diff mafft/core/suboptalign11.c @ 18:e4d75f9efb90 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/suboptalign11.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,678 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX    0
+#define USE_PENALTY_EX  1
+
+typedef struct _shuryoten
+{
+	int i;
+	int j;
+	float wm;
+	struct _shuryoten *next;
+	struct _shuryoten *prev;
+} Shuryoten;
+
+
+static int localstop;
+
+static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
+{
+	Shuryoten *s1 = (Shuryoten *)s1_arg;
+	Shuryoten *s2 = (Shuryoten *)s2_arg;
+	if      ( s1->wm > s2->wm ) return( -1 );
+	else if ( s1->wm < s2->wm ) return( 1 );
+	else                        return( 0 );
+}
+
+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[(int)(*s1)[i1]][(int)(*s2)[j]];
+}
+
+static float gentracking( int **used,
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        float **cpmx1, float **cpmx2, 
+                        int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
+{
+	int l, iin, jin, lgth1, lgth2, k, limk;
+	int ifi=0, jfi=0;
+//	char gap[] = "-";
+	char *gap;
+	gap = newgapstr;
+	static char *res1 = NULL, *res2 = NULL;
+	char *mspt1, *mspt2;
+	if( res1 == NULL )
+	{
+		res1 = (char *)calloc( N, sizeof( char ) );
+		res2 = (char *)calloc( N, sizeof( char ) );
+	}
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+	mspt1 = res1 + lgth1+lgth2;
+	*mspt1 = 0;
+	mspt2 = res2 + lgth1+lgth2;
+	*mspt2 = 0;
+	iin = endi; jin = endj;
+
+	limk = lgth1+lgth2;
+	if( used[iin][jin] ) return( -1.0 );
+	for( k=0; k<=limk; k++ ) 
+	{
+		ifi = ( ijpi[iin][jin] );
+		jfi = ( ijpj[iin][jin] );
+
+		if( used[ifi][jfi] ) return( -1.0 );
+
+		l = iin - ifi;
+		while( --l ) 
+		{
+			*--mspt1 = seq1[0][ifi+l];
+			*--mspt2 = *gap;
+			k++;
+		}
+		l= jin - jfi;
+		while( --l )
+		{
+			*--mspt1 = *gap;
+			*--mspt2 = seq2[0][jfi+l];
+			k++;
+		}
+
+		if( iin <= 0 || jin <= 0 ) break;
+		*--mspt1 = seq1[0][ifi];
+		*--mspt2 = seq2[0][jfi];
+		if( ijpi[ifi][jfi] == localstop ) break;
+		if( ijpj[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 );
+
+	iin = endi; jin = endj;
+	limk = lgth1+lgth2;
+	for( k=0; k<=limk; k++ ) 
+	{
+		ifi = ( ijpi[iin][jin] );
+		jfi = ( ijpj[iin][jin] );
+
+		used[ifi][jfi] = 1;
+		if( iin <= 0 || jin <= 0 ) break;
+		if( ijpi[ifi][jfi] == localstop ) break;
+		if( ijpj[ifi][jfi] == localstop ) break;
+
+		k++;
+		iin = ifi; jin = jfi;
+	}
+
+
+	strcpy( mseq1[0], mspt1 );
+	strcpy( mseq2[0], mspt2 );
+
+	fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );
+
+	return( 0.0 );
+}
+
+
+float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+	int k;
+	static int **used;
+	register int i, j;
+	int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+	int lgth1, lgth2;
+	int resultlen;
+	float wm = 0.0;   // by D.Mathog, 
+	float g;
+	float *currentw, *previousw;
+#if 1
+	float *wtmp;
+	int *ijpipt;
+	int *ijpjpt;
+	float *mjpt, *Mjpt, *prept, *curpt;
+	int *mpjpt, *Mpjpt;
+#endif
+	static float mi, *m;
+	static float Mi, *largeM;
+	static int **ijpi;
+	static int **ijpj;
+	static int mpi, *mp;
+	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 float **cpmx1;
+	static float **cpmx2;
+	static int **intwork;
+	static float **floatwork;
+	static int orlgth1 = 0, orlgth2 = 0;
+	float maxwm;
+	float tbk;
+	int tbki, tbkj;
+	int endali, endalj;
+//	float localthr = 0.0;
+//	float localthr2 = 0.0;
+	float fpenalty = (float)penalty;
+	float fpenalty_OP = (float)penalty_OP;
+	float fpenalty_ex = (float)penalty_ex;
+//	float fpenalty_EX = (float)penalty_EX;
+	float foffset = (float)offset;
+	float localthr = -foffset;
+	float localthr2 = -foffset;
+	static Shuryoten *shuryo = NULL;
+	int numshuryo;
+	float minshuryowm = 0.0; // by D.Mathog
+	int minshuryopos = 0; // by D.Mathog
+	float resf;
+
+
+//	fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
+
+	fprintf( stderr, "in suboptalign11\n" );
+	if( !shuryo )
+	{
+		shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
+	}
+	for( i=0; i<100; i++ )
+	{
+		shuryo[i].i = -1;
+		shuryo[i].j = -1;
+		shuryo[i].wm = 0.0;
+	}
+	numshuryo = 0;
+
+	if( orlgth1 == 0 )
+	{
+	}
+
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+	fprintf( stderr, "in suboptalign11 step 1\n" );
+
+	if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+	{
+		int ll1, ll2;
+
+	fprintf( stderr, "in suboptalign11 step 1.3\n" );
+		if( orlgth1 > 0 && orlgth2 > 0 )
+		{
+	fprintf( stderr, "in suboptalign11 step 1.4\n" );
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+//			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+	fprintf( stderr, "in suboptalign11 step 1.5\n" );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+			FreeFloatVec( largeM );
+			FreeIntVec( Mp );
+	fprintf( stderr, "in suboptalign11 step 1.6\n" );
+
+
+			FreeFloatMtx( cpmx1 );
+			FreeFloatMtx( cpmx2 );
+
+	fprintf( stderr, "in suboptalign11 step 1.7\n" );
+			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 );
+		largeM = AllocateFloatVec( ll2+2 );
+		Mp = AllocateIntVec( ll2+2 );
+
+		cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
+		cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
+
+		floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+		intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+
+		mseq1 = AllocateCharMtx( njob, ll1+ll2 );
+		mseq2 = AllocateCharMtx( njob, ll1+ll2 );
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n" );
+#endif
+
+		orlgth1 = ll1 - 100;
+		orlgth2 = ll2 - 100;
+	}
+	fprintf( stderr, "in suboptalign11 step 1.6\n" );
+
+
+
+	fprintf( stderr, "in suboptalign11 step 2\n" );
+
+	if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+	{
+		int ll1, ll2;
+
+		if( commonAlloc1 && commonAlloc2 )
+		{
+			FreeIntMtx( commonIP );
+			FreeIntMtx( commonJP );
+			FreeIntMtx( used );
+		}
+
+		ll1 = MAX( orlgth1, commonAlloc1 );
+		ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+		fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+		used = AllocateIntMtx( ll1+10, ll2+10 );
+		commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+		commonJP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n\n" );
+#endif
+
+		commonAlloc1 = ll1;
+		commonAlloc2 = ll2;
+	}
+	ijpi = commonIP;
+	ijpj = commonJP;
+
+
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+	fprintf( stderr, "in suboptalign11 step 3\n" );
+	currentw = w1;
+	previousw = w2;
+
+	match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+	match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+	lasti = lgth2+1;
+	for( j=1; j<lasti; ++j ) 
+	{
+		m[j] = currentw[j-1]; mp[j] = 0;
+		largeM[j] = currentw[j-1]; Mp[j] = 0;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+
+#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+1; j++ )
+		fprintf( stderr, "%c     ", seq2[0][j] );
+	fprintf( stderr, "\n" );
+#endif
+
+	localstop = lgth1+lgth2+1;
+	maxwm = -999.9;
+	endali = endalj = 0;
+#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
+
+	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 );
+#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;
+		Mi = previousw[0]; Mpi = 0;
+
+#if 0
+		if( mi < localthr ) mi = localthr2;
+#endif
+
+		ijpipt = ijpi[i] + 1;
+		ijpjpt = ijpj[i] + 1;
+		mjpt = m + 1;
+		Mjpt = largeM + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+		Mpjpt = Mp + 1;
+		tbk = -999999.9;
+		tbki = 0;
+		tbkj = 0;
+		lastj = lgth2+1;
+		for( j=1; j<lastj; j++ )
+		{
+			wm = *prept;
+			*ijpipt = i-1;
+			*ijpjpt = j-1;
+
+
+//			fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
+//			fprintf( stderr, "wm=%f\n", wm );
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + fpenalty;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijpipt = i - 1;
+				*ijpjpt = mpi;
+			}
+			g = *prept;
+			if( g > mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = *mjpt + fpenalty;
+#if 0
+			fprintf( stderr, "m%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijpipt = *mpjpt;
+//				*ijpjpt = j - 1;
+			}
+			g = *prept;
+			if( g > *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			*mjpt += fpenalty_ex;
+#endif
+
+
+			g =  tbk + fpenalty_OP;
+//			g =  tbk;
+			if( g > wm )
+			{
+				wm = g;
+				*ijpipt = tbki;
+				*ijpjpt = tbkj;
+//				fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
+			}
+			g = Mi;
+			if( g > tbk )
+			{
+				tbk = g;
+				tbki = i-1;
+				tbkj = Mpi;
+			}
+			g = *Mjpt;
+			if( g > tbk )
+			{
+				tbk = g;
+				tbki = *Mpjpt;
+				tbkj = j-1;
+			}
+//			tbk += fpenalty_EX;// + foffset;
+
+			g = *prept;
+			if( g > *Mjpt )
+			{
+				*Mjpt = g;
+				*Mpjpt = i-1;
+			}
+//			*Mjpt += fpenalty_EX;// + foffset;
+
+			g = *prept;
+			if( g > Mi )
+			{
+				Mi = g;
+				Mpi = j-1;
+			}
+//			Mi += fpenalty_EX;// + foffset;
+
+
+//			fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
+//			fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
+
+
+			if( maxwm < wm )
+			{
+				maxwm = wm;
+				endali = i;
+				endalj = j;
+			}
+
+#if 1
+			if( numshuryo < 100 )
+			{
+				shuryo[numshuryo].i = i;
+				shuryo[numshuryo].j = j;
+				shuryo[numshuryo].wm = wm;
+
+				if( minshuryowm > wm )
+				{
+					 minshuryowm = wm;
+					 minshuryopos = numshuryo;
+				}
+				numshuryo++;
+			}
+			else
+			{
+				if( wm > minshuryowm )
+				{
+					shuryo[minshuryopos].i = i;
+					shuryo[minshuryopos].j = j;
+					shuryo[minshuryopos].wm = wm;
+					minshuryowm = wm;
+					for( k=0; k<100; k++ )    // muda
+					{
+						if( shuryo[k].wm < minshuryowm )
+						{
+							minshuryowm = shuryo[k].wm;
+							minshuryopos = k;
+							break;
+						}
+					}
+				}
+			}
+#endif
+#if 1
+			if( wm < localthr )
+			{
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+				*ijpipt = localstop;
+//				*ijpjpt = 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;
+			ijpipt++;
+			ijpjpt++;
+			mjpt++;
+			Mjpt++;
+			prept++;
+			mpjpt++;
+			Mpjpt++;
+			curpt++;
+		}
+#if DEBUG2
+		fprintf( stderr, "\n" );
+#endif
+
+		lastverticalw[i] = currentw[lgth2-1];
+	}
+
+	for( k=0; k<100; k++ )
+	{
+		fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+	}
+
+
+#if 1
+	fprintf( stderr, "maxwm = %f\n", maxwm );
+	fprintf( stderr, "endali = %d\n", endali );
+	fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+	qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
+	for( k=0; k<100; k++ )
+	{
+		fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+	}
+
+		
+	lasti = lgth1+1;
+    for( i=0; i<lasti; i++ ) 
+    {
+        ijpi[i][0] = localstop;
+        ijpj[i][0] = localstop;
+    }
+	lastj = lgth2+1;
+    for( j=0; j<lastj; j++ ) 
+    {
+        ijpi[0][j] = localstop;
+        ijpj[0][j] = localstop;
+    }
+
+	for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;
+
+	for( k=0; k<numshuryo; k++ )
+	{
+		if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
+		fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+		resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
+		if( resf == -1.0 ) continue;
+		putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
+#if 0
+		fprintf( stderr, "\n" );
+		fprintf( stderr, ">\n%s\n", mseq1[0] );
+		fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+	}
+	for( i=0; i<20; i++ )
+	{
+		for( j=0; j<20; j++ )
+		{
+			fprintf( stderr, "%2d ", used[i][j] );
+		}
+		fprintf( stderr, "\n" );
+	}
+
+
+//	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" );
+	}
+
+
+
+
+
+	return( wm );
+}
+