diff options
| -rw-r--r-- | src/indexamajig.c | 29 |
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} }; |