X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2FpartSalignmm.c.comment;fp=binaries%2Fsrc%2Fmafft%2Fcore%2FpartSalignmm.c.comment;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=b4d200b1f2932dcd0315b9b8b1ad6c4ec7d684cb;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git

diff --git a/binaries/src/mafft/core/partSalignmm.c.comment b/binaries/src/mafft/core/partSalignmm.c.comment
deleted file mode 100644
index b4d200b..0000000
--- a/binaries/src/mafft/core/partSalignmm.c.comment
+++ /dev/null
@@ -1,1070 +0,0 @@
-#include "mltaln.h"
-#include "dp.h"
-
-#define MACHIGAI 0
-#define OUTGAP0TRY 1
-#define DEBUG 0
-#define XXXXXXX    0
-#define USE_PENALTY_EX  0
-
-static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
-{
-	int i, j, gc, gb; 
-	float feff;
-	
-	for( i=0; i<len; i++ ) ogcp[i] = 0.0;
-	for( j=0; j<clus; j++ ) 
-	{
-		feff = (float)eff[j];
-		gc = 0;
-		for( i=0; i<len; i++ ) 
-		{
-			gb = gc;
-			gc = ( seq[j][i] == '-' );
-			{
-				if( !gb *  gc ) ogcp[i] += feff;
-			}
-		}
-	}
-}
-
-static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
-{
-	int i, j, gc, gb; 
-	float feff;
-	
-	for( i=0; i<len; i++ ) fgcp[i] = 0.0;
-	for( j=0; j<clus; j++ ) 
-	{
-		feff = (float)eff[j];
-		gc = ( seq[j][0] == '-' );
-		for( i=1; i<len+1; i++ ) 
-		{
-			gb = gc;
-			gc = ( seq[j][i] == '-' );
-			{
-				if( gb * !gc ) fgcp[i-1] += feff;
-			}
-		}
-	}
-}
-
-
-			
-		
-
-static int impalloclen = 0;
-static float **impmtx = NULL;
-float part_imp_match_out_sc( int i1, int j1 )
-{
-//	fprintf( stderr, "impalloclen = %d\n", impalloclen );
-//	fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
-	return( impmtx[i1][j1] );
-#if 0
-	if( i1 == l1 || j1 == l2 ) return( 0.0 );
-	return( impmtx[i1+start1][j1+start2] );
-#endif
-}
-static void part_imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
-{
-	int j;
-	for( j=0; j<lgth2; j++ )
-	{
-		imp[j] += impmtx[i1][start2+gapmap2[j]];
-	}
-}
-
-void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
-{
-	int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
-	double effij, effijx; 
-	char *pt, *pt1, *pt2;
-	int allgap;
-	LocalHom *tmpptr;
-
-	if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
-	{
-		if( impmtx ) FreeFloatMtx( impmtx );
-		impalloclen = MAX( lgth1, lgth2 ) + 2;
-		impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
-	}
-
-
-#if 0
-	fprintf( stderr, "eff1 in _init_strict = \n" );
-	for( i=0; i<clus1; i++ )
-		fprintf( stderr, "eff1[] = %f\n", eff1[i] );
-	for( i=0; i<clus2; i++ )
-		fprintf( stderr, "eff2[] = %f\n", eff2[i] );
-#endif
-
-	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
-		impmtx[i][j] = 0.0;
-	effijx = 1.0 * fastathreshold;
-	for( i=0; i<clus1; i++ )
-	{
-		for( j=0; j<clus2; j++ )
-		{
-			effij = eff1[i] * eff2[j] * effijx;
-			tmpptr = localhom[i][j];
-			while( tmpptr )
-			{
-//				fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
-//				fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
-//				fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
-//				fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
-				pt = seq1[i];
-				tmpint = -1;
-				while( *pt != 0 )
-				{
-					if( *pt++ != '-' ) tmpint++;
-					if( tmpint == tmpptr->start1 ) break;
-				}
-				start1 = (int)( pt - seq1[i] ) - 1;
-	
-				if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
-				else
-				{
-#if MACHIGAI
-					while( *pt != 0 )
-					{
-						if( tmpint == tmpptr->end1 ) break;
-						if( *pt++ != '-' ) tmpint++;
-					}
-					end1 = (int)( pt - seq1[i] ) - 1;
-#else
-					while( *pt != 0 )
-					{
-//						fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
-						if( *pt++ != '-' ) tmpint++;
-						if( tmpint == tmpptr->end1 ) break;
-					}
-					end1 = (int)( pt - seq1[i] ) - 1;
-#endif
-				}
-	
-				pt = seq2[j];
-				tmpint = -1;
-				while( *pt != 0 )
-				{
-					if( *pt++ != '-' ) tmpint++;
-					if( tmpint == tmpptr->start2 ) break;
-				}
-				start2 = (int)( pt - seq2[j] ) - 1;
-				if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
-				else
-				{
-#if MACHIGAI
-					while( *pt != 0 )
-					{
-						if( tmpint == tmpptr->end2 ) break;
-						if( *pt++ != '-' ) tmpint++;
-					}
-					end2 = (int)( pt - seq2[j] ) - 1;
-#else
-					while( *pt != 0 )
-					{
-						if( *pt++ != '-' ) tmpint++;
-						if( tmpint == tmpptr->end2 ) break;
-					}
-					end2 = (int)( pt - seq2[j] ) - 1;
-#endif
-				}
-//				fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
-//				fprintf( stderr, "step 0\n" );
-				if( end1 - start1 != end2 - start2 )
-				{
-//					fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
-				}
-
-				k1 = start1; k2 = start2;
-				pt1 = seq1[i] + k1;
-				pt2 = seq2[j] + k2;
-				while( *pt1 && *pt2 )
-				{
-					if( *pt1 != '-' && *pt2 != '-' )
-					{
-// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
-//						impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
-//						impmtx[k1][k2] += tmpptr->importance * effij;
-						impmtx[k1][k2] += tmpptr->fimportance * effij;
-//						fprintf( stderr, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
-//						fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
-						k1++; k2++;
-						pt1++; pt2++;
-					}
-					else if( *pt1 != '-' && *pt2 == '-' )
-					{
-//						fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
-						k2++; pt2++;
-					}
-					else if( *pt1 == '-' && *pt2 != '-' )
-					{
-//						fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
-						k1++; pt1++;
-					}
-					else if( *pt1 == '-' && *pt2 == '-' )
-					{
-//						fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
-						k1++; pt1++;
-						k2++; pt2++;
-					}
-					if( k1 > end1 || k2 > end2 ) break;
-				}
-				tmpptr = tmpptr->next;
-			}
-		}
-	}
-#if 1
-	0printf( stderr, "impmtx = \n" );
-	for( k2=0; k2<lgth2; k2++ )
-		fprintf( stderr, "%6.3f ", (double)k2 );
-	fprintf( stderr, "\n" );
-	for( k1=0; k1<lgth1; k1++ )
-	{
-		fprintf( stderr, "%d", k1 );
-		for( k2=0; k2<lgth2; k2++ )
-			fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
-		fprintf( stderr, "\n" );
-	}
-	exit( 1 );
-#endif
-}
-
-void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
-{
-	int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
-	static int impalloclen = 0;
-	char *pt;
-	int allgap;
-	static char *nocount1 = NULL;
-	static char *nocount2 = NULL;
-
-	if( impalloclen < lgth1 || impalloclen < lgth2 )
-	{
-		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 );
-		impalloclen -= 2;
-	}
-
-	for( i=0; i<lgth1; i++ )
-	{
-		for( j=0; j<clus1; j++ )
-			if( seq1[j][i] == '-' ) break;
-		if( j != clus1 ) nocount1[i] = 1; 
-		else			 nocount1[i] = 0;
-	}
-	for( i=0; i<lgth2; i++ )
-	{
-		for( j=0; j<clus2; j++ )
-			if( seq2[j][i] == '-' ) break;
-		if( j != clus2 ) nocount2[i] = 1;
-		else			 nocount2[i] = 0;
-	}
-
-#if 0
-fprintf( stderr, "nocount2 =\n" );
-for( i = 0; i<impalloclen; i++ )
-{
-	fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
-}
-#endif
-
-	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
-		impmtx[i][j] = 0.0;
-	for( i=0; i<clus1; i++ )
-	{
-		fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
-		for( j=0; j<clus2; j++ )
-		{
-			fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
-			fprintf( stderr, "end1   = %d\n", localhom[i][j]->end1   );
-			fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
-			pt = seq1[i];
-			tmpint = -1;
-			while( *pt != 0 )
-			{
-				if( *pt++ != '-' ) tmpint++;
-				if( tmpint == localhom[i][j]->start1 ) break;
-			}
-			start1 = pt - seq1[i] - 1;
-
-			while( *pt != 0 )
-			{
-//				fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
-				if( *pt++ != '-' ) tmpint++;
-				if( tmpint == localhom[i][j]->end1 ) break;
-			}
-			end1 = pt - seq1[i] - 1;
-
-			pt = seq2[j];
-			tmpint = -1;
-			while( *pt != 0 )
-			{
-				if( *pt++ != '-' ) tmpint++;
-				if( tmpint == localhom[i][j]->start2 ) break;
-			}
-			start2 = pt - seq2[j] - 1;
-			while( *pt != 0 )
-			{
-				if( *pt++ != '-' ) tmpint++;
-				if( tmpint == localhom[i][j]->end2 ) break;
-			}
-			end2 = pt - seq2[j] - 1;
-//			fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
-			k1 = start1;
-			k2 = start2;
-			fprintf( stderr, "step 0\n" );
-			while( k1 <= end1 && k2 <= end2 )
-			{
-#if 0
-				if( !nocount1[k1] && !nocount2[k2] )
-					impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
-				k1++; k2++;
-#else
-				if( !nocount1[k1] && !nocount2[k2] )
-					impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
-				k1++; k2++;
-#endif
-			}
-
-			dif = ( end1 - start1 ) - ( end2 - start2 );
-			fprintf( stderr, "dif = %d\n", dif );
-			if( dif > 0 )
-			{
-				do
-				{
-					fprintf( stderr, "dif = %d\n", dif );
-					k1 = start1;
-					k2 = start2 - dif;
-					while( k1 <= end1 && k2 <= end2 )
-					{
-						if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
-							impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
-						k1++; k2++;
-					}
-				}
-				while( dif-- );
-			}
-			else
-			{
-				do
-				{
-					k1 = start1 + dif;
-					k2 = start2;
-					while( k1 <= end1 )
-					{
-						if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
-							impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
-						k1++; k2++;
-					}
-				}
-				while( dif++ );
-			}
-		}
-	}
-#if 1
-	fprintf( stderr, "impmtx = \n" );
-	for( k2=0; k2<lgth2; k2++ )
-		fprintf( stderr, "%6.3f ", (double)k2 );
-	fprintf( stderr, "\n" );
-	for( k1=0; k1<lgth1; k1++ )
-	{
-		fprintf( stderr, "%d", k1 );
-		for( k2=0; k2<lgth2; k2++ )
-			fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
-		fprintf( stderr, "\n" );
-	}
-	exit( 1 );
-#endif
-}
-
-static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
-{
-	int j, k, l;
-	float scarr[26];
-	float **cpmxpd = floatwork;
-	int **cpmxpdn = intwork;
-	int count = 0;
-
-	if( initialize )
-	{
-		for( j=0; j<lgth2; j++ )
-		{
-			count = 0;
-			for( l=0; l<26; l++ )
-			{
-				if( cpmx2[l][j] )
-				{
-					cpmxpd[count][j] = cpmx2[l][j];
-					cpmxpdn[count][j] = l;
-					count++;
-				}
-			}
-			cpmxpdn[count][j] = -1;
-		}
-	}
-
-	for( l=0; l<26; l++ )
-	{
-		scarr[l] = 0.0;
-		for( k=0; k<26; k++ )
-			scarr[l] += n_dis[k][l] * cpmx1[k][i1];
-	}
-#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤­¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
-	{
-		float *fpt, **fptpt, *fpt2;
-		int *ipt, **iptpt;
-		fpt2 = match;
-		iptpt = cpmxpdn;
-		fptpt = cpmxpd;
-		while( lgth2-- )
-		{
-			*fpt2 = 0.0;
-			ipt=*iptpt,fpt=*fptpt;
-			while( *ipt > -1 )
-				*fpt2 += scarr[*ipt++] * *fpt++;
-			fpt2++,iptpt++,fptpt++;
-		} 
-	}
-#else
-	for( j=0; j<lgth2; j++ )
-	{
-		match[j] = 0.0;
-		for( k=0; cpmxpdn[k][j]>-1; k++ )
-			match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
-	} 
-#endif
-}
-
-static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw, 
-						char **seq1, char **seq2, 
-                        char **mseq1, char **mseq2, 
-                        float **cpmx1, float **cpmx2, 
-                        short **ijp, int icyc, int jcyc,
-						int start1, int end1, int start2, int end2,
-						int *gapmap1, int *gapmap2 )
-{
-	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
-	char gap[] = "-";
-	float wm;
-	lgth1 = strlen( seq1[0] );
-	lgth2 = strlen( seq2[0] );
-
-#if 0
-	for( i=0; i<lgth1; i++ ) 
-	{
-		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
-	}
-#endif
- 
-	if( outgap == 1 )
-		;
-	else
-	{
-		wm = lastverticalw[0];
-		for( i=0; i<lgth1; i++ )
-		{
-			if( lastverticalw[i] >= wm )
-			{
-				wm = lastverticalw[i];
-				iin = i; jin = lgth2-1;
-				ijp[lgth1][lgth2] = +( lgth1 - i );
-			}
-		}
-		for( j=0; j<lgth2; j++ )
-		{
-			if( lasthorizontalw[j] >= wm )
-			{
-				wm = lasthorizontalw[j];
-				iin = lgth1-1; jin = j;
-				ijp[lgth1][lgth2] = -( lgth2 - j );
-			}
-		}
-	}
-
-    for( i=0; i<lgth1+1; i++ ) 
-    {
-        ijp[i][0] = i + 1;
-    }
-    for( j=0; j<lgth2+1; j++ ) 
-    {
-        ijp[0][j] = -( j + 1 );
-    }
-
-	for( i=0; i<icyc; i++ )
-	{
-		mseq1[i] += lgth1+lgth2;
-		*mseq1[i] = 0;
-	}
-	for( j=0; j<jcyc; j++ )
-	{
-		mseq2[j] += lgth1+lgth2;
-		*mseq2[j] = 0;
-	}
-	iin = lgth1; jin = lgth2;
-	*impwmpt = 0.0;
-	for( k=0; k<=lgth1+lgth2; k++ ) 
-	{
-		if( ijp[iin][jin] < 0 ) 
-		{
-			ifi = iin-1; jfi = jin+ijp[iin][jin];
-		}
-		else if( ijp[iin][jin] > 0 )
-		{
-			ifi = iin-ijp[iin][jin]; jfi = jin-1;
-		}
-		else
-		{
-			ifi = iin-1; jfi = jin-1;
-		}
-		l = iin - ifi;
-		while( --l ) 
-		{
-			for( i=0; i<icyc; i++ )
-				*--mseq1[i] = seq1[i][ifi+l];
-			for( j=0; j<jcyc; j++ ) 
-				*--mseq2[j] = *gap;
-			k++;
-		}
-		l= jin - jfi;
-		while( --l )
-		{
-			for( i=0; i<icyc; i++ ) 
-				*--mseq1[i] = *gap;
-			for( j=0; j<jcyc; j++ ) 
-				*--mseq2[j] = seq2[j][jfi+l];
-			k++;
-		}
-		if( iin != lgth1 && jin != lgth2 ) // ??
-		{
-			*impwmpt += part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
-//			fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
-		}
-		if( iin <= 0 || jin <= 0 ) break;
-		for( i=0; i<icyc; i++ ) 
-			*--mseq1[i] = seq1[i][ifi];
-		for( j=0; j<jcyc; j++ ) 
-			*--mseq2[j] = seq2[j][jfi];
-		k++;
-		iin = ifi; jin = jfi;
-	}
-}
-static float Atracking( float *lasthorizontalw, float *lastverticalw, 
-						char **seq1, char **seq2, 
-                        char **mseq1, char **mseq2, 
-                        float **cpmx1, float **cpmx2, 
-                        short **ijp, int icyc, int jcyc )
-{
-	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk;
-	char gap[] = "-";
-	float wm = 0.0;
-	lgth1 = strlen( seq1[0] );
-	lgth2 = strlen( seq2[0] );
-
-#if 0
-	for( i=0; i<lgth1; i++ ) 
-	{
-		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
-	}
-#endif
- 
-	if( outgap == 1 )
-		;
-	else
-	{
-		wm = lastverticalw[0];
-		for( i=0; i<lgth1; i++ )
-		{
-			if( lastverticalw[i] >= wm )
-			{
-				wm = lastverticalw[i];
-				iin = i; jin = lgth2-1;
-				ijp[lgth1][lgth2] = +( lgth1 - i );
-			}
-		}
-		for( j=0; j<lgth2; j++ )
-		{
-			if( lasthorizontalw[j] >= wm )
-			{
-				wm = lasthorizontalw[j];
-				iin = lgth1-1; jin = j;
-				ijp[lgth1][lgth2] = -( lgth2 - j );
-			}
-		}
-	}
-
-    for( i=0; i<lgth1+1; i++ ) 
-    {
-        ijp[i][0] = i + 1;
-    }
-    for( j=0; j<lgth2+1; j++ ) 
-    {
-        ijp[0][j] = -( j + 1 );
-    }
-
-	for( i=0; i<icyc; i++ )
-	{
-		mseq1[i] += lgth1+lgth2;
-		*mseq1[i] = 0;
-	}
-	for( j=0; j<jcyc; j++ )
-	{
-		mseq2[j] += lgth1+lgth2;
-		*mseq2[j] = 0;
-	}
-	iin = lgth1; jin = lgth2;
-	lastk = lgth1+lgth2;
-	for( k=0; k<=lastk; k++ ) 
-	{
-		if( ijp[iin][jin] < 0 ) 
-		{
-			ifi = iin-1; jfi = jin+ijp[iin][jin];
-		}
-		else if( ijp[iin][jin] > 0 )
-		{
-			ifi = iin-ijp[iin][jin]; jfi = jin-1;
-		}
-		else
-		{
-			ifi = iin-1; jfi = jin-1;
-		}
-		l = iin - ifi;
-		while( --l ) 
-		{
-			for( i=0; i<icyc; i++ )
-				*--mseq1[i] = seq1[i][ifi+l];
-			for( j=0; j<jcyc; j++ ) 
-				*--mseq2[j] = *gap;
-			k++;
-		}
-		l= jin - jfi;
-		while( --l )
-		{
-			for( i=0; i<icyc; i++ ) 
-				*--mseq1[i] = *gap;
-			for( j=0; j<jcyc; j++ ) 
-				*--mseq2[j] = seq2[j][jfi+l];
-			k++;
-		}
-		if( iin <= 0 || jin <= 0 ) break;
-		for( i=0; i<icyc; i++ ) 
-			*--mseq1[i] = seq1[i][ifi];
-		for( j=0; j<jcyc; j++ ) 
-			*--mseq2[j] = seq2[j][jfi];
-		k++;
-		iin = ifi; jin = jfi;
-	}
-	return( 0.0 );
-}
-
-float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2 )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-//	int k;
-	register int i, j;
-	int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
-	int lgth1, lgth2;
-	int resultlen;
-	float wm = 0.0;   /* int ?????? */
-	float g;
-	float *currentw, *previousw;
-#if 1
-	float *wtmp;
-	short *ijppt;
-	float *mjpt, *prept, *curpt;
-	int *mpjpt;
-#endif
-	static float mi, *m;
-	static short **ijp;
-	static int mpi, *mp;
-	static float *w1, *w2;
-	static float *match;
-	static float *initverticalw;    /* kufuu sureba iranai */
-	static float *lastverticalw;    /* kufuu sureba iranai */
-	static char **mseq1;
-	static char **mseq2;
-	static char **mseq;
-	static float *ogcp1;
-	static float *ogcp2;
-	static float *fgcp1;
-	static float *fgcp2;
-	static float **cpmx1;
-	static float **cpmx2;
-	static int **intwork;
-	static float **floatwork;
-	static int orlgth1 = 0, orlgth2 = 0;
-	float fpenalty = (float)penalty;
-	float fpenalty_ex = (float)penalty_ex;
-	float *fgcp2pt;
-	float *ogcp2pt;
-	float fgcp1va;
-	float ogcp1va;
-
-
-
-#if 0
-	fprintf( stderr, "eff in SA+++align\n" );
-	for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
-#endif
-	if( orlgth1 == 0 )
-	{
-		mseq1 = AllocateCharMtx( njob, 0 );
-		mseq2 = AllocateCharMtx( njob, 0 );
-	}
-
-
-	lgth1 = strlen( seq1[0] );
-	lgth2 = strlen( seq2[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 );
-
-			FreeFloatVec( ogcp1 );
-			FreeFloatVec( ogcp2 );
-			FreeFloatVec( fgcp1 );
-			FreeFloatVec( fgcp2 );
-
-
-			FreeFloatMtx( cpmx1 );
-			FreeFloatMtx( cpmx2 );
-
-			FreeFloatMtx( floatwork );
-			FreeIntMtx( intwork );
-		}
-
-		ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
-		ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
-
-#if DEBUG
-		fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
-#endif
-
-		w1 = AllocateFloatVec( ll2+2 );
-		w2 = AllocateFloatVec( ll2+2 );
-		match = AllocateFloatVec( ll2+2 );
-
-		initverticalw = AllocateFloatVec( ll1+2 );
-		lastverticalw = AllocateFloatVec( ll1+2 );
-
-		m = AllocateFloatVec( ll2+2 );
-		mp = AllocateIntVec( ll2+2 );
-
-		mseq = AllocateCharMtx( njob, ll1+ll2 );
-
-		ogcp1 = AllocateFloatVec( ll1+2 );
-		ogcp2 = AllocateFloatVec( ll2+2 );
-		fgcp1 = AllocateFloatVec( ll1+2 );
-		fgcp2 = AllocateFloatVec( ll2+2 );
-
-		cpmx1 = AllocateFloatMtx( 26, ll1+2 );
-		cpmx2 = AllocateFloatMtx( 26, ll2+2 );
-
-		floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); 
-		intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); 
-
-#if DEBUG
-		fprintf( stderr, "succeeded\n" );
-#endif
-
-		orlgth1 = ll1 - 100;
-		orlgth2 = ll2 - 100;
-	}
-
-
-	for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
-	for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
-
-
-	if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
-	{
-		int ll1, ll2;
-
-		if( commonAlloc1 && commonAlloc2 )
-		{
-			FreeShortMtx( 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 = AllocateShortMtx( ll1+10, ll2+10 );
-
-#if DEBUG
-		fprintf( stderr, "succeeded\n\n" );
-#endif
-
-		commonAlloc1 = ll1;
-		commonAlloc2 = ll2;
-	}
-	ijp = commonIP;
-
-	cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
-	cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
-
-	OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
-	OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
-	FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
-	FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
-
-	for( i=0; i<lgth1; i++ ) 
-	{
-		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
-		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
-	}
-	for( i=0; i<lgth2; i++ ) 
-	{
-		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
-		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
-	}
-#if 0
-	for( i=0; i<lgth1; i++ ) 
-		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
-#endif
-
-	currentw = w1;
-	previousw = w2;
-
-
-	match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
-
-
-	match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
-#if 0 // -> tbfast.c
-	if( localhom )
-		imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
-
-#endif
-
-	if( outgap == 1 )
-	{
-		for( i=1; i<lgth1+1; i++ )
-		{
-			initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
-		}
-		for( j=1; j<lgth2+1; j++ )
-		{
-			currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
-		}
-	}
-#if OUTGAP0TRY
-	else
-	{
-		for( j=1; j<lgth2+1; j++ )
-			currentw[j] -= offset * j / 2.0;
-		for( i=1; i<lgth1+1; i++ )
-			initverticalw[i] -= offset * i / 2.0;
-	}
-#endif
-
-	for( j=1; j<lgth2+1; ++j ) 
-	{
-		m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
-	}
-
-	lastverticalw[0] = currentw[lgth2-1];
-
-	if( outgap ) lasti = lgth1+1; else lasti = lgth1;
-
-#if XXXXXXX
-fprintf( stderr, "currentw = \n" );
-for( i=0; i<lgth1+1; i++ )
-{
-	fprintf( stderr, "%5.2f ", currentw[i] );
-}
-fprintf( stderr, "\n" );
-fprintf( stderr, "initverticalw = \n" );
-for( i=0; i<lgth2+1; i++ )
-{
-	fprintf( stderr, "%5.2f ", initverticalw[i] );
-}
-fprintf( stderr, "\n" );
-fprintf( stderr, "fcgp\n" );
-for( i=0; i<lgth1; i++ ) 
-	fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
-for( i=0; i<lgth2; i++ ) 
-	fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
-#endif
-
-	for( i=1; i<lasti; i++ )
-	{
-		wtmp = previousw; 
-		previousw = currentw;
-		currentw = wtmp;
-
-		previousw[0] = initverticalw[i-1];
-
-		match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, 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 );
-//			imp_match_out_vead( currentw, i, lgth2 );
-			part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
-		}
-#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];
-
-
-		mi = previousw[0] + ogcp2[1]; mpi = 0;
-
-		ijppt = ijp[i] + 1;
-		mjpt = m + 1;
-		prept = previousw;
-		curpt = currentw + 1;
-		mpjpt = mp + 1;
-		fgcp2pt = fgcp2;
-		ogcp2pt = ogcp2+1;
-		fgcp1va = fgcp1[i-1];
-		ogcp1va = ogcp1[i];
-		for( j=1; j<lgth2+1; j++ )
-		{
-			wm = *prept;
-			*ijppt = 0;
-
-#if 0
-			fprintf( stderr, "%5.0f->", wm );
-#endif
-			g = mi + *fgcp2pt;
-#if 0
-			fprintf( stderr, "%5.0f?", g );
-#endif
-			if( g > wm )
-			{
-				wm = g;
-				*ijppt = -( j - mpi );
-			}
-			g = *prept + *ogcp2pt;
-			if( g >= mi )
-			{
-				mi = g;
-				mpi = j-1;
-			}
-#if USE_PENALTY_EX
-			mi += fpenalty_ex;
-#endif
-
-			g = *mjpt + fgcp1va;
-#if 0 
-			fprintf( stderr, "%5.0f?", g );
-#endif
-			if( g > wm )
-			{
-				wm = g;
-				*ijppt = +( i - *mpjpt );
-			}
-			g = *prept + ogcp1va;
-			if( g >= *mjpt )
-			{
-				*mjpt = g;
-				*mpjpt = i-1;
-			}
-#if USE_PENALTY_EX
-			m[j] += fpenalty_ex;
-#endif
-
-#if 0
-			fprintf( stderr, "%5.0f ", wm );
-#endif
-			*curpt += wm;
-			ijppt++;
-			mjpt++;
-			prept++;
-			mpjpt++;
-			curpt++;
-			fgcp2pt++;
-			ogcp2pt++;
-		}
-		lastverticalw[i] = currentw[lgth2-1];
-	}
-
-#if OUTGAP0TRY
-	if( !outgap )
-	{
-		for( j=1; j<lgth2+1; j++ )
-			currentw[j] -= offset * ( lgth2 - j ) / 2.0;
-		for( i=1; i<lgth1+1; i++ )
-			lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
-	}
-#endif
-		
-	/*
-	fprintf( stderr, "\n" );
-	for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
-	fprintf( stderr, "#####\n" );
-	for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
-	fprintf( stderr, "====>" );
-	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
-	for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
-	*/
-	if( localhom )
-	{
-		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
-	}
-	else
-		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
-
-//	fprintf( stderr, "### impmatch = %f\n", *impmatch );
-
-	resultlen = strlen( mseq1[0] );
-	if( alloclen < resultlen || resultlen > N )
-	{
-		fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
-		ErrorExit( "LENGTH OVER!\n" );
-	}
-
-
-	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
-	for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
-	/*
-	fprintf( stderr, "\n" );
-	for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
-	fprintf( stderr, "#####\n" );
-	for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
-	*/
-
-
-	return( wm );
-}
-