+#else
+ pfac = calcpfac_gapex_noidatend( gaplen1, gaplen2, i, 1, i, seq1[0], seq2[0], 1 );
+#if DEBUG
+ reporterr( "%c-%c, INITIAL igap extension check, pfac = %f\n\n", '=', seq2[0][j], pfac );
+#endif
+ mi = previousw[0] + fpenalty * pfac;
+ mpi=0;
+#endif
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ if( trywarp )
+ {
+ prevwmrecordspt = prevwmrecords;
+ wmrecordspt = wmrecords+1;
+ wmrecords1pt = wmrecords;
+ warpipt = warpi + 1;
+ warpjpt = warpj + 1;
+ }
+
+
+
+
+// reporterr( "\n\ni=%d, %c\n", i, seq1[0][i] );
+ for( j=1; j<lastj; j++ )
+ {
+
+#if DEBUG
+ reporterr( "***** %c%d-%c%d ******* \n", seq1[0][i], i, seq2[0][j], j );
+ reporterr( "mpi=%d (%c), *mpjpt=%d (%c)\n", mpi, seq2[0][mpi], *mpjpt, seq1[0][*mpjpt] );
+#endif
+
+
+// Hitsuyou na bun dake tsuika
+#if USEGAPLENMTX
+ extendgaplenpartly( gaplen1mtx[i-1][mpi], gaplen1, i, i );
+ extendgaplenpartly( gaplen2mtx[i-1][mpi], gaplen2, j, j );
+ extendgaplenpartly( gaplen1mtx[*mpjpt][j-1], gaplen1, i, i );
+ extendgaplenpartly( gaplen2mtx[*mpjpt][j-1], gaplen2, j, j );
+ extendgaplenpartly( gaplen1mtx[i-1][j-1], gaplen1, i, i );
+ extendgaplenpartly( gaplen2mtx[i-1][j-1], gaplen2, j, j );
+#endif
+#if USEGAPLENHALF
+ extendgaplenpartly( gaplen1half[i-1][mpi], gaplen1+i-1, 1, 1 );
+ extendgaplenpartly( gaplen2half[i-1][mpi], gaplen2+mpi, j-mpi, j-mpi );
+ extendgaplenpartly( gaplen1half[*mpjpt][j-1], gaplen1+*mpjpt, i-*mpjpt, i-*mpjpt );
+ extendgaplenpartly( gaplen2half[*mpjpt][j-1], gaplen2+j-1, 1, 1 );
+ extendgaplenpartly( gaplen1half[i-1][j-1], gaplen1+i-1, 1, 1 );
+ extendgaplenpartly( gaplen2half[i-1][j-1], gaplen2+j-1, 1, 1 );
+
+#endif
+
+// reporterr( "extending gaplen1icurr\n" );
+ extendgaplencompactx( gaplen1icurr[i-1], gaplen1+i-1, 1 ); // iruhazu
+// reporterr( "extending gaplen2icurr\n" );
+ extendgaplencompactx( gaplen2icurr[i-1], gaplen2, j ); // iruhazu
+// reporterr( "extending gaplen1jprev[j-1], j-1=%d\n", j-1 );
+ extendgaplencompactx( gaplen1jprev[j-1], gaplen1, i );
+// reporterr( "extending gaplen1jcurr, j-1=%d\n", j-1 );
+ extendgaplencompactx( gaplen1jcurr[j-1], gaplen1, i );
+// reporterr( "extending gaplen2jprev\n" );
+ extendgaplencompactx( gaplen2jprev[j-1], gaplen2+j-1, 1 );
+// reporterr( "extending gaplen2jcurr\n" );
+ extendgaplencompactx( gaplen2jcurr[j-1], gaplen2+j-1, 1 );
+// reporterr( "extending gaplen1jbest[j-1]\n" );
+ extendgaplencompactx( gaplen1jbest[j-1], gaplen1, i );
+// reporterr( "extending gaplen1jbestkamo[j-1]\n" );
+ extendgaplencompactx( gaplen1jbestkamo[j-1], gaplen1, i );
+// reporterr( "extending gaplen1jprev[mpi], j-1=%d\n", j-1 );
+ extendgaplencompactx( gaplen1jprev[mpi], gaplen1, i ); // full
+// reporterr( "extending gaplen2jprev[mpi]\n" );
+ extendgaplencompactx( gaplen2jprev[mpi], gaplen2+mpi, j-mpi ); // half
+// reporterr( "extending gaplen1ibestkamo[i-1]\n" );
+ extendgaplencompactx( gaplen1ibestkamo[i-1], gaplen1+i-1, 1 );
+// reporterr( "extending gaplen2ibestkamo[i-1]\n" );
+ extendgaplencompactx( gaplen2ibestkamo[i-1], gaplen2, j );
+
+
+#if DEBUG
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jcurr[j]=\n", i, j );
+ showgaplen( gaplen2jcurr[j], 100 );
+
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jcurr[j-1]=\n", i, j );
+ showgaplen( gaplen2jcurr[j-1], 100 );
+
+
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jprev[j]=\n", i, j );
+ showgaplen( gaplen2jprev[j], 100 );
+
+ reporterr( "at the head of j loop, i,j=%d,%d, gaplen2jprev[j-1]=\n", i, j );
+ showgaplen( gaplen2jprev[j-1], 100 );
+#endif
+
+
+#ifdef xxxenablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+ cleargaplens( gaplens );
+ if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
+ if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+#if USEGAPLENHALF
+// i==248, j==80 wo check
+#if DEBUG80
+ if( j==80 )
+ {
+ reporterr( "When i==%d, j==%d,\n", i, j );
+ reporterr( "gaplen2jprev[j-1=%d]=\n", j-1 );
+ showgaplen( gaplen2jprev[j-1], lgth1 );
+ reporterr( "gaplen2half[i-1=%d][j-1=%d]=\n", i-1, j-1 );
+ showgaplen( gaplen2half[i-1][j-1], lgth1 );
+ }
+ if( j==79 )
+ {
+ reporterr( "When i==%d, j==%d,\n", i, j );
+ reporterr( "gaplen2jprev[j-1=%d]=\n", j-1 );
+ showgaplen( gaplen2jprev[j-1], lgth1 );
+ reporterr( "gaplen2half[i-1=%d][j-1=%d]=\n", i-1, j-1 );
+ showgaplen( gaplen2half[i-1][j-1], lgth1 );
+ }
+#endif
+#endif
+
+
+// pfac = calcpfac( gaplen1jprev[j-1], gaplen2jprev[j-1], i, j, seq1[0], seq2[0] );
+//reporterr( "#### COMPACT, i,j=%d,%d\n", i, j );
+ pfac = calcpfacnoidatend( gaplen1jprev[j-1], gaplen2jprev[j-1], i, 1, seq1[0], seq2[0]+j, one ); // 1j->full, 2j->half
+#if USEGAPLENMTX
+//reporterr( "#### FULL, i,j=%d,%d\n", i, j );
+ pfactmp = calcpfac( gaplen1mtx[i-1][j-1], gaplen2mtx[i-1][j-1], i, j, seq1[0], seq2[0], one );
+#endif
+#if USEGAPLENHALF
+//reporterr( "#### HALF, i,j=%d/%d,%d/%d\n", i, lgth1, j, lgth2 );
+// showgaplen( gaplen2half[i-1][j-1], lgth2-j );
+ pfactmp = calcpfac( gaplen1half[i-1][j-1], gaplen2half[i-1][j-1], 1, 1, seq1[0]+i, seq2[0]+j, zero );
+#endif
+#if USEGAPLENMTX + USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(straight) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+ PFACERROR = 1;
+ exit( 1 );
+ }
+#endif
+//if( i==50 && j==135 ) exit( 1 );
+
+
+// reporterr( "i,j=%d,%d, *prept = %f\n", i, j, *prept );
+
+#if ALGZSTRAIGHT
+ wm = *prept; // Machigai!!
+#else
+ wm = *prept + fpenalty * pfac;
+#endif
+ *ijppt = 0;
+
+
+#if DEBUG
+ if( i == j )
+ {
+ fprintf( stderr, "\n i=%d, j=%d %c, %c ", i, j, seq1[0][i], seq2[0][j] );
+ fprintf( stderr, "%5.0f, pfac for straight =%f\n", wm, pfac );
+ }
+#endif
+ newgaplen = j-mpi-1;
+
+
+//if( i == 53 && j == 93 ) exit( 1 );
+
+
+
+
+// pfac = calcpfac_gap_incomplete( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], newgaplen, i, j, seq1[0], seq2[0], 0 ); // i-1
+ pfac = calcpfac_gap_noidatend( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], newgaplen, 1, j, seq1[0]+i-1, seq2[0], 0 ); // i-1
+#if USEGAPLENMTX
+ pfactmp = calcpfac_gap_incomplete( gaplen1mtx[i-1][mpi], gaplen2mtx[i-1][mpi], newgaplen, i, j, seq1[0], seq2[0], 1 );
+#endif
+#if USEGAPLENHALF
+ pfactmp = calcpfac_gap_incomplete( gaplen1half[i-1][mpi], gaplen2half[i-1][mpi], newgaplen, 1, j-mpi, seq1[0]+i-1, seq2[0]+mpi, 1 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(igap) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+ PFACERROR = 1;
+ }
+#endif
+
+
+#if DEBUG
+ reporterr( "%c-%c pfac for igap end incomplete = %f\n", seq1[0][i], seq2[0][j], pfac );
+ reporterr( "mi when igap end checking = %f\n", mi );
+ reporterr( "wm = %f, mi+fpenalty*pfac=%f\n", wm, mi+fpenalty*pfac );
+#endif
+
+
+#if ALGZGAP
+ if( (g=mi+*fgcp2pt*gf1va) > wm )
+#else
+ if( (g=mi+fpenalty*pfac) > wm )
+#endif
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+#if DEBUG80
+ reporterr( "Selected as igap end! wm = %f, mi = %f\n", wm, mi );
+ fprintf( stderr, "Jump from %d-%d (%c-%c) to %d (%c-%c)!\n", i, j, seq1[0][i], seq2[0][j], mpi, seq1[0][i-1], seq2[0][mpi] );
+#endif
+ }
+
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+// if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
+
+#if 0
+// reporterr( "Checking %c, (current pos = %c)\n", seq2[0][j+1], seq2[0][j] );
+ sfac = 1.0;
+ for( k=0; gaplen2[j+1]&&(gl=gaplen2[j+1][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ {
+// reporterr( ".len = %d, .relend = %d\n", gaplen2[j+1][k].len, gaplen2[j+1][k].relend );
+ if( gl - 1 == gaplen2[j+1][k].relend )
+ {
+ sfac -= gaplen2[j+1][k].freq;
+// reporterr( "Hit! sfac = %f\n", sfac );
+ }
+ }
+ sfac2 = 1.0;
+ for( k=0; gaplen1[i+1]&&(gl=gaplen1[i+1][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ if( gaplen1[i+1][k].relend != -1 ) sfac2 -= gaplen1[i+1][k].freq;
+ sfac *= sfac2;
+#else
+// sfac = 0.0;
+#endif
+
+
+
+#if ALGZGAP
+ if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
+#else
+// if( (g=*prept + fpenalty * sfac ) >= mi )
+ if( (g=*prept ) >= mi )
+#endif
+ {
+// mpibk = mpi;
+// mi = g - fpenalty * sfac;
+ mi = g;
+ mpi = j-1;
+#if DEBUG80
+ reporterr( "Selected as igap start! %c%d-%c%d, mi=%f, g=%f\n", seq1[0][i-1], i-1, seq2[0][mpi], mpi, mi, g );
+#endif
+
+#if FREEFREQUENTLY
+// freegaplenpartly( gaplen1ibestkamo[i-1], 0, i-1 );
+ freegaplenpartly( gaplen2ibestkamo[i-1], j-3, j-2 );
+#endif
+// freegaplenpartly( gaplen1jprev[mpibk], 0, lgth2 ); // full
+// freegaplenpartly( gaplen2jprev[mpibk], 0, lgth2-mpibk ); // half
+// if( gaplen1jprev[mpibk] ) FreeGaplenMtx( gaplen1jprev[mpibk], 0 );
+// gaplen1jprev[mpibk] = NULL;
+// if( gaplen2jprev[mpibk] ) FreeGaplenMtx( gaplen2jprev[mpibk], 0 );
+// gaplen2jprev[mpibk] = NULL;
+
+
+// addnewgaplen( gaplen1ibestkamo[i-1], gaplen1jprev[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2ibestkamo[i-1], gaplen2jprev[j-1], gaplen2, lgth2, -1, 0 );
+// copygaplenrestricted( gaplen1ibestkamo[i-1], gaplen1jprev[j-1], lgth1, -1, 0, i, i ); // i-1, i
+ copygaplencompactx( gaplen1ibestkamo[i-1], gaplen1jprev[j-1], lgth1, -1, 0, 1, i ); // half
+// copygaplenrestricted( gaplen2ibestkamo[i-1], gaplen2jprev[j-1], lgth2, -1, 0, j, j ); // mpi, j
+ copygaplencompactx( gaplen2ibestkamo[i-1], gaplen2jprev[j-1], lgth2, -1, 0, j, 1 ); //half
+
+
+ }
+
+
+
+
+
+
+// reporterr( "g=%f, *prept=%f, mi=%f\n", g, *prept, mi );
+
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if ALGZGAP
+ pfac = 0.0; // CHUUI!
+#else
+
+// pfac = calcpfac_gapex( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], i, j, j-mpi, seq1[0], seq2[0], 1 ); // i-1
+ pfac = calcpfac_gapex_noidatend( gaplen1ibestkamo[i-1], gaplen2ibestkamo[i-1], 1, j, j-mpi, seq1[0]+i, seq2[0], 1 ); // 1ibest->half, 2ibest->full
+#if USEGAPLENMTX
+ pfactmp = calcpfac_gapex( gaplen1mtx[i-1][mpi], gaplen2mtx[i-1][mpi], i, j, j-mpi, seq1[0], seq2[0], 1 );
+#endif
+#if USEGAPLENHALF
+ pfactmp = calcpfac_gapex( gaplen1half[i-1][mpi], gaplen2half[i-1][mpi], 1, j-mpi, j-mpi, seq1[0]+i, seq2[0]+mpi, 1 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(igapex) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+ PFACERROR = 1;
+ }
+#endif
+
+
+
+
+
+
+
+#if DEBUG
+ reporterr( "%c-%c, igap extension check, pfac = %f\n\n", '=', seq2[0][j], pfac );
+#endif
+#endif
+// reporterr( "mi = %f -> ", mi );
+ mi += fpenalty * pfac;
+// reporterr( "mi = %f\n", mi );
+
+
+// reporterr( "using %d-%d, %d, %d\n", *mpjpt, j-1, i, j );
+ newgaplen = i-*mpjpt-1;
+// pfac = calcpfac_gap_incomplete( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], newgaplen, j, i, seq2[0], seq1[0], 0 ); // j-1 deha???
+
+
+ pfac = calcpfac_gap_noidatend( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], newgaplen, 1, i, seq2[0]+j-1, seq1[0], 1 ); // 2jbestkamo->half, 1jbestkamo->full
+#if USEGAPLENMTX
+ pfactmp = calcpfac_gap_incomplete( gaplen2mtx[*mpjpt][j-1], gaplen1mtx[*mpjpt][j-1], newgaplen, j, i, seq2[0], seq1[0], 1 );
+#endif
+#if USEGAPLENHALF
+ pfactmp = calcpfac_gap_incomplete( gaplen2half[*mpjpt][j-1], gaplen1half[*mpjpt][j-1], newgaplen, 1, i-*mpjpt, seq2[0]+j-1, seq1[0]+*mpjpt, 1 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(jgap) pfac=%f, but pfactmp=%f (i,j=%d,%d)\n", pfac, pfactmp, i, j );
+// exit( 1 );
+ PFACERROR = 1;
+ }
+#endif
+
+#if ALGZGAP
+ if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
+#else
+ if( (g=*mjpt + fpenalty*pfac) > wm )
+#endif
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+
+
+#if FREEFREQUENTLY
+ freegaplenpartly( gaplen1jbest[j-1], i-3, i-2 );
+// freegaplenpartly( gaplen2jbest[j-1], j-3, j-2 );
+#endif
+
+
+#if DEBUG
+ reporterr( "Selected as jgap end!, pfac = %f\n", pfac );
+ fprintf( stderr, "Jump from %d (%c) to %d (%c)!\n", j, seq1[0][j], *mpjpt, seq1[0][*mpjpt] );
+#endif
+// addnewgaplen( gaplen1jbest[j-1], gaplen1jbestkamo[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jbest[j-1], gaplen2jbestkamo[j-1], gaplen2, lgth2, -1, 0 );
+ copygaplencompactx( gaplen1jbest[j-1], gaplen1jbestkamo[j-1], lgth1, -1, 0, i, i );// *mpjpt, i
+// copygaplenrestricted( gaplen2jbest[j-1], gaplen2jbestkamo[j-1], lgth2, -1, 0, j, j ); // j-1, j
+ copygaplencompactx( gaplen2jbest[j-1], gaplen2jbestkamo[j-1], lgth2, -1, 0, 1, 1 ); // half!
+
+
+
+
+ }
+
+
+// extendgaplenpartly( gaplen1jbest[j-1], gaplen1, i, i ); // tmptmptmp
+// extendgaplenpartly( gaplen2jbest[j-1], gaplen2, 0, 0 ); // tmptmptmp
+
+#if 0
+ sfac = 1.0;
+ for( l=0; gaplen1[i+1]&&(gl=gaplen1[i+1][l].len)!=-1; l++ ) // ososugi! hash ni atode henkou
+ if( gl - 1 == gaplen1[i+1][l].relend ) sfac -= gaplen1[i+1][l].freq;
+ sfac2 = 1.0;
+ for( k=0; gaplen2[j+1]&&(gl=gaplen2[j+1][k].len)!=-1; k++ ) // ososugi! hash ni atode henkou
+ if( gaplen2[j+1][k].relend != -1 ) sfac2 -= gaplen2[j+1][k].freq;
+ sfac *= sfac2;
+#else
+// sfac = 0.0;
+#endif
+
+#if DEBUG
+ reporterr( " (jgap start check i=%d) -> *prept=%f, *mjpt=%f\n", i, seq1[0][i], seq2[0][j], *prept, *mjpt );
+#endif
+
+#if ALGZGAP
+ if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
+#else
+// if( (g=*prept + fpenalty * sfac ) >= *mjpt )
+ if( (g=*prept ) >= *mjpt )
+#endif
+ {
+// *mjpt = g - fpenalty * sfac;
+ *mjpt = g;
+ *mpjpt = i-1;
+#if DEBUG
+ reporterr( "Selected as jgap start!\n" );
+#endif
+
+
+#if FREEFREQUENTLY
+ freegaplenpartly( gaplen1jbestkamo[j-1], i-3, i-2 );
+// freegaplenpartly( gaplen2jbestkamo[j-1], j-3, j-2 );
+#endif
+
+
+// addnewgaplen( gaplen1jbestkamo[j-1], gaplen1jprev[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], gaplen2, lgth2, -1, 0 );
+// reporterr( "copying gaplen1jbestkamo[%d-1] from galpen1jprev, j=%d, i=%d\n", j, j, i );
+ copygaplencompactx( gaplen1jbestkamo[j-1], gaplen1jprev[j-1], lgth1, -1, 0, i, i ); // *mpjpt, i
+// copygaplenrestricted( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], lgth2, -1, 0, j, j ); // j-1, j
+// copygaplencompactx( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], lgth2, -1, 0, j, 1 ); // half!
+// reporterr( "copying gaplen2jbestkamo[%d-1] from galpen2jprev\n", j );
+ copygaplencompactx( gaplen2jbestkamo[j-1], gaplen2jprev[j-1], lgth2-j, -1, 0, 1, 1 ); // ryouhou half!
+
+
+// if( j==2 && i==1 ) exit( 1 );
+
+
+
+ }
+
+// extendgaplenpartly( gaplen1ibestkamo[i-1], gaplen1, 0, 0 ); // tmptmptmp
+// extendgaplenpartly( gaplen2ibestkamo[i-1], gaplen2, j, j ); // tmptmptmp
+
+
+// extendgaplenpartly( gaplen1jbestkamo[j-1], gaplen1, i, i ); // tmptmptmp
+// extendgaplenpartly( gaplen2jbestkamo[j-1], gaplen2, 0, 0 ); // tmptmptmp
+
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if ALGZGAP
+ pfac = 0.0;
+#else
+
+// pfactmp = calcpfac_gapex( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], j, i, i-*mpjpt, seq2[0], seq1[0], 0 ); // j-1
+ pfactmp = calcpfac_gapex_noidatend( gaplen2jbestkamo[j-1], gaplen1jbestkamo[j-1], 1, i, i-*mpjpt, seq2[0]+j, seq1[0], 0 ); // 2jbestkamo->half, 1jbestkamo->full
+#if USEGAPLENMTX
+ pfac = calcpfac_gapex( gaplen2mtx[*mpjpt][j-1], gaplen1mtx[*mpjpt][j-1], j, i, i-*mpjpt, seq2[0], seq1[0], 0 );
+#endif
+#if USEGAPLENHALF
+ pfac = calcpfac_gapex( gaplen2half[*mpjpt][j-1], gaplen1half[*mpjpt][j-1], 1, i-*mpjpt, i-*mpjpt, seq2[0]+j, seq1[0]+*mpjpt, 0 );
+#endif
+#if USEGAPLENMTX || USEGAPLENHALF
+ if( pfac != pfactmp )
+ {
+ reporterr( "(jgapex) pfac=%f, but pfactmp=%f (i,j=%d,%d) diff=%f\n", pfac, pfactmp, i, j, pfac-pfactmp );
+// exit( 1 );
+ PFACERROR = 1;
+ }
+#endif
+ pfac = pfactmp;
+#if DEBUG
+ reporterr( "%c-%c, jgap extension check (j=%d), pfac = %f\n", seq1[0][i], '=', j, pfac );
+#endif
+#endif
+ m[j] += fpenalty * pfac;
+
+
+
+ if( trywarp )
+ {
+#if USE_PENALTY_EX
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
+#else
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
+#endif
+ {
+// fprintf( stderr, "WARP!!\n" );
+ if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
+ {
+ *ijppt = warpbase + warpn - 1;
+ }
+ else
+ {
+ *ijppt = warpbase + warpn;
+ warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
+ warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
+ warpis[warpn] = prevwarpi[j-1];
+ warpjs[warpn] = prevwarpj[j-1];
+ warpn++;
+ }
+ wm = g;
+ }
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ curm = *curpt + wm;
+
+ if( *wmrecords1pt > *wmrecordspt )
+ {
+ *wmrecordspt = *wmrecords1pt;
+ *warpipt = *(warpipt-1);
+ *warpjpt = *(warpjpt-1);
+ }
+ if( curm > *wmrecordspt )
+ {
+ *wmrecordspt = curm;
+ *warpipt = i;
+ *warpjpt = j;
+ }
+ wmrecordspt++;
+ wmrecords1pt++;
+ warpipt++;
+ warpjpt++;
+ }
+
+#if DEBUG
+ reporterr( "extention-x 1j???, before extention-x, j=%d\n", j );
+ showgaplen( gaplen1jcurr[j], 100 );
+#endif
+ extendgaplencompactx( gaplen1jcurr[j], gaplen1, i );
+
+#if DEBUG
+ reporterr( "after extention-x\n" );
+ showgaplen( gaplen1jcurr[j], 100 );
+ reporterr( "extention-x 2j???\n" );
+#endif
+ extendgaplencompactx( gaplen2jcurr[j], gaplen2+j, 0 );
+
+
+#if 1
+ if( *ijppt < 0 )
+ {
+#if DEBUG
+ reporterr( "Path: %d-%d->%d-%d, i=%d (%c), j=%d (%c), *ijppt=%d\n", i, j, i-1, j+*ijppt, i, seq1[0][i], j, seq2[0][j], *ijppt );
+ reporterr( "Inserting %d gaps to gaplen1 and copying gaplen2 (%c%d-%c%d)\n", -*ijppt-1, seq1[0][i], i, seq2[0][j], j );
+#endif
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[i][j], gaplen1mtx[i-1][j+*ijppt], gaplen1, lgth1, i, -*ijppt-1 );
+// addnewgaplen( gaplen2mtx[i][j], gaplen2mtx[i-1][j+*ijppt], gaplen2, lgth2, -1, 0 );
+ copygaplenrestricted( gaplen1mtx[i][j], gaplen1mtx[i-1][j+*ijppt], lgth1, i, -*ijppt-1, i, i ); // 0, lgth1
+ copygaplenrestricted( gaplen2mtx[i][j], gaplen2mtx[i-1][j+*ijppt], lgth2, -1, 0, j, j ); // 0, lgth2
+#endif
+#if USEGAPLENHALF
+ copygaplenrestricted_zurasu( gaplen1half[i][j], gaplen1half[i-1][j+*ijppt], lgth1, 0, -*ijppt-1, 0, 0, 1, 1 ); // 0, lgth1
+ copygaplenrestricted_zurasu( gaplen2half[i][j], gaplen2half[i-1][j+*ijppt], lgth2, -1, 0, 0, 0, -*ijppt, -*ijppt ); // 0, lgth2
+#endif
+// addnewgaplen( gaplen1jcurr[j], gaplen1jprev[j+*ijppt], gaplen1, lgth1, i, -*ijppt-1 );
+// addnewgaplen( gaplen2jcurr[j], gaplen2jprev[j+*ijppt], gaplen2, lgth2, -1, 0 );
+// reporterr( "copying gaplen1jcurr from gaplen1jbest, with a %d insertion\n", -*ijppt-1 );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1jprev[j+*ijppt], lgth1, i, -*ijppt-1, i, i ); // scope: i+*ijppt+1, i ?
+// reporterr( "copy end\n" );
+// copygaplenrestricted( gaplen2jcurr[j], gaplen2jprev[j+*ijppt], lgth2, -1, 0, j, j );
+ copygaplencompactx( gaplen2jcurr[j], gaplen2jprev[j+*ijppt], lgth2, -1, 0, 0, -*ijppt ); // half! ryouho zureteru
+ }
+ else if( *ijppt > 0 )
+ {
+#if DEBUG
+ reporterr( "Path: %d-%d->%d-%d, i=%d (%c), j=%d (%c), *ijppt=%d\n", i, j, i-*ijppt, j-1, i, seq1[0][i], j, seq2[0][j], *ijppt );
+ reporterr( "Copying gaplen1 inserting %d gaps to gaplen2 (%c%d-%c%d)\n", *ijppt-1, seq1[0][i], i, seq2[0][j], j );
+#endif
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[i][j], gaplen1mtx[i-*ijppt][j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2mtx[i][j], gaplen2mtx[i-*ijppt][j-1], gaplen2, lgth2, j, *ijppt-1 );
+ copygaplenrestricted( gaplen1mtx[i][j], gaplen1mtx[i-*ijppt][j-1], lgth1, -1, 0, i, i ); // 0, lgth1
+ copygaplenrestricted( gaplen2mtx[i][j], gaplen2mtx[i-*ijppt][j-1], lgth2, j, *ijppt-1, j, j ); // 0, lgth2
+#endif
+#if USEGAPLENHALF
+ copygaplenrestricted_zurasu( gaplen1half[i][j], gaplen1half[i-*ijppt][j-1], lgth1, -1, 0, 0, 0, *ijppt, *ijppt ); // 0, lgth1
+ copygaplenrestricted_zurasu( gaplen2half[i][j], gaplen2half[i-*ijppt][j-1], lgth2, 0, *ijppt-1, 0, 0, 1, 1 ); // 0, lgth2
+#endif
+// addnewgaplen( gaplen1jcurr[j], gaplen1jbest[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jcurr[j], gaplen2jbest[j-1], gaplen2, lgth2, j, *ijppt-1 );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1jbest[j-1], lgth1, -1, 0, i, i );
+// copygaplenrestricted( gaplen2jcurr[j], gaplen2jbest[j-1], lgth2, j, *ijppt-1, j, j ); // j-*ijppt+1?
+// copygaplenrestricted_zurasu( gaplen2jcurr[j], gaplen2jbest[j-1], lgth2, 0, *ijppt-1, 0, 0, j, j ); // 2jcurr->half, but 2jbest->full, imanotokoro
+ copygaplencompactx( gaplen2jcurr[j], gaplen2jbest[j-1], lgth2, 0, *ijppt-1, 0, 1 ); //ryouhou half
+
+ }
+ else
+#endif
+ {
+#if DEBUG
+ reporterr( "Path: %d-%d->%d-%d, i=%d (%c), j=%d (%c), *ijppt=%d\n", i, j, i-1, j-1, i, seq1[0][i], j, seq2[0][j], *ijppt );
+ reporterr( "Copying gaplen1 and gaplen2 (%c%d-%c%d)\n", seq1[0][i], i, seq2[0][j], j );
+#endif
+#if USEGAPLENMTX
+// addnewgaplen( gaplen1mtx[i][j], gaplen1mtx[i-1][j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2mtx[i][j], gaplen2mtx[i-1][j-1], gaplen2, lgth2, -1, 0 );
+ copygaplenrestricted( gaplen1mtx[i][j], gaplen1mtx[i-1][j-1], lgth1, -1, 0, i, i ); // 0, lgth1
+ copygaplenrestricted( gaplen2mtx[i][j], gaplen2mtx[i-1][j-1], lgth2, -1, 0, j, j ); // 0, lgth2
+#endif
+#if USEGAPLENHALF
+ copygaplenrestricted_zurasu( gaplen1half[i][j], gaplen1half[i-1][j-1], lgth1, -1, 0, 0, 0, 1, 1 ); // 0, lgth1
+ copygaplenrestricted_zurasu( gaplen2half[i][j], gaplen2half[i-1][j-1], lgth2, -1, 0, 0, 0, 1, 1 ); // 0, lgth2
+#endif
+// addnewgaplen( gaplen1jcurr[j], gaplen1jprev[j-1], gaplen1, lgth1, -1, 0 );
+// addnewgaplen( gaplen2jcurr[j], gaplen2jprev[j-1], gaplen2, lgth2, -1, 0 );
+ copygaplencompactx( gaplen1jcurr[j], gaplen1jprev[j-1], lgth1, -1, 0, i, i );
+// copygaplenrestricted( gaplen2jcurr[j], gaplen2jprev[j-1], lgth2, -1, 0, j, j );
+ copygaplencompactx( gaplen2jcurr[j], gaplen2jprev[j-1], lgth2, -1, 0, 0, 1 ); // half
+ }
+
+#if DEBUG
+ reporterr( "at the end of j loop, gaplen1jcurr[%d] = \n", j );
+ showgaplen( gaplen1jcurr[j], 100 );
+ reporterr( "at the end of j loop, gaplen1prev[%d] = \n", j );
+ showgaplen( gaplen1jprev[j], 100 );
+#endif
+
+
+
+#if 1
+ freegaplenpartly( gaplen1jcurr[j-1], i-3, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // half!
+ freegaplenpartly( gaplen1jbestkamo[j-1], i-3, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbestkamo[j-1], j-3, j-2 ); // -1 dehanaku -2??
+ freegaplenpartly( gaplen1jbest[j-1], i-3, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbest[j-1], j-3, j-2 ); // -1 dehanaku -2??
+#else
+ freegaplenpartly( gaplen1jprev[j-1], 0, i-2 ); // -1 dehanaku -2??
+ freegaplenpartly( gaplen1jcurr[j-1], 0, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jcurr[j-1], j-3, j-2 ); // half!
+ freegaplenpartly( gaplen1jbestkamo[j-1], 0, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbestkamo[j-1], j-3, j-2 ); // -1 dehanaku -2??
+ freegaplenpartly( gaplen1jbest[j-1], 0, i-2 ); // -1 dehanaku -2??
+// freegaplenpartly( gaplen2jbest[j-1], j-3, j-2 ); // -1 dehanaku -2??
+#endif
+
+
+#if USEGAPLENMTX
+// freegaplenpartly( gaplen1mtx[i-1][j-1], 0, i-2 );
+// freegaplenpartly( gaplen2mtx[i-1][j-1], 0, j-2 );
+#endif
+
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if 1
+// freegaplenpartly( gaplen1icurr[i-1], i-1, i-1 );
+ freegaplenpartly( gaplen1icurr[i-1], 0, lgth1-i );
+ freegaplenpartly( gaplen2icurr[i-1], 0, lgth2 );
+// freegaplenpartly( gaplen1ibestkamo[i-1], i-1, i-1 );
+ freegaplenpartly( gaplen1ibestkamo[i-1], 0, lgth1-i );
+ freegaplenpartly( gaplen2ibestkamo[i-1], 0, lgth2 );
+#endif
+
+ if( trywarp )
+ {
+ fltncpy( prevwmrecords, wmrecords, lastj );
+ intncpy( prevwarpi, warpi, lastj );
+ intncpy( prevwarpj, warpj, lastj );
+ }
+#if 0
+ fprintf( stderr, "i=%d, %15.5f \n", i, wm );
+#endif
+//if( i == 2 ) exit( 1 );
+ }
+
+ if( trywarp )
+ {
+// fprintf( stderr, "wm = %f\n", wm );
+// fprintf( stderr, "warpn = %d\n", warpn );
+ free( wmrecords );
+ free( prevwmrecords );
+ free( warpi );
+ free( warpj );
+ free( prevwarpi );
+ free( prevwarpj );
+ }
+
+
+#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, ijp, icyc, jcyc, warpis, warpjs, warpbase );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase );
+
+ if( warpis ) free( warpis );
+ if( warpjs ) free( warpjs );
+
+// 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] );
+#if 0
+ 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] );
+#endif
+
+// reporterr( "clearing\n" );
+ cleargaplens( gaplens );
+ if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
+ if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+
+#if USEGAPLENMTX
+/* maikai free */
+ reporterr( "Freeing!\n" );
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen1mtx[i][j] ) FreeGaplenMtx( gaplen1mtx[i][j], 0 );
+ gaplen1mtx[i][j] = NULL;
+ }
+ free( gaplen1mtx[i] );
+ gaplen1mtx[i] = NULL;
+ }
+ free( gaplen1mtx );
+ gaplen1mtx = NULL;
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen2mtx[i][j] ) FreeGaplenMtx( gaplen2mtx[i][j], 0 );
+ gaplen2mtx[i][j] = NULL;
+ }
+ free( gaplen2mtx[i] );
+ gaplen2mtx[i] = NULL;
+ }
+ free( gaplen2mtx );
+ gaplen2mtx = NULL;
+#endif
+
+
+#if USEGAPLENHALF
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen1half[i][j] ) FreeGaplenMtx( gaplen1half[i][j], 0 );
+ gaplen1half[i][j] = NULL;
+ }
+ free( gaplen1half[i] );
+ gaplen1half[i] = NULL;
+ }
+ free( gaplen1half );
+ gaplen1half = NULL;
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ for( j=0; j<lgth2+1; j++ )
+ {
+ if( gaplen2half[i][j] ) FreeGaplenMtx( gaplen2half[i][j], 0 );
+ gaplen2half[i][j] = NULL;
+ }
+ free( gaplen2half[i] );
+ gaplen2half[i] = NULL;
+ }
+ free( gaplen2half );
+ gaplen2half = NULL;
+#endif
+/* maikai free */
+
+
+#if WMCHECK
+ fprintf( stderr, "wm = %f\n", wm - *impmatch);
+ fprintf( stderr, "*impmatch = %f\n", *impmatch);
+
+ int kenzan = 0;
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ kenzan += pairgapcount( mseq1[i], mseq2[j] );
+ }
+
+
+ reporterr( "kenzan = %d -> %f\n", kenzan, (double)kenzan /( icyc*jcyc ) );
+
+ double pairscore, nogappairscore, diff;
+ char **pseq;
+ pseq = AllocateCharMtx( 2, strlen( seq1[0] ) + 1 );
+ pairscore = nogappairscore = 0.0;
+#if 1
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ strcpy( pseq[0], seq1[i] );
+ strcpy( pseq[1], seq2[j] );
+ commongappick( 2, pseq );
+ c = which[i][j];
+ pairscore += eff1[i] * eff2[j] * naivepairscore11_dynmtx( matrices[c], pseq[0], pseq[1], penalty );
+ nogappairscore += eff1[i] * eff2[j] * naivepairscore11_dynmtx( matrices[c], pseq[0], pseq[1], 0 );
+ }
+#else
+ for( c=0; c<maxdistclass; c++ )
+ {
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ strcpy( pseq[0], seq1[i] );
+ strcpy( pseq[1], seq2[j] );
+ commongappick( 2, pseq );
+ pairscore += eff1s[c][i] * eff2s[c][j] * naivepairscore11_dynmtx( matrices[c], pseq[0], pseq[1], penalty );
+ nogappairscore += eff1s[c][i] * eff2s[c][j] * naivepairscore11_dynmtx( matrices[c], pseq[0], pseq[1], 0 );
+ }
+ }
+#endif
+
+ FreeCharMtx( pseq );
+ diff = (pairscore - wm + *impmatch ) / (double)strlen( seq1[0] );
+ reporterr( "pairscore = %f\n", (double)pairscore );
+ reporterr( "pairscore-nogappairscore = %f\n", (double)(pairscore-nogappairscore) );
+ reporterr( "pairscore-nogappairscore / penalty = %f\n", (double)(pairscore-nogappairscore)/(double)(fpenalty) );
+ reporterr( "diff = %f\n\n", diff );
+
+#if 1
+ if( ( !trywarp && fabs( diff ) > 0.01 ) || PFACERROR )
+// if( abs( pairscore - wm +*impmatch ) > 0.01 )
+#else
+ if( abs( pairscore - wm +*impmatch ) > 0.01 )
+#endif
+// if( abs( pairscore - wm +*impmatch ) > 0.01 )
+ {
+ for( i=0; i<icyc; i++ )
+ printf( ">group1\n%s\n", seq1[i] );
+ for( j=0; j<jcyc; j++ )
+ printf( ">group2\n%s\n", seq2[j] );
+ exit( 1 );
+ }
+#else
+ reporterr( "\n" );
+#endif
+
+#if 0
+// if( strlen( seq1[0] ) - lgth1 > 100 && icyc > 1 || strlen( seq2[0] ) - lgth2 > 100 & jcyc > 1 )
+ if( strstr( seq1[0], "LNDDAT" ) && icyc == 1 || strstr( seq2[0], "LNDDAT" ) && jcyc==1)
+ {
+ for( i=0; i<icyc; i++ )
+ printf( ">group1\n%s\n", seq1[i] );
+ for( j=0; j<jcyc; j++ )
+ printf( ">group2\n%s\n", seq2[j] );
+ exit( 1 );
+ }
+#endif
+
+
+ return( wm );
+}
git://source.jalview.org / jabaws.git / blobdiff