all subcommand headers: adding a namespace to wrap a main and to hold the about and footer messages

Author: andrewdavidsmith

src/bound_pop.hpp

@@ -21,7 +21,15 @@
 #ifndef SRC_BOUND_POP_HPP_
 #define SRC_BOUND_POP_HPP_
 
-int
-bound_pop_main(int argc, char *argv[]);
+namespace bound_pop {
+
+const auto about_msg = R"(
+Estimate a bound on the size of the population using the initial sample.
+)";
+
+auto
+main(int argc, char *argv[]) -> int;
+
+};  // namespace bound_pop
 
 #endif  // SRC_BOUND_POP_HPP_

src/c_curve.hpp

@@ -21,7 +21,15 @@
 #ifndef SRC_C_CURVE_HPP_
 #define SRC_C_CURVE_HPP_
 
-int
-c_curve_main(int argc, char *argv[]);
+namespace c_curve {
+
+static constexpr auto about_msg = R"(
+Generate the full complexity curve for observed data (no extrapolation).
+)";
+
+auto
+main(int argc, char *argv[]) -> int;
+
+};  // namespace c_curve
 
 #endif  // SRC_C_CURVE_HPP_

src/gc_extrap.hpp

@@ -1,27 +1,42 @@
-/* Copyright (C) 2013-2024 University of Southern California and
+/* Copyright (C) 2013-2025 University of Southern California and
  *                         Andrew D. Smith and Timothy Daley
  *
  * Authors: Timothy Daley and Andrew Smith
  *
- * This program is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
+ * This program is free software: you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
  *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * General Public License for more details.
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+ * more details.
  *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see
- * <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License along
+ * with this program. If not, see <http://www.gnu.org/licenses/>.
  */
 
 #ifndef SRC_GC_EXTRAP_HPP_
 #define SRC_GC_EXTRAP_HPP_
 
-int
-gc_extrap_main(int argc, char *argv[]);
+namespace gc_extrap {
+
+static constexpr auto about_msg = R"(
+Estimate the size of the part of the genome to be covered by mapped reads.
+)";
+
+static constexpr auto footer_msg = R"(
+This approach is described in Daley & Smith (2014). The method is the same as
+for lc_extrap: using rational function approximation to a power-series
+expansion for the number of "unobserved" bases in the initial sample. The
+gc_extrap method is adapted to deal with individual nucleotides rather than
+distinct reads.
+)";
+
+auto
+main(int argc, char *argv[]) -> int;
+
+};  // namespace gc_extrap
 
 #endif  // SRC_GC_EXTRAP_HPP_

src/lc_extrap.hpp

@@ -21,7 +21,23 @@
 #ifndef SRC_LC_EXTRAP_HPP_
 #define SRC_LC_EXTRAP_HPP_
 
-int
-lc_extrap_main(int argc, char *argv[]);
+namespace lc_extrap {
+
+constexpr auto about_msg = R"(
+Estimate a complexity curve (e.g., for a sequencing library).
+)";
+
+constexpr auto footer_msg = R"(
+This is the approach described in Daley & Smith (2013). The method applies
+rational function approximation via continued fractions with the original goal
+of estimating the number of distinct reads that a sequencing library would
+yield upon deeper sequencing.  This method has been used for many different
+purposes since then.
+)";
+
+auto
+main(int argc, char *argv[]) -> int;
+
+};  // namespace lc_extrap
 
 #endif  // SRC_LC_EXTRAP_HPP_

src/pop_size.hpp

@@ -21,7 +21,22 @@
 #ifndef SRC_POP_SIZE_HPP_
 #define SRC_POP_SIZE_HPP_
 
-int
-pop_size_main(int argc, char *argv[]);
+namespace pop_size {
+
+static constexpr auto about_msg = R"(
+Estimate the population size using a small sample from the population.
+)";
+
+static constexpr auto footer_msg = R"(
+Estimate the total population size using the approach described in Daley &
+Smith (2013), extrapolating to very long range. Default parameters assume that
+the initial sample represents at least 1e-9 of the population, which is
+sufficient for every example application we have seen.
+)";
+
+auto
+main(int argc, char *argv[]) -> int;
+
+};  // namespace pop_size
 
 #endif  // SRC_POP_SIZE_HPP_