Clean up code, add more cpp11 features for performance

 - Fix typos in global.xmh
 - Remove dead zeta.cpp file
 - Establish a constexpr army
 - Convert NULL to nullptr

src/include/dawg/details/global.xmh

@@ -21,13 +21,13 @@ XM( (output)(block)(before),  std::string, ,
 XM( (output)(block)(after),   std::string, ,
 	"Text that will be written after every replicate.")
 XM( (output)(block)(between), std::string, ,
-	"Text that will be written betwee replicates.")
+	"Text that will be written between replicates.")
 
 //XM( (output)(vars),   bool, true)
 XM( (output)(file),   std::string, ,
 	"Path to the output file.")
 XM( (output)(split),  bool, false,
-	"Ouput each replicate to its own file.")
+	"Output each replicate to its own file.")
 XM( (output)(append), bool, false,
 	"Append results to existing file.")
 XM(  (output)(label), bool, false,

src/include/dawg/mutt.h

@@ -105,7 +105,7 @@ inline boost::uint32_t create_random_seed() {
 	boost::uint32_t v = static_cast<boost::uint32_t>(getpid());
 	v += ((v << 15) + (v >> 3)) + 0x6ba658b3; // Spread 5-decimal PID over 32-bit number
 	v^=(v<<17); v^=(v>>13); v^=(v<<5);
-	v += static_cast<boost::uint32_t>(time(NULL));
+	v += static_cast<boost::uint32_t>(time(nullptr));
 	v^=(v<<17); v^=(v>>13); v^=(v<<5);
 	return (v == 0) ? 0x6a27d958 : (v & 0x7FFFFFFF); // return at most a 31-bit seed
 }

src/include/dawg/output.h

@@ -18,7 +18,7 @@ namespace dawg {
 
 class output {
 public:
-	output() : do_op(&output::print_aln), p_out(NULL), format_id(0),
+	output() : do_op(&output::print_aln), p_out(nullptr), format_id(0),
 		rep(0), label_width(0),
 		do_append(false), do_split(false), do_label(false),
 		split_id_offset(0) { }
@@ -28,7 +28,7 @@ class output {
 
 	inline bool operator()(const alignment& aln) {
 		open_next();
-		if(p_out == NULL)
+		if(p_out == nullptr)
 			return false;
 		std::ostream &out = *p_out;
 		if(!do_split)
@@ -92,7 +92,7 @@ class output {
 
 template<class T>
 bool output::set_format(T format) {
-	static const char format_keys[][10] = {
+	static constexpr char format_keys[][10] = {
 		"aln", "poo", "fasta", "fsa",
 		"nexus", "phylip"
 	};

src/include/dawg/rate.h

@@ -22,7 +22,7 @@ class rate_model {
 
 	template<typename It>
 	bool create(const std::string &rname, It first, It last) {
-		static std::string name_keys[] = {
+		static const std::string name_keys[] = {
 			std::string("const"),
 			std::string("gamma-invariant"),
             std::string("zero")

src/include/dawg/residue.h

@@ -29,12 +29,12 @@ class residue {
 	typedef boost::uint64_t data_type;
 
 
-	static const data_type base_mask      =  UINT64_C(0x00000000000000FF);
-	static const data_type branch_mask    =  UINT64_C(0x0000FFFFFFFFFF00);
-	static const data_type rate_mask	  =  UINT64_C(0xFFFF000000000000);
-	static const data_type rate_shift     =  48;
-	static const data_type base_bit_width =  8;
-	static const data_type branch_inc     =  0x100;
+	static constexpr data_type base_mask      =  UINT64_C(0x00000000000000FF);
+	static constexpr data_type branch_mask    =  UINT64_C(0x0000FFFFFFFFFF00);
+	static constexpr data_type rate_mask	  =  UINT64_C(0xFFFF000000000000);
+	static constexpr data_type rate_shift     =  48;
+	static constexpr data_type base_bit_width =  8;
+	static constexpr data_type branch_inc     =  0x100;
 
 	inline data_type base() const { return data_ & base_mask; }
 	inline void base(data_type b) { data_ = (b & base_mask) | (data_ & ~base_mask); }
@@ -85,10 +85,10 @@ class residue_exchange {
 
 	inline bool model(unsigned int type, unsigned int code, bool rna,
 			bool lowercase, bool markins, bool keepempty) {
-		static const char sIns[] = "-+";
+		static constexpr char sIns[] = "-+";
 		// table for going from base->char
 		// TODO: Allow codons to be translated into aa
-		static const char mods[] =
+		static constexpr char mods[] =
 			"ACGT!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!-" // DNA
 			"acgt!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!-" // dna
 			"ACGU!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!-" // RNA
@@ -122,7 +122,7 @@ class residue_exchange {
 		;
 		// tables for going from char->base
 		// 1 genetic code is 80 elements long
-		static const char rmods[] = {
+		static constexpr char rmods[] = {
 			-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, 0,-1, 1, // DNA & RNA
 			-1,-1,-1, 2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, 3, 3,-1,-1,
 			-1,-1,-1,-1,-1,-1,-1,-1,-1, 0,-1, 1,-1,-1,-1, 2,-1,-1,-1,-1,
@@ -214,7 +214,7 @@ class residue_exchange {
 
 	// cod64 -> codon number
 	static inline unsigned int cod64_to_codon(char c) {
-		static const char a[] = {
+		static constexpr char a[] = {
 			// cod64 -> codon number
 			54,55,56,57,58,59,60,61,62,63,-1,-1,-1,11,-1,-1,10, 0, 1, 2,
 			 3, 4, 5, 6, 7, 8, 9,12,13,15,16,14,17,18,19,20,21,22,23,24,
@@ -260,7 +260,7 @@ class residue_exchange {
 	explicit residue_exchange(int m=DNA) { model(m,0,0,false,false,false); }
 
 	inline static const char* get_protein_code(unsigned int code) {
-		static const char s[] = 
+		static constexpr char s[] =
 			"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
 			"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
 			"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG"

src/include/dawg/subst.h

@@ -157,7 +157,7 @@ class subst_model {
 
 template<typename It1, typename It2>
 bool subst_model::create(const char *mod_name, unsigned int code, It1 first1, It1 last1, It2 first2, It2 last2) {
-	static const char name_keys[][16] = {
+	static constexpr char name_keys[][16] = {
 		"jc",  "gtr", "k2p", "hky", "f84", "f81", "tn", "tn-f04",
 		"equ", "aagtr", "lg", "wag", "wagstar", "jtt-dcmut", "dayhoff-dcmut", "molphy",
 		"codgtr", "codmg", "codmg-equ", "codmg-aap", "codmg-cp",

src/include/dawg/trick.h

@@ -104,15 +104,15 @@ inline void trick::section::conv(const std::string& ss, std::string& r) {
 }
 
 inline void trick::section::conv(const std::string& ss, double& r) {
-	r = strtod(ss.c_str(), NULL);
+	r = strtod(ss.c_str(), nullptr);
 }
 
 inline void trick::section::conv(const std::string& ss, unsigned int& r) {
-	r = strtoul(ss.c_str(), NULL, 0);
+	r = strtoul(ss.c_str(), nullptr, 0);
 }
 
 inline void trick::section::conv(const std::string& ss, int& r) {
-	r = strtol(ss.c_str(), NULL, 0);
+	r = strtol(ss.c_str(), nullptr, 0);
 }
 
 // A value is false if it is equal to 0, f, false, off, no, or blank

src/lib/mutt.cpp

@@ -83,7 +83,7 @@ double dawg::mutt::rand_gamma(double a, double b) {
  ************************************************************/
 
 /* tabulated values for the height of the Ziggurat levels */
-static const double ytab[128] = {
+static constexpr double ytab[128] = {
   1, 0.963598623011, 0.936280813353, 0.913041104253,
   0.892278506696, 0.873239356919, 0.855496407634, 0.838778928349,
   0.822902083699, 0.807732738234, 0.793171045519, 0.779139726505,
@@ -120,7 +120,7 @@ static const double ytab[128] = {
 
 /* tabulated values for 2^24 times x[i]/x[i+1],
  * used to accept for U*x[i+1]<=x[i] without any floating point operations */
-static const boost::uint32_t ktab[128] = {
+static constexpr boost::uint32_t ktab[128] = {
   0, 12590644, 14272653, 14988939,
   15384584, 15635009, 15807561, 15933577,
   16029594, 16105155, 16166147, 16216399,
@@ -156,7 +156,7 @@ static const boost::uint32_t ktab[128] = {
 };
 
 /* tabulated values of 2^{-24}*x[i] */
-static const double wtab[128] = {
+static constexpr double wtab[128] = {
   1.62318314817e-08, 2.16291505214e-08, 2.54246305087e-08, 2.84579525938e-08,
   3.10340022482e-08, 3.33011726243e-08, 3.53439060345e-08, 3.72152672658e-08,
   3.8950989572e-08, 4.05763964764e-08, 4.21101548915e-08, 4.35664624904e-08,

src/lib/output.cpp

@@ -26,20 +26,20 @@ bool dawg::output::open(const char *file_name, unsigned int max_rep,
 	last_rep = max_rep;
 	rep = 0;
 	cs_range format(file_name, file_name);
-	const char *mid = NULL;
-	if(file_name != NULL && file_name[0] != '\0') {
+	const char *mid = nullptr;
+	if(file_name != nullptr && file_name[0] != '\0') {
 		mid = strchr(file_name, ':');
 #ifdef BOOST_WINDOWS
-		if(mid != NULL && mid != file_name+1) {
+		if(mid != nullptr && mid != file_name+1) {
 #else
-		if(mid != NULL) {
+		if(mid != nullptr) {
 #endif		
 			// format:file
 			format = boost::make_iterator_range(file_name, mid);
 			file_name = mid+1;
 			// find extension point for later
 			mid = strrchr(file_name, '.');
-		} else if((mid = strrchr(file_name, '.')) != NULL) {
+		} else if((mid = strrchr(file_name, '.')) != nullptr) {
 			// file.format
 			format = boost::make_iterator_range(mid+1, (const char*)strchr(mid+1, '\0'));
 		}
@@ -52,7 +52,7 @@ bool dawg::output::open(const char *file_name, unsigned int max_rep,
 	current_label.assign(label_width, '0');
 	do_label = label;
 
-	if(file_name != NULL && file_name[0] != '\0' && strcmp(file_name, "-") != 0) {
+	if(file_name != nullptr && file_name[0] != '\0' && strcmp(file_name, "-") != 0) {
 		// set append and split options before we open the file
 		do_append = append;
 		do_split  = split;
@@ -62,7 +62,7 @@ bool dawg::output::open(const char *file_name, unsigned int max_rep,
 				return DAWG_ERROR("unable to open output file \'" << file_name << "\'.");
 		} else {
 			// setup output_filename
-			if(mid == NULL) {
+			if(mid == nullptr) {
 				split_file_name.assign(file_name);
 				split_file_name.append(1, '-');
 				split_file_name.append(current_label);
@@ -91,7 +91,7 @@ bool dawg::output::open_file(const char* file_name) {
 		(do_append ? ios_base::app : ios_base::trunc);
 	fout.open(file_name, om);
 	if(!fout.is_open()) {
-		set_ostream(NULL);
+		set_ostream(nullptr);
 		return false;
 	}
 	set_ostream(fout);
@@ -214,7 +214,7 @@ void dawg::output::print_phylip(const alignment& aln) {
 void dawg::output::print_nexus(const alignment& aln) {
 	ostream &out = *p_out;
 
-	static char datatypes[][10] = {
+	static constexpr char datatypes[][10] = {
 		"DNA", "RNA", "PROTEIN", "DNA",
 		"DNA", "RNA", "PROTEIN", "DNA"
 	};

src/lib/parse.cpp

@@ -16,7 +16,7 @@ using namespace dawg;
 
 bool trick::parse_file(trick& p, const char *cs) {
 	bool ret;
-	if(cs == NULL || strcmp(cs, "")==0 || strcmp(cs, "-")==0) {
+	if(cs == nullptr || strcmp(cs, "")==0 || strcmp(cs, "-")==0) {
 		ret = p.parse_stream(std::cin);
 	} else {
 		std::ifstream is(cs);

tests/Unit/Dawg/testu01.cpp

@@ -95,15 +95,15 @@ unif01_Gen *create_gen(unsigned int u) {
 	g->seed(u);
 	gen->state = g;
 	gen->name = &name[0];
-	gen->param = NULL;
+	gen->param = nullptr;
 	gen->GetU01 =  &get_u01;
 	gen->GetBits = &get_bits;
 	gen->Write = &write_gen;
 	return gen;
 }
 
 void delete_gen(unif01_Gen *gen) {
-	if(NULL == gen)
+	if(nullptr == gen)
 		return;
 	delete static_cast<mutt_gen_default*>(gen->state);
 	delete gen;