Imported Upstream version 1.6.3upstream/1.6.3

3 files changed, 81 insertions, 19 deletions

diff --git a/cgats/cgats.c b/cgats/cgats.c
index baf9992..84ff2c9 100644
--- a/cgats/cgats.c
+++ b/cgats/cgats.c
@@ -14,6 +14,34 @@
  * see the License.txt file in this directory for licensing details.
  */
 
+/*
+
+	Should add a function to promote a field type, ie.
+	promote integer to float, to avoid misrecognition
+	problems.
+
+
+	To make this more portable for independent use,
+	should save/set/restore LC_NUMERIC locale before
+	printf/scanf from file. e.g.
+
+		include <locale.h>
+		char *old_locale, *saved_locale;
+     
+		old_locale = setlocale (LC_NUMERIC, NULL);
+		saved_locale = strdup (old_locale);
+		if (saved_locale == NULL)
+			error ("Out of memory");
+		setlocale (LC_NUMERIC, "C");
+
+		.... read or write ...
+     
+		setlocale (LC_NUMERIC, saved_locale);
+		free (saved_locale);
+
+	Also apply to pars.c
+ */
+
 #define _CGATS_C_				/* Turn on implimentation code */
 
 #include <stdio.h>
@@ -23,8 +51,8 @@
 #undef DEBUG				/* Debug only in slected places */
 
 #ifdef DEBUG
-# define DBGA g_log, 0 		/* First argument to DBGF() */
-# define DBGF(xx)	a1logd xx
+# define DBGA stderr
+# define DBGF(xx)	fprintf xx
 #else
 # define DBGF(xx)
 #endif
@@ -40,7 +68,7 @@ extern void error(const char *fmt, ...), warning(const char *fmt, ...);
 #include "pars.h"
 #include "cgats.h"
 
-#define REAL_SIGDIG 5		/* Number of significant digits in real representation */
+#define REAL_SIGDIG 6		/* Number of significant digits in real representation */
 
 static int cgats_read(cgats *p, cgatsFile *fp);
 static int find_kword(cgats *p, int table, const char *ksym);
@@ -374,6 +402,14 @@ cgats_read(cgats *p, cgatsFile *fp) {
 		if (tp == NULL)
 			break;		/* EOF */
 
+		/* This seems unlikely and will cause err() to barf */
+		if (strlen(tp) > CGATS_ERRM_LENGTH/2) {
+			tp[CGATS_ERRM_LENGTH/2] = '\000';
+			err(p,-1,"Read line got symbol '%s' that's too long\n",tp);
+			pp->del(pp);
+			return p->errc;
+		}
+
 		switch(rstate) {
 			case R_IDENT: 		/* Expecting file identifier */
 			case R_KWORDS: {	/* Expecting keyword, field def or data */
@@ -938,16 +974,19 @@ add_field(cgats *p, int table, const char *fsym, data_type ftype) {
 
 	p->errc = 0;
 	p->err[0] = '\000';
-	if (table < 0 || table >= p->ntables)
+	if (table < 0 || table >= p->ntables) {
 		return err(p,-1,"cgats.add_field(), table parameter out of range");
+	}
 	t = &p->t[table];
 
-	if (t->nsets != 0)
+	if (t->nsets != 0) {
 		return err(p,-1,"cgats.add_field(), attempt to add field to non-empty table");
+	}
 
 	/* Check the field name is reasonable */
-	if (cs_has_ws(fsym))
+	if (cs_has_ws(fsym)) {
 		return err(p,-1,"cgats.add_kword(), field name '%s'is illegal",fsym);
+	}
 
 	if (ftype == none_t)
 		ftype = cs_t;					/* Fudge - unknown type yet, used for reads */
@@ -956,22 +995,27 @@ add_field(cgats *p, int table, const char *fsym, data_type ftype) {
 		st = standard_field(fsym);
 		if (st == nqcs_t && ftype == cs_t)	/* Fudge - standard type to non-quoted if normal */
 			ftype = nqcs_t;
-		if (st != none_t && st != ftype)
+		if (st != none_t && st != ftype) {
 			return err(p,-1,"cgats.add_field(): unexpected data type for standard field name");
+		}
 	}
 
 	t->nfields++;
 	if (t->nfields > t->nfieldsa) {
-		/* Allocate fields in groups of 4 */
-		t->nfieldsa += 4;
-		if ((t->fsym = (char **)al->realloc(al, t->fsym, t->nfieldsa * sizeof(char *))) == NULL)
+		/* Allocate fields in groups of 32 */
+		t->nfieldsa += 32;
+		if ((t->fsym = (char **)al->realloc(al, t->fsym, t->nfieldsa * sizeof(char *))) == NULL) {
 			return err(p,-2,"cgats.add_field(), realloc failed!");
+		}
 		if ((t->ftype = (data_type *)al->realloc(al, t->ftype, t->nfieldsa * sizeof(data_type)))
-		                                                                               == NULL)
+		                                                                               == NULL) {
 			return err(p,-2,"cgats.add_field(), realloc failed!");
+		}
 	}
-	if ((t->fsym[t->nfields-1] = (char *)alloc_copy_data_type(al, cs_t, (void *)fsym)) == NULL)
+	if ((t->fsym[t->nfields-1] = (char *)alloc_copy_data_type(al, cs_t, (void *)fsym)) == NULL) {
 		return err(p,-2,"cgats.alloc_copy_data_type() malloc fail");
+	}
+
 	t->ftype[t->nfields-1] = ftype;
 
 	return t->nfields-1;
diff --git a/cgats/cgats.h b/cgats/cgats.h
index 2a6b1fd..7537a48 100644
--- a/cgats/cgats.h
+++ b/cgats/cgats.h
@@ -20,7 +20,7 @@
 #define CGATSLIB_VERSION 0x020005
 #define CGATSLIB_VERSION_STR "2.05"
 
-#define CGATS_ERRM_LENGTH 200
+#define CGATS_ERRM_LENGTH 2000
 
 #ifdef __cplusplus
 	extern "C" {
diff --git a/cgats/pars.c b/cgats/pars.c
index 606957c..a0e694c 100644
--- a/cgats/pars.c
+++ b/cgats/pars.c
@@ -41,6 +41,8 @@ extern void error(const char *fmt, ...), warning(const char *fmt, ...);
 
 #include "pars.h"
 
+#undef DEBUG			/* Print each token returned */
+
 static void del_parse(parse *p);
 static int read_line(parse *p);
 static void reset_del(parse *p);
@@ -420,6 +422,9 @@ read_line(parse *p) {
 		if ((c = p->fp->getch(p->fp)) == EOF) {
 			if (p->bo == 0) {	/* If there is nothing in the buffer */
 				p->line = 0;
+#ifdef DEBUG
+				printf("pars: read_line() got EOF\n");
+#endif
 				return 0;
 			}
 			c = 0;			/* Finish the line */
@@ -443,16 +448,16 @@ read_line(parse *p) {
 		}
 
 		if (c == '\r') {
-			p->line++;		/* Increment line number */
+			p->line++;			/* Increment line number */
 			p->ltflag = 1;		/* Remember to allow 1 of '\n' before next line */
 			if (p->q == 0)
-				c = 0;		/* Finish the line */
+				c = 0;			/* Finish the line */
 		} else if (p->q == 0 && (p->delf[c] & PARS_COMM) != 0) {	/* Hit a comment */
-			p->line++;		/* Increment line number */
+			p->line++;			/* Increment line number */
 			p->ltflag = 2;		/* Remember to flush all chars up to end of line */
-			c = 0;			/* Finish the line */
+			c = 0;				/* Finish the line */
 		} else if (c == '\n') {
-			p->line++;		/* Increment line number */
+			p->line++;			/* Increment line number */
 			if (p->q == 0)
 				c = 0;			/* Finish the the line */
 		}
@@ -477,6 +482,9 @@ read_line(parse *p) {
 	} while (c != 0);	/* Null means we've done the end of the line */
 	p->to = 0;			/* Reset token pointer to the start of the line buffer */
 	p->q = 0;			/* Reset quoted flag */
+#ifdef DEBUG
+	printf("pars: read_line() got buffer '%s'\n",p->b);
+#endif
 	return 1;
 }
 
@@ -525,8 +533,12 @@ get_token(parse *p) {
 
 	p->errc = 0;		/* Reset error status */
 	p->err[0] = '\000';
-	if (p->b == NULL)
+	if (p->b == NULL) {
+#ifdef DEBUG
+		printf("pars: read_token() NULL buffe\n");
+#endif
 		return NULL;
+	}
 	p->token++;		/* Increment token number */
 	p->q = 0;
 	do {
@@ -566,8 +578,14 @@ get_token(parse *p) {
 	p->q = 0;
 	if (tbo <= 1) {
 		p->token = 0;
+#ifdef DEBUG
+		printf("pars: read_token() got nothing useful\n");
+#endif
 		return NULL;		/* Haven't read anything useful */
 	}
+#ifdef DEBUG
+	printf("pars: read_token() returning '%s'\n",p->tb);
+#endif
 	return p->tb;
 }