diff mafft/core/Lalign11.c @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/Lalign11.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,1150 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX    0
+#define USE_PENALTY_EX  1
+
+
+static TLS int localstop; // 060910
+
+#if 1
+static void match_calc_mtx( double **mtx, float *match, char **s1, char **s2, int i1, int lgth2 ) 
+{
+	char *seq2 = s2[0];
+	double *doubleptr = mtx[(int)s1[0][i1]];
+
+	while( lgth2-- )
+		*match++ = doubleptr[(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+	int j;
+
+	for( j=0; j<lgth2; j++ )
+		match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+#if 0
+static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+	int j, k, l;
+	float scarr[nalphabets];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	int count = 0;
+
+	if( initialize )
+	{
+		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];
+	}
+#if 0 /* これを使うときはfloatworkのアロケートを逆にする */
+	{
+		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
+}
+#endif
+
+static float Ltracking( float *lasthorizontalw, float *lastverticalw, 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        int **ijp, int *off1pt, int *off2pt, int endi, int endj,
+						int *warpis, int *warpjs, int warpbase )
+{
+	int i, j, l, iin, jin, lgth1, lgth2, k, limk;
+	int ifi=0, jfi=0; // by D.Mathog, a guess
+//	char gap[] = "-";
+	char *gap;
+	gap = newgapstr;
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+	{
+		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+	}
+#endif
+ 
+    for( i=0; i<lgth1+1; i++ ) 
+    {
+        ijp[i][0] = localstop;
+    }
+    for( j=0; j<lgth2+1; j++ ) 
+    {
+        ijp[0][j] = localstop;
+    }
+
+	mseq1[0] += lgth1+lgth2;
+	*mseq1[0] = 0;
+	mseq2[0] += lgth1+lgth2;
+	*mseq2[0] = 0;
+	iin = endi; jin = endj;
+	limk = lgth1+lgth2;
+	for( k=0; k<=limk; k++ ) 
+	{
+		if( ijp[iin][jin] >= warpbase )
+		{
+//			fprintf( stderr, "WARP!\n" );
+			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 1 // sentou de warp?
+		if( ifi == -warpbase && jfi == -warpbase )
+		{
+			l = iin;
+			while( --l >= 0 ) 
+			{
+				*--mseq1[0] = seq1[0][l];
+				*--mseq2[0] = *gap;
+				k++;
+			}
+			l= jin;
+			while( --l >= 0 )
+			{
+				*--mseq1[0] = *gap;
+				*--mseq2[0] = seq2[0][l];
+				k++;
+			}
+			break;
+		}
+		else
+#endif
+		{
+			l = iin - ifi;
+			while( --l > 0 ) 
+			{
+				*--mseq1[0] = seq1[0][ifi+l];
+				*--mseq2[0] = *gap;
+				k++;
+			}
+			l= jin - jfi;
+			while( --l > 0 )
+			{
+				*--mseq1[0] = *gap;
+				*--mseq2[0] = seq2[0][jfi+l];
+				k++;
+			}
+		}
+
+
+		if( iin <= 0 || jin <= 0 ) break;
+		*--mseq1[0] = seq1[0][ifi];
+		*--mseq2[0] = seq2[0][jfi];
+		if( ijp[ifi][jfi] == localstop ) break;
+		k++;
+		iin = ifi; jin = jfi;
+	}
+	if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+	if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+//	fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+//	fprintf( stderr, "\n" );
+//	fprintf( stderr, "%s\n", mseq1[0] );
+//	fprintf( stderr, "%s\n", mseq2[0] );
+
+
+	return( 0.0 );
+}
+
+
+float L__align11( double **n_dynamicmtx, float scoreoffset, char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	int i, j;
+	int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+	int lgth1, lgth2;
+	int resultlen;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+#if 1
+	float *wtmp;
+	int *ijppt;
+	float *mjpt, *prept, *curpt;
+	int *mpjpt;
+#endif
+	static TLS float mi, *m;
+	static TLS int **ijp;
+	static TLS int mpi, *mp;
+	static TLS float *w1, *w2;
+	static TLS float *match;
+	static TLS float *initverticalw;    /* kufuu sureba iranai */
+	static TLS float *lastverticalw;    /* kufuu sureba iranai */
+	static TLS char **mseq1;
+	static TLS char **mseq2;
+	static TLS char **mseq;
+//	static TLS int **intwork;
+//	static TLS float **floatwork;
+	static TLS int orlgth1 = 0, orlgth2 = 0;
+	static TLS double **amino_dynamicmtx = NULL; // ??
+	float maxwm;
+	int endali = 0, endalj = 0; // by D.Mathog, a guess
+//	int endali, endalj;
+	float localthr = -offset + scoreoffset * 600; // 2013/12/13
+	float localthr2 = -offset + scoreoffset * 600; // 2013/12/13
+//	float localthr = -offset;
+//	float localthr2 = -offset;
+	float fpenalty = (float)penalty;
+	float fpenalty_ex = (float)penalty_ex;
+	float fpenalty_shift = (float)penalty_shift;
+	float fpenalty_tmp; // atode kesu
+
+	int *warpis = NULL;
+	int *warpjs = NULL;
+	int *warpi = NULL;
+	int *warpj = NULL;
+	int *prevwarpi = NULL;
+	int *prevwarpj = NULL;
+	float *wmrecords = NULL;
+	float *prevwmrecords = NULL;
+	int warpn = 0;
+	int warpbase;
+	float curm = 0.0;
+	float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+	int *warpipt, *warpjpt;
+
+
+
+	if( seq1 == NULL )
+	{
+		if( orlgth1 > 0 && orlgth2 > 0 )
+		{
+			orlgth1 = 0;
+			orlgth2 = 0;
+			free( mseq1 );
+			free( mseq2 );
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+
+			FreeCharMtx( mseq );
+			if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
+
+		}
+		return( 0.0 );
+	}
+
+
+	if( orlgth1 == 0 )
+	{
+		mseq1 = AllocateCharMtx( njob, 0 );
+		mseq2 = AllocateCharMtx( njob, 0 );
+	}
+
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+
+	warpbase = lgth1 + lgth2;
+	warpis = NULL;
+	warpjs = NULL;
+	warpn = 0;
+	if( trywarp )
+	{
+		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++ ) prevwmrecords[i] = 0.0;
+		for( i=0; i<lgth2+1; i++ ) wmrecords[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( 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 );
+			if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
+
+
+//			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 );
+
+
+//		floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+//		intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n" );
+#endif
+		amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
+		orlgth1 = ll1 - 100;
+		orlgth2 = ll2 - 100;
+	}
+
+    for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
+		amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
+
+
+	mseq1[0] = mseq[0];
+	mseq2[0] = mseq[1];
+
+
+	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
+	for( i=0; i<lgth1; i++ ) 
+		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
+
+	match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
+
+
+	lasti = lgth2+1;
+	for( j=1; j<lasti; ++j ) 
+	{
+		m[j] = currentw[j-1]; mp[j] = 0;
+#if 0
+		if( m[j] < localthr ) m[j] = localthr2;
+#endif
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	lasti = lgth1+1;
+
+#if 0
+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" );
+#endif
+#if DEBUG2
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "       " );
+	for( j=0; j<lgth2; j++ )
+		fprintf( stderr, "%c     ", seq2[0][j] );
+	fprintf( stderr, "\n" );
+#endif
+
+	localstop = lgth1+lgth2+1;
+	maxwm = -999999999.9;
+#if DEBUG2
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "%c   ", seq1[0][0] );
+
+	for( j=0; j<lgth2+1; j++ )
+		fprintf( stderr, "%5.0f ", currentw[j] );
+	fprintf( stderr, "\n" );
+#endif
+
+	for( i=1; i<lasti; i++ )
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+		fprintf( stderr, "%c   ", seq1[0][i] );
+		fprintf( stderr, "%5.0f ", currentw[0] );
+#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 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]; mpi = 0;
+
+#if 0
+		if( mi < localthr ) mi = localthr2;
+#endif
+
+		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+		lastj = lgth2+1;
+
+		if( trywarp )
+		{
+			prevwmrecordspt = prevwmrecords;
+			wmrecordspt = wmrecords+1;
+			wmrecords1pt = wmrecords;
+			warpipt = warpi + 1;
+			warpjpt = warpj + 1;
+		}
+		for( j=1; j<lastj; j++ )
+		{
+			wm = *prept;
+			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( (g=mi+fpenalty) > wm )
+			{
+				wm = g;
+				*ijppt = -( j - mpi );
+			}
+			if( *prept > mi )
+			{
+				mi = *prept;
+				mpi = j-1;
+			}
+
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( (g=*mjpt+fpenalty) > wm )
+			{
+				wm = g;
+				*ijppt = +( i - *mpjpt );
+			}
+			if( *prept > *mjpt )
+			{
+				*mjpt = *prept;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			*mjpt += fpenalty_ex;
+#endif
+
+			if( maxwm < wm )
+			{
+				maxwm = wm;
+				endali = i;
+				endalj = j;
+			}
+#if 1
+			if( wm < localthr )
+			{
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f, localthr = %f\n", i, j, *curpt, localthr );
+				*ijppt = localstop;
+				wm = localthr2;
+			}
+#endif
+#if 0
+			fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if 0
+			fprintf( stderr, "wm (%d,%d) = %5.0f\n", i, j, wm );
+//			fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+			if( trywarp )
+			{
+				fpenalty_tmp = fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] );
+//				fprintf( stderr, "fpenalty_shift = %f\n", fpenalty_tmp );
+
+//				fprintf( stderr, "\n\n\nwarp to %c-%c (%d-%d) from %c-%c (%d-%d) ? prevwmrecords[%d] = %f + %f <- wm = %f\n", seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], prevwarpi[j-1], prevwarpj[j-1], seq1[0][i], seq2[0][j], i, j, j, prevwmrecords[j-1], fpenalty_tmp, wm );
+//				if( (g=prevwmrecords[j-1] + fpenalty_shift )> wm )
+				if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
+				{
+//					fprintf( stderr, "Yes! Warp!! from %d-%d (%c-%c) to  %d-%d (%c-%c) fpenalty_tmp = %f! warpn = %d\n", i, j, seq1[0][i], seq2[0][j-1], prevwarpi[j-1], prevwarpj[j-1],seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], fpenalty_tmp, warpn );
+					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;
+				}
+				else
+				{
+				}
+
+				curm = *curpt + wm;
+	
+//				fprintf( stderr, "###### curm = %f at %c-%c, i=%d, j=%d\n", curm, seq1[0][i], seq2[0][j], i, j ); 
+	
+//				fprintf( stderr, "copy from i, j-1? %f > %f?\n", wmrecords[j-1], curm );
+//				if( wmrecords[j-1] > wmrecords[j] )
+				if( *wmrecords1pt > *wmrecordspt )
+				{
+//					fprintf( stderr, "yes\n" );
+//					wmrecords[j] = wmrecords[j-1];
+					*wmrecordspt = *wmrecords1pt;
+//					warpi[j] = warpi[j-1];
+//					warpj[j] = warpj[j-1];
+					*warpipt  = *(warpipt-1);
+					*warpjpt  = *(warpjpt-1);
+//					fprintf( stderr, "warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
+				}
+//				else
+//				{
+//					fprintf( stderr, "no\n" );
+//				}
+	
+//				fprintf( stderr, " curm = %f at %c-%c\n", curm, seq1[0][i], seq2[0][j] ); 
+//				fprintf( stderr, " wmrecords[%d] = %f\n", j, wmrecords[j] ); 
+//				fprintf( stderr, "replace?\n" );
+	
+//				if( curm > wmrecords[j] )
+				if( curm > *wmrecordspt )
+				{
+//					fprintf( stderr, "yes at %d-%d (%c-%c), replaced warp: warpi[j]=%d, warpj[j]=%d warpn=%d, wmrecords[j] = %f -> %f\n", i, j, seq1[0][i], seq2[0][j], i, j, warpn, wmrecords[j], curm );
+//					wmrecords[j] = curm;
+					*wmrecordspt = curm;
+//					warpi[j] = i;
+//					warpj[j] = j;
+					*warpipt = i;
+					*warpjpt = j;
+				}
+//				else
+//				{
+//					fprintf( stderr, "No! warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
+//				}
+//				fprintf( stderr, "%d-%d (%c-%c) curm = %5.0f, wmrecords[j]=%f\n", i, j, seq1[0][i], seq2[0][j], curm, wmrecords[j] );
+				wmrecordspt++;
+				wmrecords1pt++;
+				warpipt++;
+				warpjpt++;
+			}
+
+			*curpt++ += wm;
+			ijppt++;
+			mjpt++;
+			prept++;
+			mpjpt++;
+		}
+#if DEBUG2
+		fprintf( stderr, "\n" );
+#endif
+
+		lastverticalw[i] = currentw[lgth2-1];
+		if( trywarp )
+		{
+			fltncpy( prevwmrecords, wmrecords, lastj );
+			intncpy( prevwarpi, warpi, lastj );
+			intncpy( prevwarpj, warpj, lastj );
+		}
+
+	}
+//	fprintf( stderr, "\nwm = %f\n", wm );
+	if( trywarp )
+	{
+//		if( warpn ) fprintf( stderr, "warpn = %d\n", warpn );
+		free( wmrecords );
+		free( prevwmrecords );
+		free( warpi );
+		free( warpj );
+		free( prevwarpi );
+		free( prevwarpj );
+	}
+
+#if 0
+	fprintf( stderr, "maxwm = %f\n", maxwm );
+	fprintf( stderr, "endali = %d\n", endali );
+	fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+	if( ijp[endali][endalj] == localstop )
+	{
+		strcpy( seq1[0], "" );
+		strcpy( seq2[0], "" );
+		*off1pt = *off2pt = 0;
+		fprintf( stderr, "maxwm <- 0.0 \n" );
+		return( 0.0 );
+	}
+		
+	Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj, warpis, warpjs, warpbase );
+	if( warpis ) free( warpis );
+	if( warpjs ) free( warpjs );
+
+
+	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" );
+	}
+
+
+	strcpy( seq1[0], mseq1[0] );
+	strcpy( seq2[0], mseq2[0] );
+
+#if 0
+	fprintf( stderr, "wm=%f\n", wm );
+	fprintf( stderr, ">\n%s\n", mseq1[0] );
+	fprintf( stderr, ">\n%s\n", mseq2[0] );
+
+	fprintf( stderr, "maxwm = %f\n", maxwm );
+	fprintf( stderr, "   wm = %f\n",    wm );
+#endif
+
+	return( maxwm );
+}
+
+
+float L__align11_noalign( double **n_dynamicmtx, char **seq1, char **seq2 )
+// warp mitaiou
+{
+//	int k;
+	int i, j;
+	int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+	int lgth1, lgth2;
+//	int resultlen;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+#if 1
+	float *wtmp;
+//	int *ijppt;
+	float *mjpt, *prept, *curpt;
+//	int *mpjpt;
+#endif
+	static TLS float mi, *m;
+//	static TLS int **ijp;
+//	static TLS int mpi, *mp;
+	static TLS float *w1, *w2;
+	static TLS float *match;
+	static TLS float *initverticalw;    /* kufuu sureba iranai */
+	static TLS float *lastverticalw;    /* kufuu sureba iranai */
+//	static TLS char **mseq1;
+//	static TLS char **mseq2;
+//	static TLS char **mseq;
+//	static TLS int **intwork;
+//	static TLS float **floatwork;
+	static TLS int orlgth1 = 0, orlgth2 = 0;
+	static TLS double **amino_dynamicmtx = NULL; // ??
+	float maxwm;
+//	int endali = 0, endalj = 0; // by D.Mathog, a guess
+//	int endali, endalj;
+	float localthr = -offset;
+	float localthr2 = -offset;
+//	float localthr = 100;
+//	float localthr2 = 100;
+	float fpenalty = (float)penalty;
+	float fpenalty_ex = (float)penalty_ex;
+
+	if( seq1 == NULL )
+	{
+		if( orlgth1 > 0 && orlgth2 > 0 )
+		{
+			orlgth1 = 0;
+			orlgth2 = 0;
+//			free( mseq1 );
+//			free( mseq2 );
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+
+			FreeFloatVec( m );
+//			FreeIntVec( mp );
+
+//			FreeCharMtx( mseq );
+			if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
+
+		}
+		return( 0.0 );
+	}
+
+
+//	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 );
+
+
+
+//			FreeFloatMtx( floatwork );
+//			FreeIntMtx( intwork );
+			if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = 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 );
+
+
+//		floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+//		intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n" );
+#endif
+		amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
+		orlgth1 = ll1 - 100;
+		orlgth2 = ll2 - 100;
+	}
+
+    for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
+		amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
+
+
+
+//	mseq1[0] = mseq[0];
+//	mseq2[0] = mseq[1];
+
+
+//	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
+	for( i=0; i<lgth1; i++ ) 
+		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
+
+	match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
+
+
+	lasti = lgth2+1;
+	for( j=1; j<lasti; ++j ) 
+	{
+		m[j] = currentw[j-1]; 
+//		mp[j] = 0;
+#if 0
+		if( m[j] < localthr ) m[j] = localthr2;
+#endif
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	lasti = lgth1+1;
+
+#if 0
+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" );
+#endif
+#if DEBUG2
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "       " );
+	for( j=0; j<lgth2; j++ )
+		fprintf( stderr, "%c     ", seq2[0][j] );
+	fprintf( stderr, "\n" );
+#endif
+
+	localstop = lgth1+lgth2+1;
+	maxwm = -999999999.9;
+#if DEBUG2
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "%c   ", seq1[0][0] );
+
+	for( j=0; j<lgth2+1; j++ )
+		fprintf( stderr, "%5.0f ", currentw[j] );
+	fprintf( stderr, "\n" );
+#endif
+
+	for( i=1; i<lasti; i++ )
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+		fprintf( stderr, "%c   ", seq1[0][i] );
+		fprintf( stderr, "%5.0f ", currentw[0] );
+#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 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]; 
+//		mpi = 0;
+
+#if 0
+		if( mi < localthr ) mi = localthr2;
+#endif
+
+//		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+//		mpjpt = mp + 1;
+		lastj = lgth2+1;
+		for( j=1; j<lastj; j++ )
+		{
+			wm = *prept;
+//			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( (g=mi+fpenalty) > wm )
+			{
+				wm = g;
+//				*ijppt = -( j - mpi );
+			}
+			if( *prept > mi )
+			{
+				mi = *prept;
+//				mpi = j-1;
+			}
+
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( (g=*mjpt+fpenalty) > wm )
+			{
+				wm = g;
+//				*ijppt = +( i - *mpjpt );
+			}
+			if( *prept > *mjpt )
+			{
+				*mjpt = *prept;
+//				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			*mjpt += fpenalty_ex;
+#endif
+
+			if( maxwm < wm )
+			{
+				maxwm = wm;
+//				endali = i;
+//				endalj = j;
+			}
+#if 1
+			if( wm < localthr )
+			{
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+//				*ijppt = localstop;
+				wm = localthr2;
+			}
+#endif
+#if 0
+			fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+			fprintf( stderr, "%5.0f ", wm );
+//			fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+			*curpt++ += wm;
+//			ijppt++;
+			mjpt++;
+			prept++;
+//			mpjpt++;
+		}
+#if DEBUG2
+		fprintf( stderr, "\n" );
+#endif
+
+		lastverticalw[i] = currentw[lgth2-1];
+	}
+
+
+#if 0
+	fprintf( stderr, "maxwm = %f\n", maxwm );
+	fprintf( stderr, "endali = %d\n", endali );
+	fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+
+#if 0 // IRUKAMO!!!!
+	if( ijp[endali][endalj] == localstop )
+	{
+		strcpy( seq1[0], "" );
+		strcpy( seq2[0], "" );
+		*off1pt = *off2pt = 0;
+		fprintf( stderr, "maxwm <- 0.0 \n" );
+		return( 0.0 );
+	}
+#else
+	if( maxwm < localthr )
+	{
+		fprintf( stderr, "maxwm <- 0.0 \n" );
+		return( 0.0 );
+	}
+#endif
+		
+//	Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj );
+
+
+//	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" );
+//	}
+
+
+//	strcpy( seq1[0], mseq1[0] );
+//	strcpy( seq2[0], mseq2[0] );
+
+#if 0
+	fprintf( stderr, "wm=%f\n", wm );
+	fprintf( stderr, ">\n%s\n", mseq1[0] );
+	fprintf( stderr, ">\n%s\n", mseq2[0] );
+
+	fprintf( stderr, "maxwm = %f\n", maxwm );
+	fprintf( stderr, "   wm = %f\n",    wm );
+#endif
+
+	return( maxwm );
+}