X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2FSalignmm.c;h=06e402eb9b07d91a210180f514d0eb97ad3bd952;hb=063b30bb5e8161134ae764742636ab538e10eea7;hp=11700400a0174a6ea320d831e86a3e9a60203db9;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/binaries/src/mafft/core/Salignmm.c b/binaries/src/mafft/core/Salignmm.c
index 1170040..06e402e 100644
--- a/binaries/src/mafft/core/Salignmm.c
+++ b/binaries/src/mafft/core/Salignmm.c
@@ -2,15 +2,15 @@
 #include "dp.h"
 
 #define MACHIGAI 0
-#define OUTGAP0TRY 1
+#define OUTGAP0TRY 0
 #define DEBUG 0
 #define XXXXXXX    0
 #define USE_PENALTY_EX  0
 #define FASTMATCHCALC 1
 
 
-static float **impmtx = NULL;
-static int impalloclen = 0;
+static TLS float **impmtx = NULL;
+static TLS int impalloclen = 0;
 float imp_match_out_sc( int i1, int j1 )
 {
 //	fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
@@ -79,10 +79,22 @@ void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgt
 	float effij_kozo;
 	double effijx;
 	char *pt, *pt1, *pt2;
-	static char *nocount1 = NULL;
-	static char *nocount2 = NULL;
+	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 );
@@ -295,11 +307,11 @@ for( i = 0; i<impalloclen; i++ )
 void 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;
+	static TLS int impalloclen = 0;
 	char *pt;
 	int allgap;
-	static char *nocount1 = NULL;
-	static char *nocount2 = NULL;
+	static TLS char *nocount1 = NULL;
+	static TLS char *nocount2 = NULL;
 
 	if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
 	{
@@ -761,7 +773,8 @@ static float Atracking( float *lasthorizontalw, float *lastverticalw,
 						char **seq1, char **seq2, 
                         char **mseq1, char **mseq2, 
                         float **cpmx1, float **cpmx2, 
-                        int **ijp, int icyc, int jcyc )
+                        int **ijp, int icyc, int jcyc,
+						int tailgp )
 {
 	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 	float wm;
@@ -780,7 +793,7 @@ static float Atracking( float *lasthorizontalw, float *lastverticalw,
 	}
 #endif
  
-	if( outgap == 1 )
+	if( tailgp == 1 )
 		;
 	else
 	{
@@ -864,7 +877,7 @@ static float Atracking( float *lasthorizontalw, float *lastverticalw,
 	return( 0.0 );
 }
 
-float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *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;
@@ -885,25 +898,25 @@ float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc,
 	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 *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;
+	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 float *ogcp1;
+	static TLS float *ogcp2;
+	static TLS float *fgcp1;
+	static TLS float *fgcp2;
+	static TLS float **cpmx1;
+	static TLS float **cpmx2;
+	static TLS int **intwork;
+	static TLS float **floatwork;
+	static TLS int orlgth1 = 0, orlgth2 = 0;
 	float fpenalty = (float)penalty;
 	float *fgcp2pt;
 	float *ogcp2pt;
@@ -911,12 +924,93 @@ float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc,
 	float ogcp1va;
 
 
+	if( seq1 == NULL )
+	{
+		if( orlgth1 )
+		{
+//			fprintf( stderr, "## Freeing local arrays in A__align\n" );
+			orlgth1 = 0;
+			orlgth2 = 0;
+
+			imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+
+			free( mseq1 );
+			free( mseq2 );
+			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 );
+
+		}
+		else
+		{
+//			fprintf( stderr, "## Not allocated\n" );
+		}
+		return( 0.0 );
+	}
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+#if 1
+	if( lgth1 == 0 || lgth2 == 0 )
+	{
+		fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+	}
+	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] = '-';
+//			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] = '-';
+//			fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+		}
+		return( 0.0 );
+	}
+#endif
+
 
 #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 )
 	{
@@ -925,14 +1019,6 @@ float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc,
 	}
 
 
-	lgth1 = strlen( seq1[0] );
-	lgth2 = strlen( seq2[0] );
-#if 0
-	if( lgth1 == 0 || lgth2 == 0 )
-	{
-		fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
-	}
-#endif
 
 	if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 	{
@@ -1105,7 +1191,7 @@ float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc,
 
 #endif
 
-	if( outgap == 1 )
+	if( headgp == 1 )
 	{
 		for( i=1; i<lgth1+1; i++ )
 		{
@@ -1135,7 +1221,7 @@ float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc,
 	else
 		lastverticalw[0] = currentw[lgth2-1];
 
-	if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+	if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
 
 #if XXXXXXX
 fprintf( stderr, "currentw = \n" );
@@ -1159,6 +1245,16 @@ for( i=0; i<lgth2; i++ )
 
 	for( i=1; i<lasti; i++ )
 	{
+
+#ifdef enablemultithread
+//		fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+		if( chudanpt && *chudanpt != chudanref ) 
+		{
+//			fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+			*chudanres = 1;
+			return( -1.0 );
+		}
+#endif
 		wtmp = previousw; 
 		previousw = currentw;
 		currentw = wtmp;
@@ -1211,6 +1307,15 @@ fprintf( stderr, "\n" );
 		lastj = lgth2+1;
 		for( j=1; j<lastj; j++ )
 		{
+#ifdef xxxenablemultithread
+//			fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+			if( chudanpt && *chudanpt != chudanref ) 
+			{
+//				fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+				*chudanres = 1;
+				return( -1.0 );
+			}
+#endif
 			wm = *prept;
 			*ijppt = 0;
 
@@ -1291,7 +1396,7 @@ fprintf( stderr, "\n" );
 		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
 	}
 	else
-		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, tailgp );
 
 //	fprintf( stderr, "### impmatch = %f\n", *impmatch );
 
@@ -1305,12 +1410,12 @@ fprintf( stderr, "\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
 
 //	fprintf( stderr, "wm = %f\n", wm );
 
@@ -1338,25 +1443,25 @@ float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int
 	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 *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;
+	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 float *ogcp1;
+	static TLS float *ogcp2;
+	static TLS float *fgcp1;
+	static TLS float *fgcp2;
+	static TLS float **cpmx1;
+	static TLS float **cpmx2;
+	static TLS int **intwork;
+	static TLS float **floatwork;
+	static TLS int orlgth1 = 0, orlgth2 = 0;
 	float *fgcp2pt;
 	float *ogcp2pt;
 	float fgcp1va;
@@ -1537,7 +1642,7 @@ float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int
 
 #endif
 
-	if( outgap == 1 )
+	if( 1 ) // tsuneni outgap=1
 	{
 		for( i=1; i<lgth1+1; i++ )
 		{
@@ -1568,7 +1673,7 @@ float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int
 	else
 		lastverticalw[0] = currentw[lgth2-1];
 
-	if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+	if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap=1
 
 #if XXXXXXX
 fprintf( stderr, "currentw = \n" );
@@ -1727,7 +1832,7 @@ fprintf( stderr, "\n" );
 		Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
 	}
 	else
-		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, 1 );
 
 //	fprintf( stderr, "### impmatch = %f\n", *impmatch );
 
@@ -1753,40 +1858,3 @@ fprintf( stderr, "\n" );
 	return( wm );
 }
 
-float translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen )
-{
-    int i;
-    float wm;
-    char **result;
-    char *seq = NULL, **aseq = NULL;
-    double *effarr = NULL;
-    int nseq = 0;
-	int resultlen;
-
-    if     ( clus1 == 1 && clus2 != 1 ) 
-    {
-        seq = mseq1[0]; aseq = mseq2; effarr = effarr2; nseq = clus2+1;
-#if 0
-		printf( "effarr in transl... = \n" );
-		for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
-#endif
-    }
-    else if( clus1 != 1 && clus2 == 1 ) 
-    {
-        seq = mseq2[0]; aseq = mseq1; effarr = effarr1; nseq = clus1+1;
-    }
-    else ErrorExit( "ERROR in translate_and_Calign" );
-
-    result = Calignm1( &wm, aseq, seq, effarr, nseq-2, 0 );
-
-	resultlen = strlen( result[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<nseq-1; i++ ) strcpy( aseq[i], result[i] );
-    strcpy( seq, result[nseq-1] );
-
-    return( 0.0 );
-}