diff mafft/core/MSalign11.c @ 18:e4d75f9efb90 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/MSalign11.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,665 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX    0
+#define USE_PENALTY_EX  0
+
+static void extendmseq( char **mseq1, char **mseq2, char **seq1, char **seq2, int i, int j, int prevhiti, int prevhitj )
+{
+//	char gap[] = "-";
+	char *gap;
+	gap = newgapstr;
+	int l;
+
+	fprintf( stderr, "i=%d, prevhiti=%d\n", i, prevhiti );
+	fprintf( stderr, "j=%d, prevhitj=%d\n", j, prevhitj );
+	l = prevhiti - i - 1;
+	fprintf( stderr, "l=%d\n", l );
+	while( l>0 ) 
+	{
+		*--mseq1[0] = seq1[0][i+l--];
+		*--mseq2[0] = *gap;
+	}
+	l= prevhitj - j - 1;
+	fprintf( stderr, "l=%d\n", l );
+	while( l>0 )
+	{
+		*--mseq1[0] = *gap;
+		*--mseq2[0] = seq2[0][j+l--];
+	}
+	if( i < 0 || j < 0 ) return;
+	*--mseq1[0] = seq1[0][i];
+	*--mseq2[0] = seq2[0][j];
+	fprintf( stderr, "added %c to mseq1, mseq1 = %s \n", seq1[0][i], mseq1[0] );
+	fprintf( stderr, "added %c to mseq2, mseq2 = %s \n", seq2[0][j], mseq2[0] );
+}
+
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+	char tmpc = s1[0][i1];
+	char *seq2 = s2[0];
+
+	while( lgth2-- )
+		*match++ = amino_dis[(int)tmpc][(int)*seq2++];
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw, 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        float **cpmx1, float **cpmx2, 
+                        int **ijp )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+//	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] = i + 1;
+    }
+    for( j=0; j<lgth2+1; j++ ) 
+    {
+        ijp[0][j] = -( j + 1 );
+    }
+
+
+	mseq1[0] += lgth1+lgth2;
+	*mseq1[0] = 0;
+	mseq2[0] += lgth1+lgth2;
+	*mseq2[0] = 0;
+	iin = lgth1; jin = lgth2;
+	limk = lgth1+lgth2 + 1;
+	for( k=0; k<limk; 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 ) 
+		{
+			*--mseq1[0] = seq1[0][ifi+l];
+			*--mseq2[0] = *gap;
+			k++;
+		}
+		l= jin - jfi;
+		while( --l )
+		{
+			*--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];
+		k++;
+		iin = ifi; jin = jfi;
+	}
+	return( 0.0 );
+}
+
+void backdp( float **WMMTX, float wmmax, float *maxinw, float *maxinh, int lgth1, int lgth2, int alloclen, float *w1, float *w2, float *initverticalw, float *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 )
+{
+	register int i, j;
+	int prevhiti, prevhitj;
+//	int lasti, lastj; 
+	float g;
+	float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)penalty_ex;
+#endif
+	float *currentw, *previousw, *wtmp;
+	float mi;
+	int mpi;
+	int *mpjpt;
+	float *mjpt, *prept, *curpt;
+	float wm = 0.0;
+	float forwwm;
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 );
+	match_calc( currentw, seq1, seq2, lgth1-1, lgth2 );
+
+
+	prevhiti = iin;
+	prevhitj = jin;
+	fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 );
+	fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 );
+	extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 );
+
+	for( i=0; i<lgth1-1; i++ )
+	{
+		initverticalw[i] += fpenalty;
+		WMMTX[i][lgth2-1] += fpenalty;
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		currentw[j] += fpenalty;
+		WMMTX[lgth1-1][j] += fpenalty;
+	}
+
+
+#if 0
+	fprintf( stderr, "initverticalw = \n" );
+	for( i=0; i<lgth1; i++ )
+		fprintf( stderr, "% 8.2f", initverticalw[i] );
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "currentw = \n" );
+	for( i=0; i<lgth2; i++ )
+		fprintf( stderr, "% 8.2f", currentw[i] );
+	fprintf( stderr, "\n" );
+#endif
+
+	for( j=lgth2-1; j>0; --j ) 
+	{
+		m[j-1] = currentw[j]; 
+		mp[j] = 0; // iranai
+	}
+
+	for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+	//m[lgth2-1] ga, irunoka iranainoka irahai.
+
+	for( i=lgth1-2; i>-1; i-- )
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[lgth2-1] = initverticalw[i+1];
+
+		match_calc( currentw, seq1, seq2, i, lgth2 );
+
+#if 0
+		fprintf( stderr, "i=%d, currentw = \n", i );
+		for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] );
+		fprintf( stderr, "\n" );
+#endif
+
+		currentw[lgth2-1] = initverticalw[i];
+
+		mi = previousw[lgth2-1]; 
+		mpi = lgth2-1; //iranai
+
+
+		mjpt = m + lgth2 - 2;
+		prept = previousw + lgth2 - 1;
+		curpt = currentw + lgth2 - 2;
+		mpjpt = mp + lgth2 - 2;
+
+		for( j=lgth2-2; j>-1; j-- )
+		{
+
+//			fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] );
+			wm = *prept;
+			g = mi + fpenalty;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+			}
+			g = *prept;
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j+1; //iranai
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fpenalty;
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+			}
+			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1; //iranai
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+#if 0
+			fprintf( stderr, "*curpt = %5.0f \n", *curpt );
+#endif
+
+//			forwwm = wm + MIN( maxinw[i], maxinh[j] );
+			forwwm = wm + MIN( maxinw[i], maxinh[j] );
+			WMMTX[i][j] = forwwm;
+			if( forwwm == wmmax && i<prevhiti && j<prevhitj ) 
+			{
+				fprintf( stderr, "hit!\n" );
+				extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj );
+				if( forwwm == wmmax )
+				{
+					*--mseq1[0] = 'u';
+					*--mseq2[0] = 'u';
+				}
+				prevhiti = i;
+				prevhitj = j;
+			}
+			*curpt += wm;
+
+			mjpt--;
+			prept--;
+			mpjpt--;
+			curpt--;
+		}
+	}
+	extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj );
+}
+
+
+float MSalign11( char **seq1, char **seq2, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	register int i, j;
+	int lasti, lastj;
+	int iin = 0, jin = 0;  // by Mathog, a guess
+	int lgth1, lgth2;
+	int resultlen;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+	float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)penalty_ex;
+#endif
+	float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess
+	float *maxinh = NULL; // by D.Mathog, guess
+#if 1
+	float wmmax;
+	float *wtmp;
+	int *ijppt;
+	float *mjpt, *prept, *curpt;
+	int *mpjpt;
+#endif
+	static float mi, *m;
+	static int **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 **cpmx1;
+	static float **cpmx2;
+	static int **intwork;
+	static float **WMMTX;
+	static float **floatwork;
+	static int orlgth1 = 0, orlgth2 = 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( maxinw );
+			FreeFloatVec( maxinh );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+
+			FreeCharMtx( mseq );
+
+
+			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 );
+		maxinw = AllocateFloatVec( ll1+2 );
+
+
+		m = AllocateFloatVec( ll2+2 );
+		mp = AllocateIntVec( ll2+2 );
+		maxinh = AllocateFloatVec( ll2+2 );
+
+		mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+		cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
+		cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
+
+		floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+		intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n" );
+#endif
+
+		orlgth1 = ll1 - 100;
+		orlgth2 = ll2 - 100;
+	}
+
+
+	mseq1[0] = mseq[0];
+	mseq2[0] = mseq[1];
+
+
+	if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+	{
+		int ll1, ll2;
+
+		if( commonAlloc1 && commonAlloc2 )
+		{
+			FreeIntMtx( commonIP );
+			FreeFloatMtx( WMMTX );
+		}
+
+		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 );
+		WMMTX = AllocateFloatMtx( 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( initverticalw, seq2, seq1, 0, lgth1 );
+
+
+	match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+	WMMTX[0][0] = initverticalw[0];
+
+	maxinh[0] = initverticalw[0];
+	for( i=1; i<lgth1+1; i++ )
+	{
+		initverticalw[i] += fpenalty;
+		WMMTX[i][0] = initverticalw[i];
+		if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
+	}
+	maxinw[0] = currentw[0];
+	for( j=1; j<lgth2+1; j++ )
+	{
+		currentw[j] += fpenalty;
+		WMMTX[0][j] = currentw[j];
+		if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
+	}
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+		m[j] = currentw[j-1]; mp[j] = 0;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	lasti = lgth1+1;
+
+	for( i=1; i<lasti; i++ )
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc( currentw, seq1, seq2, i, lgth2 );
+
+		currentw[0] = initverticalw[i];
+
+		mi = previousw[0]; mpi = 0;
+
+		maxinwpt = maxinw + i;
+		*maxinwpt = currentw[0];
+
+		fprintf( stderr, "currentw[0]  = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
+
+		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+		lastj = lgth2+1;
+
+		for( j=1; j<lastj; j++ )
+		{
+			wm = *prept;
+			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + fpenalty;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijppt = -( j - mpi );
+			}
+			g = *prept;
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fpenalty;
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijppt = +( i - *mpjpt );
+			}
+			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+#if 0
+			fprintf( stderr, "%5.0f ", wm );
+#endif
+			*curpt += wm;
+
+			WMMTX[i][j] = *curpt;
+
+
+			if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt;
+			if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt;
+//			fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
+
+			ijppt++;
+			mjpt++;
+			prept++;
+			mpjpt++;
+			curpt++;
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+	}
+
+	wmmax = -999.9;
+	for( i=0; i<lgth1; i++ )
+	{
+		g = lastverticalw[i];
+		if( g > wmmax ) 
+		{
+			wmmax = g;
+			iin = i;
+			jin = lgth2-1;
+		}
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		g = currentw[j];
+		if( g > wmmax )
+		{
+			wmmax = g;
+			iin = lgth1-1;
+			jin = j;
+		}
+	}
+
+	for( i=0; i<lgth1; i++ )
+		fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
+	for( j=0; j<lgth2; j++ )
+		fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
+
+	fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
+	if( iin == lgth1 - 1 && jin == lgth2 - 1 )
+		;
+	else
+		wmmax += fpenalty;
+
+	fprintf( stderr, "wmmax = %f\n", wmmax );
+
+#if 0
+	for( i=0; i<lgth1; i++ )
+	{
+		for( j=0; j<lgth2; j++ )
+		{
+			fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+		}
+		fprintf( stderr, "\n" );
+	}
+#endif
+
+	mseq1[0] += lgth1+lgth2;
+	*mseq1[0] = 0;
+	mseq2[0] += lgth1+lgth2;
+	*mseq2[0] = 0;
+
+	backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
+
+	fprintf( stderr, "\n" );
+#if 1
+	fprintf( stderr, "\n" );
+	fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
+	fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
+#endif
+
+#if 0
+	for( i=0; i<lgth1; i++ )
+	{
+		for( j=0; j<lgth2; j++ )
+		{
+			fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+		}
+		fprintf( stderr, "\n" );
+	}
+#endif
+
+	mseq1[0] = mseq[0];
+	mseq2[0] = mseq[1];
+	mseq1[0] += lgth1+lgth2;
+	*mseq1[0] = 0;
+	mseq2[0] += lgth1+lgth2;
+	*mseq2[0] = 0;
+
+	Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
+
+
+	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 1
+	fprintf( stderr, "\n" );
+	fprintf( stderr, ">\n%s\n", mseq1[0] );
+	fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+
+
+	return( wm );
+}
+