X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2FHalignmm.c;h=bec9de2739b507f1aa19dac0119f5f216505da4f;hb=063b30bb5e8161134ae764742636ab538e10eea7;hp=2d58cd7ceb5763da523cd0b4a96c4d41379c1ff6;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/binaries/src/mafft/core/Halignmm.c b/binaries/src/mafft/core/Halignmm.c
index 2d58cd7..bec9de2 100644
--- a/binaries/src/mafft/core/Halignmm.c
+++ b/binaries/src/mafft/core/Halignmm.c
@@ -8,7 +8,7 @@
 #define USE_PENALTY_EX  0
 #define FASTMATCHCALC 1
 
-static float **impmtx = NULL;
+static TLS float **impmtx = NULL;
 
 #if 0 // by D.Mathog
 static float countnocountxx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int offset2 )
@@ -180,12 +180,12 @@ static void imp_match_out_vead_tateH( float *imp, int j1, int lgth1 )
 void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
 {
 	int i, j, k1, k2, tmpint, start1, start2, end1, end2;
-	static int impalloclen = 0;
+	static TLS int impalloclen = 0;
 	float effij;
 	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( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
@@ -718,39 +718,39 @@ float H__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 Gappat **gappat1;
-	static Gappat **gappat2;
-	static float *digf1;
-	static float *digf2;
-	static float *diaf1;
-	static float *diaf2;
-	static float *gapz1;
-	static float *gapz2;
-	static float *gapf1;
-	static float *gapf2;
-	static float *ogcp1g;
-	static float *ogcp2g;
-	static float *fgcp1g;
-	static float *fgcp2g;
-	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 Gappat **gappat1;
+	static TLS Gappat **gappat2;
+	static TLS float *digf1;
+	static TLS float *digf2;
+	static TLS float *diaf1;
+	static TLS float *diaf2;
+	static TLS float *gapz1;
+	static TLS float *gapz2;
+	static TLS float *gapf1;
+	static TLS float *gapf2;
+	static TLS float *ogcp1g;
+	static TLS float *ogcp2g;
+	static TLS float *fgcp1g;
+	static TLS float *fgcp2g;
+	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 tmppenal;
 	float cumpenal;