Merge new upstream release

17 files changed, 117 insertions, 28 deletions

diff --git a/cgats/Jamfile b/cgats/Jamfile
index 813269a..813269a 100644..100755
--- a/cgats/Jamfile
+++ b/cgats/Jamfile
diff --git a/cgats/License.txt b/cgats/License.txt
index 7655233..7655233 100644..100755
--- a/cgats/License.txt
+++ b/cgats/License.txt
diff --git a/cgats/Makefile b/cgats/Makefile
index 5312104..5312104 100644..100755
--- a/cgats/Makefile
+++ b/cgats/Makefile
diff --git a/cgats/Makefile.IBMNT b/cgats/Makefile.IBMNT
index 26a2bd2..26a2bd2 100644..100755
--- a/cgats/Makefile.IBMNT
+++ b/cgats/Makefile.IBMNT
diff --git a/cgats/Makefile.OSX b/cgats/Makefile.OSX
index fb1c88f..fb1c88f 100644..100755
--- a/cgats/Makefile.OSX
+++ b/cgats/Makefile.OSX
diff --git a/cgats/Makefile.UNIX b/cgats/Makefile.UNIX
index 91d6005..91d6005 100644..100755
--- a/cgats/Makefile.UNIX
+++ b/cgats/Makefile.UNIX
diff --git a/cgats/Makefile.WNT b/cgats/Makefile.WNT
index 4ca291d..4ca291d 100644..100755
--- a/cgats/Makefile.WNT
+++ b/cgats/Makefile.WNT
diff --git a/cgats/Readme.txt b/cgats/Readme.txt
index 94f3e3d..94f3e3d 100644..100755
--- a/cgats/Readme.txt
+++ b/cgats/Readme.txt
diff --git a/cgats/afiles b/cgats/afiles
index dc20cb4..e185eb7 100644..100755
--- a/cgats/afiles
+++ b/cgats/afiles
@@ -7,6 +7,7 @@ pars.c
 pars.h
 parsstd.c
 cgatsstd.c
+test.txt
 Jamfile
 Makefile
 Makefile.WNT
diff --git a/cgats/cgats.c b/cgats/cgats.c
index a39ec04..3e6e642 100644..100755
--- a/cgats/cgats.c
+++ b/cgats/cgats.c
@@ -68,7 +68,8 @@ extern void error(const char *fmt, ...), warning(const char *fmt, ...);
 #include "pars.h"
 #include "cgats.h"
 
-#define REAL_SIGDIG 6		/* Number of significant digits in real representation */
+#undef  EMIT_KEYWORDS		/* [und] Emit unknown keywords by default */
+#define REAL_SIGDIG 6		/* [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);
@@ -147,6 +148,10 @@ cgatsAlloc *al			/* memory allocator */
 	p->write_name = NULL;
 #endif
 
+#ifdef EMIT_KEYWORDS
+	p->emit_keywords = 1;
+#endif
+
 	return p;
 }
 
@@ -668,6 +673,7 @@ cgats_read(cgats *p, cgatsFile *fp) {
 						for (j = 0; j < ct->nsets; j++) {
 							data_type ty;
 							ty = guess_type(((char *)ct->rfdata[j][i]));
+
 							if (ty == cs_t) {
 								bt = cs_t;
 								break;		/* Early out */
@@ -678,7 +684,7 @@ cgats_read(cgats *p, cgatsFile *fp) {
 								if (bt == i_t)
 									bt = ty;
 							} else { /* ty == i_t */
-								bt = ty;
+								/* This is the default */
 							}
 						}
 						/* Got guessed type bt. Sanity check against known field types */
@@ -1446,7 +1452,7 @@ cgats_write(cgats *p, cgatsFile *fp) {
 
 			/* Keyword and data if it is present */
 			if (t->ksym[i] != NULL && t->kdata[i] != NULL) {
-				if (!standard_kword(t->ksym[i])) {	/* Do the right thing */
+				if (p->emit_keywords && !standard_kword(t->ksym[i])) {	/* Do the right thing */
 					if ((qs = quote_cs(al, t->ksym[i])) == NULL) {
 						al->free(al, sfield);
 						return err(p,-2,"quote_cs() malloc failed!");
@@ -1485,7 +1491,7 @@ cgats_write(cgats *p, cgatsFile *fp) {
 	
 			/* Declare any non-standard fields */
 			for (field = 0; field < t->nfields; field++) {
-				if (!sfield[field])	/* Non-standard */ {
+				if (p->emit_keywords && !sfield[field])	/* Non-standard */ {
 					char *qs;
 					if ((qs = quote_cs(al, t->fsym[field])) == NULL) {
 						al->free(al, sfield);
@@ -1931,21 +1937,22 @@ real_format(double value, int nsd, char *fmt) {
 		xtot++;
 	}
 	if (value < 1.0) {
+		int thr = -5;
 		ndigs = (int)(log10(value));
-		if (ndigs <= -2) {
+		if (ndigs <= thr) {
 			sprintf(fmt,"%%%d.%de",xtot,tot-2);
 			return;
 		}
 		sprintf(fmt,"%%%d.%df",xtot-ndigs,nsd-ndigs);
 		return;
 	} else {
+		int thr = -0;
 		ndigs = (int)(log10(value));
-		if (ndigs >= (nsd -1))
-			{
+		if (ndigs >= (nsd + thr)) {
 			sprintf(fmt,"%%%d.%de",xtot,tot-2);
 			return;
-			}
-		sprintf(fmt,"%%%d.%df",xtot,(nsd-1)-ndigs);
+		}
+		sprintf(fmt,"%%%d.%df",xtot,(nsd + thr)-ndigs);
 		return;
 	}
 }
@@ -2090,24 +2097,29 @@ main(int argc, char *argv[]) {
 		 || pp->add_field(pp, 0, "XYZ_X", r_t) < 0)
 			error("Initial error: '%s'",pp->err);
 	
-		if (pp->add_set(pp, 0, "1", "A1",  0.000012345678) < 0
-		 || pp->add_set(pp, 0, "2", "A2",  0.00012345678) < 0
-		 || pp->add_set(pp, 0, "3 ", "A#5",0.0012345678) < 0
-		 || pp->add_set(pp, 0, "4", "A5",  0.012345678) < 0
-		 || pp->add_set(pp, 0, "5", "A5",  0.12345678) < 0
-		 || pp->add_set(pp, 0, "5", "A5",  0.00000000) < 0
-		 || pp->add_set(pp, 0, "6", "A5",  1.2345678) < 0
-		 || pp->add_set(pp, 0, "7", "A5",  12.345678) < 0
-		 || pp->add_set(pp, 0, "8", "A5",  123.45678) < 0
-		 || pp->add_set(pp, 0, "9", "A5",  1234.5678) < 0
-		 || pp->add_set(pp, 0, "10", "A5", 12345.678) < 0
-		 || pp->add_set(pp, 0, "12", "A5", 123456.78) < 0
-		 || pp->add_set(pp, 0, "13", "A5", 1234567.8) < 0
-		 || pp->add_set(pp, 0, "14", "A5", 12345678.0) < 0
-		 || pp->add_set(pp, 0, "15", "A5", 123456780.0) < 0
-		 || pp->add_set(pp, 0, "16", "A5", 1234567800.0) < 0
-		 || pp->add_set(pp, 0, "17", "A5", 12345678000.0) < 0
-		 || pp->add_set(pp, 0, "18", "A5", 123456780000.0) < 0)
+		if (pp->add_set(pp, 0, "1", "A1",  0.000000012345678) < 0
+		 || pp->add_set(pp, 0, "2", "A1",  0.00000012345678) < 0
+		 || pp->add_set(pp, 0, "3", "A1",  0.0000012345678) < 0
+		 || pp->add_set(pp, 0, "4", "A1",  0.000012345678) < 0
+		 || pp->add_set(pp, 0, "5", "A1",  0.000012345678) < 0
+		 || pp->add_set(pp, 0, "6", "A2",  0.00012345678) < 0
+		 || pp->add_set(pp, 0, "7", "A5",0.0012345678) < 0
+		 || pp->add_set(pp, 0, "8", "A5",  0.012345678) < 0
+		 || pp->add_set(pp, 0, "9", "A5",  0.12345678) < 0
+		 || pp->add_set(pp, 0, "10", "A5",  0.00000000) < 0
+		 || pp->add_set(pp, 0, "11", "A5",  1.2345678) < 0
+		 || pp->add_set(pp, 0, "12", "A5",  12.345678) < 0
+		 || pp->add_set(pp, 0, "13", "A5",  123.45678) < 0
+		 || pp->add_set(pp, 0, "14", "A5",  1234.5678) < 0
+		 || pp->add_set(pp, 0, "15", "A5", 12345.678) < 0
+		 || pp->add_set(pp, 0, "16", "A5", 123456.78) < 0
+		 || pp->add_set(pp, 0, "17", "A5", 1234567.8) < 0
+		 || pp->add_set(pp, 0, "18", "A5", 12345678.0) < 0
+		 || pp->add_set(pp, 0, "19", "A5", 123456780.0) < 0
+		 || pp->add_set(pp, 0, "20", "A5", 1234567800.0) < 0
+		 || pp->add_set(pp, 0, "21", "A5", 12345678000.0) < 0
+		 || pp->add_set(pp, 0, "22", "A5", 123456780000.0) < 0
+		 || pp->add_set(pp, 0, "23", "A5", 1234567800000.0) < 0)
 			error("Adding set error '%s'",pp->err);
 		
 		if (pp->add_table(pp, cgats_5, 0) < 0			/* Start the second table */
diff --git a/cgats/cgats.h b/cgats/cgats.h
index 7537a48..bc0cdd7 100644..100755
--- a/cgats/cgats.h
+++ b/cgats/cgats.h
@@ -87,6 +87,9 @@ struct _cgats {
 	int nothers;		/* Number of other identifiers */
 	char **others;		/* Other file type identifiers */
 
+	/* Options */
+	int emit_keywords;	/* NZ to emit "KEYWORD" for non-standard keywords (default no) */
+
 	/* Public Methods */
 	int (*set_cgats_type)(struct _cgats *p, const char *osym);
 											/* Define the (one) variable CGATS type */
diff --git a/cgats/cgatsstd.c b/cgats/cgatsstd.c
index d8fbb34..d8fbb34 100644..100755
--- a/cgats/cgatsstd.c
+++ b/cgats/cgatsstd.c
diff --git a/cgats/makezip.ksh b/cgats/makezip.ksh
index 8cc5f6c..8cc5f6c 100644..100755
--- a/cgats/makezip.ksh
+++ b/cgats/makezip.ksh
diff --git a/cgats/pars.c b/cgats/pars.c
index a0e694c..8a4e4b9 100644..100755
--- a/cgats/pars.c
+++ b/cgats/pars.c
@@ -606,7 +606,7 @@ main() {
 		error("Failed to create parse object with file 'test.txt'");
 
 	/* Setup our token parsing charaters */
-	pp->add_del(pp, " ,\to"," ,\t", "#", "\"");
+	pp->add_del(pp, " ,\t"," ,\t", "#", "\"");
 
 	for (;;) {
 		char *tp;
diff --git a/cgats/pars.h b/cgats/pars.h
index 83bbdad..83bbdad 100644..100755
--- a/cgats/pars.h
+++ b/cgats/pars.h
diff --git a/cgats/parsstd.c b/cgats/parsstd.c
index 4443e0a..4443e0a 100644..100755
--- a/cgats/parsstd.c
+++ b/cgats/parsstd.c
diff --git a/cgats/test.txt b/cgats/test.txt
new file mode 100755
index 0000000..5036d32
--- /dev/null
+++ b/cgats/test.txt
@@ -0,0 +1,73 @@
+CGATS.5
+
+# Comment only test comment
+KEYWORD "TEST_KEY_WORD"
+TEST_KEY_WORD "try this out"	# Keyword comment
+KEYWORD "TEST_KEY_WORD2"
+TEST_KEY_WORD2 "try this"" out """" huh !"
+ORIGINATOR "Not specified"
+DESCRIPTOR "Not specified"
+CREATED "November 16, 2000"
+INSTRUMENTATION "Not specified"
+MEASUREMENT_SOURCE "Not specified"
+PRINT_CONDITIONS "Not specified"
+
+KEYWORD "SAMPLE_LOC"
+NUMBER_OF_FIELDS 3
+BEGIN_DATA_FORMAT
+SAMPLE_ID SAMPLE_LOC XYZ_X 
+END_DATA_FORMAT
+
+NUMBER_OF_SETS 22
+BEGIN_DATA
+1 A1 1.2346e-09 
+2 A1 1.2346e-08 
+3 A1 1.2346e-07 
+4 A1 1.2346e-06 
+5 A1 1.2346e-05 
+6 A2 1.2346e-04 
+"7 " "A#5" 1.2346e-03 
+8 A5 0.012346 
+9 A5 0.12346 
+10 A5 0.0000 
+11 A5 1.2346 
+12 A5 12.346 
+13 A5 123.46 
+14 A5 1234.6 
+16 A5 1.2346e+04 
+17 A5 1.2346e+05 
+18 A5 1.2346e+06 
+19 A5 1.2346e+07 
+20 A5 1.2346e+08 
+21 A5 1.2346e+09 
+22 A5 1.2346e+10 
+23 A5 1.2346e+11 
+END_DATA
+
+
+# Second Comment only test comment
+
+NUMBER_OF_SETS 22
+BEGIN_DATA
+1 A4 -1.2346e-09 
+2 A4 -1.2346e-08 
+3 A4 -1.2346e-07 
+4 A4 -1.2346e-06 
+5 A4 -1.2346e-05 
+6 A5 -1.2346e-04 
+7 A5 -1.2346e-03 
+8 A5 -0.012346 
+9 A5 -0.12346 
+10 A5 -1.2346 
+11 A5 -12.346 
+12 A5 -123.46 
+13 A5 -1234.6 
+14 A5 -1.2346e+04 
+15 A5 -1.2346e+05 
+16 A5 -1.2346e+06 
+17 A5 -1.2346e+07 
+18 A5 -1.2346e+08 
+19 A5 -1.2346e+09 
+20 A5 -1.2346e+10 
+21 A5 -1.2346e+11 
+E7D_DATA