fixes #39

include/digest/data_structure.hpp

@@ -115,7 +115,7 @@ template <uint32_t k> struct Naive {
 	std::array<uint64_t, k> arr;
 	unsigned int i = 0;
 
-	Naive(uint32_t) {};
+	Naive(uint32_t){};
 	Naive(const Naive &other) = default;
 	Naive &operator=(const Naive &other) = default;
 
@@ -183,7 +183,7 @@ template <uint32_t k> struct Naive2 {
 	unsigned int last = 0;
 	std::vector<uint64_t> arr = std::vector<uint64_t>(k);
 
-	Naive2(uint32_t) {};
+	Naive2(uint32_t){};
 	Naive2(const Naive2 &other) = default;
 	Naive2 &operator=(const Naive2 &other) = default;
 

include/digest/digester.hpp

@@ -207,7 +207,7 @@ template <BadCharPolicy P> class Digester {
 	 * @throws BadConstructionException thrown if the starting position is
 	 * greater than the length of the string
 	 */
-	void new_seq(const char *seq, size_t len, size_t start) {
+	virtual void new_seq(const char *seq, size_t len, size_t start) {
 		this->seq = seq;
 		this->len = len;
 		this->offset = 0;
@@ -231,7 +231,7 @@ template <BadCharPolicy P> class Digester {
 	 * @throws BadConstructionException thrown if the starting position is
 	 * greater than the length of the string
 	 */
-	void new_seq(const std::string &seq, size_t pos) {
+	virtual void new_seq(const std::string &seq, size_t pos) {
 		new_seq(seq.c_str(), seq.size(), pos);
 	}
 

include/digest/window_minimizer.hpp

@@ -131,6 +131,16 @@ template <BadCharPolicy P, class T> class WindowMin : public Digester<P> {
 		}
 	}
 
+	void new_seq(const char *seq, size_t len, size_t start) override {
+		ds = T(large_window);
+		Digester<P>::new_seq(seq, len, start);
+	}
+
+	void new_seq(const std::string &seq, size_t pos) override {
+		ds = T(large_window);
+		Digester<P>::new_seq(seq.c_str(), seq.size(), pos);
+	}
+
 	/**
 	 *
 	 * @return unsigned, the value of large_window
@@ -139,16 +149,18 @@ template <BadCharPolicy P, class T> class WindowMin : public Digester<P> {
 
 	// function is mainly to help with tests
 	/**
-	 * @brief gets the size of the internal rmq data structure being used. Mainly used to help with tests (so you probably shouldn't use it).
-	 * 
+	 * @brief gets the size of the internal rmq data structure being used.
+	 * Mainly used to help with tests (so you probably shouldn't use it).
+	 *
 	 * @return size_t, the size of the internal rmq data structure object
 	 */
 	size_t get_ds_size() { return ds_size; }
 
 	// function is mainly to help with tests
 	/**
-	 * @brief checks if we have generated the first minimizer. Mainly used to help with tests (so you probably shouldn't use it).
-	 * 
+	 * @brief checks if we have generated the first minimizer. Mainly used to
+	 * help with tests (so you probably shouldn't use it).
+	 *
 	 * @return bool, if we have already obtained a minimizer
 	 */
 	bool get_is_minimized() { return is_minimized; }

pybind/bindings.cpp

@@ -1,15 +1,20 @@
+#include <digest_utils.hpp>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
-#include <digest_utils.hpp>
 
 namespace py = pybind11;
 
 PYBIND11_MODULE(Digest, m) {
-    m.doc() = "bindings for Digest";
-    m.def("window_minimizer", &window_minimizer, "A function that runs window minimizer digestion",
-            py::arg("seq"), py::arg("k") = 31, py::arg("w") = 11, py::arg("include_hash") = false);
-    m.def("modimizer", &modimizer, "A function that runs mod-minimizer digestion",
-            py::arg("seq"), py::arg("k") = 31, py::arg("mod") = 100, py::arg("include_hash") = false);
-    m.def("syncmer", &syncmer, "A function that runs syncmer digestion",
-            py::arg("seq"), py::arg("k") = 31, py::arg("w") = 11, py::arg("include_hash") = false);
+	m.doc() = "bindings for Digest";
+	m.def("window_minimizer", &window_minimizer,
+		  "A function that runs window minimizer digestion", py::arg("seq"),
+		  py::arg("k") = 31, py::arg("w") = 11,
+		  py::arg("include_hash") = false);
+	m.def("modimizer", &modimizer,
+		  "A function that runs mod-minimizer digestion", py::arg("seq"),
+		  py::arg("k") = 31, py::arg("mod") = 100,
+		  py::arg("include_hash") = false);
+	m.def("syncmer", &syncmer, "A function that runs syncmer digestion",
+		  py::arg("seq"), py::arg("k") = 31, py::arg("w") = 11,
+		  py::arg("include_hash") = false);
 }

pybind/digest_utils.hpp

@@ -1,50 +1,52 @@
-#include <digest/window_minimizer.hpp>
-#include <digest/syncmer.hpp>
 #include <digest/mod_minimizer.hpp>
+#include <digest/syncmer.hpp>
+#include <digest/window_minimizer.hpp>
 #include <variant>
 
-std::variant<std::vector<uint32_t>, std::vector<std::pair<uint32_t, uint32_t>>> window_minimizer (
-        const std::string &seq, unsigned k, unsigned large_window, bool include_hash=false) {
-    digest::WindowMin<digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive> digester (seq, k, large_window);
-    if (include_hash) {
-        std::vector<std::pair<uint32_t, uint32_t>> output;
-        digester.roll_minimizer(seq.length(), output);
-        return output;
-    }
-    else {
-        std::vector<uint32_t> output;
-        digester.roll_minimizer(seq.length(), output);
-        return output;
-    }
+std::variant<std::vector<uint32_t>, std::vector<std::pair<uint32_t, uint32_t>>>
+window_minimizer(const std::string &seq, unsigned k, unsigned large_window,
+				 bool include_hash = false) {
+	digest::WindowMin<digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive>
+		digester(seq, k, large_window);
+	if (include_hash) {
+		std::vector<std::pair<uint32_t, uint32_t>> output;
+		digester.roll_minimizer(seq.length(), output);
+		return output;
+	} else {
+		std::vector<uint32_t> output;
+		digester.roll_minimizer(seq.length(), output);
+		return output;
+	}
 }
-//std::vector<std::pair<size_t, size_t>> output;
+// std::vector<std::pair<size_t, size_t>> output;
 
-std::variant<std::vector<uint32_t>, std::vector<std::pair<uint32_t, uint32_t>>> modimizer (
-        const std::string &seq, unsigned k, uint32_t mod, bool include_hash=false) {
-    digest::ModMin<digest::BadCharPolicy::SKIPOVER> digester (seq, k, mod);
-    if (include_hash) {
-        std::vector<std::pair<uint32_t, uint32_t>> output;
-        digester.roll_minimizer(seq.length(), output);
-        return output;
-    }
-    else {
-        std::vector<uint32_t> output;
-        digester.roll_minimizer(seq.length(), output);
-        return output;
-    }
+std::variant<std::vector<uint32_t>, std::vector<std::pair<uint32_t, uint32_t>>>
+modimizer(const std::string &seq, unsigned k, uint32_t mod,
+		  bool include_hash = false) {
+	digest::ModMin<digest::BadCharPolicy::SKIPOVER> digester(seq, k, mod);
+	if (include_hash) {
+		std::vector<std::pair<uint32_t, uint32_t>> output;
+		digester.roll_minimizer(seq.length(), output);
+		return output;
+	} else {
+		std::vector<uint32_t> output;
+		digester.roll_minimizer(seq.length(), output);
+		return output;
+	}
 }
 
-std::variant<std::vector<uint32_t>, std::vector<std::pair<uint32_t, uint32_t>>> syncmer (
-        const std::string &seq, unsigned k, unsigned large_window, bool include_hash=false) {
-    digest::Syncmer<digest::BadCharPolicy::WRITEOVER, digest::ds::Adaptive> digester (seq, k, large_window);
-    if (include_hash) {
-        std::vector<std::pair<uint32_t, uint32_t>> output;
-        digester.roll_minimizer(seq.length(), output);
-        return output;
-    }
-    else {
-        std::vector<uint32_t> output;
-        digester.roll_minimizer(seq.length(), output);
-        return output;
-    }
+std::variant<std::vector<uint32_t>, std::vector<std::pair<uint32_t, uint32_t>>>
+syncmer(const std::string &seq, unsigned k, unsigned large_window,
+		bool include_hash = false) {
+	digest::Syncmer<digest::BadCharPolicy::WRITEOVER, digest::ds::Adaptive>
+		digester(seq, k, large_window);
+	if (include_hash) {
+		std::vector<std::pair<uint32_t, uint32_t>> output;
+		digester.roll_minimizer(seq.length(), output);
+		return output;
+	} else {
+		std::vector<uint32_t> output;
+		digester.roll_minimizer(seq.length(), output);
+		return output;
+	}
 }

tests/test/test.cpp

@@ -1246,7 +1246,7 @@ TEST_CASE("ModMin Testing") {
 	{ F(digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive, 32) }           \
 	{ F(digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive, 33) }           \
 	{ F(digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive, 63) }           \
-	{F(digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive, 64)}
+	{ F(digest::BadCharPolicy::SKIPOVER, digest::ds::Adaptive, 64) }
 
 TEST_CASE("WindowMin Testing") {
 	SECTION("Constructor Testing") {