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-rw-r--r--src/indexamajig.c29
1 files changed, 16 insertions, 13 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 980f23f1..4d0b227a 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -219,28 +219,40 @@ int main(int argc, char *argv[])
/* Long options */
const struct option longopts[] = {
+
+ /* Options with long and short versions */
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
{"indexing", 1, NULL, 'z'},
{"geometry", 1, NULL, 'g'},
{"beam", 1, NULL, 'b'},
+ {"pdb", 1, NULL, 'p'},
+ {"prefix", 1, NULL, 'x'},
+ {"threshold", 1, NULL, 't'},
+ {"image", 1, NULL, 'e'},
+
+ /* Long-only options with no arguments */
{"filter-cm", 0, &iargs.config_cmfilter, 1},
{"filter-noise", 0, &iargs.config_noisefilter, 1},
{"verbose", 0, &iargs.config_verbose, 1},
- {"pdb", 1, NULL, 'p'},
- {"prefix", 1, NULL, 'x'},
{"no-sat-corr", 0, &iargs.config_satcorr, 0},
{"sat-corr", 0, &iargs.config_satcorr, 1},
- {"threshold", 1, NULL, 't'},
{"no-check-prefix", 0, &config_checkprefix, 0},
{"no-closer-peak", 0, &iargs.config_closer, 0},
{"closer-peak", 0, &iargs.config_closer, 1},
- {"image", 1, NULL, 'e'},
{"basename", 0, &config_basename, 1},
{"bg-sub", 0, &iargs.config_bgsub, 1},
{"no-bg-sub", 0, &iargs.config_bgsub, 0},
+ {"no-peaks-in-stream", 0, &iargs.stream_peaks, 0},
+ {"no-refls-in-stream", 0, &iargs.stream_refls, 0},
+ {"res-cutoff", 0, &iargs.res_cutoff, 1},
+ {"integrate-saturated",0, &iargs.integrate_saturated,1},
+ {"use-saturated", 0, &iargs.use_saturated, 1},
+ {"no-revalidate", 0, &iargs.no_revalidate, 1},
+ {"integrate-found", 0, &iargs.integrate_found, 1},
+ /* Long-only options with arguments */
{"peaks", 1, NULL, 2},
{"cell-reduction", 1, NULL, 3},
{"min-gradient", 1, NULL, 4},
@@ -254,16 +266,7 @@ int main(int argc, char *argv[])
{"min-integration-snr",1, NULL, 12},
{"tolerance", 1, NULL, 13},
{"int-radius", 1, NULL, 14},
- {"no-peaks-in-stream", 1, &iargs.stream_peaks, 0},
- {"no-refls-in-stream", 1, &iargs.stream_refls, 0},
- {"res-cutoff", 1, &iargs.res_cutoff, 1},
-
- /* FIXME: Add '--no-peaks' and '--no-reflections' */
- {"integrate-saturated",0, &iargs.integrate_saturated,1},
- {"use-saturated", 0, &iargs.use_saturated, 1},
- {"no-revalidate", 0, &iargs.no_revalidate, 1},
- {"integrate-found", 0, &iargs.integrate_found, 1},
{0, 0, NULL, 0}
};