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-rwxr-xr-x[-rw-r--r--]cgats/Jamfile0
-rwxr-xr-x[-rw-r--r--]cgats/License.txt0
-rwxr-xr-x[-rw-r--r--]cgats/Makefile0
-rwxr-xr-x[-rw-r--r--]cgats/Makefile.IBMNT0
-rwxr-xr-x[-rw-r--r--]cgats/Makefile.OSX0
-rwxr-xr-x[-rw-r--r--]cgats/Makefile.UNIX0
-rwxr-xr-x[-rw-r--r--]cgats/Makefile.WNT0
-rwxr-xr-x[-rw-r--r--]cgats/Readme.txt0
-rwxr-xr-x[-rw-r--r--]cgats/afiles1
-rwxr-xr-x[-rw-r--r--]cgats/cgats.c66
-rwxr-xr-x[-rw-r--r--]cgats/cgats.h3
-rwxr-xr-x[-rw-r--r--]cgats/cgatsstd.c0
-rwxr-xr-x[-rw-r--r--]cgats/makezip.ksh0
-rwxr-xr-x[-rw-r--r--]cgats/pars.c2
-rwxr-xr-x[-rw-r--r--]cgats/pars.h0
-rwxr-xr-x[-rw-r--r--]cgats/parsstd.c0
-rwxr-xr-xcgats/test.txt73
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
generated by cgit v1.2.3 (git 2.25.1) at 2024-04-27 18:06:17 +0000