resources, fix progress' implementations move to std::thread

configure.ac

@@ -32,6 +32,19 @@ AS_IF([test x"$CCP4" != x""],
 		LDFLAGS="$LDFLAGS -L${CCP4}/lib"
 	  ])
 
+AC_ARG_VAR([USE_RSRC], [Use resources to store internal data, requires mrc])
+AC_ARG_VAR([MRC], [Specify a location for the mrc executable])
+
+dnl We really like to use mrc
+if test "x$MRC" = "x"; then
+	AC_PATH_PROG([MRC], [mrc])
+fi
+if test "x$MRC" = "x"; then
+	AC_MSG_WARN([mrc not found, building without support for resources.])
+else
+	USE_RSRC=1
+fi
+
 AX_BOOST_BASE([1.73])
 AX_BOOST_REGEX
 
@@ -123,5 +136,4 @@ AX_CHECK_LIBRARY([LIBBZ2], [bzlib.h], [bz2], [],
 # 	[enable_debug=auto])
 
 dnl Process files
-AC_OUTPUT([GNUmakefile
-		   libcif++.pc])
+AC_OUTPUT([GNUmakefile])

include/cif++/AtomType.hpp

@@ -14,7 +14,6 @@ enum AtomType : uint8_t
 	Nn = 0,		// Unknown
 	
 	H = 1,		// Hydro­gen
-	D = 129,	// Deuterium
 	He = 2,		// He­lium
 
 	Li = 3,		// Lith­ium
@@ -140,6 +139,8 @@ enum AtomType : uint8_t
 	Md = 101,	// Mende­levium
 	No = 102,	// Nobel­ium
 	Lr = 103,	// Lawren­cium
+
+	D = 129,	// Deuterium
 };
 
 // --------------------------------------------------------------------

src/AtomType.cpp

@@ -17,7 +17,6 @@ const AtomTypeInfo kKnownAtoms[] =
 {
 	{ Nn,	"Unknown",			"Nn",	0,		false, {	kNA,	kNA,	kNA,	kNA,	kNA,	kNA,	kNA } },  //	0	Nn	 Unknown        
 	{ H,	"Hydrogen",			"H",	1.008,	false, {	53,		25,		37,		32,		kNA,	kNA,	120 } },  //	1	H	 Hydro­gen         
-	{ D,	"Deuterium",		"D",	2.014,	false, {	53,		25,		37,		32,		kNA,	kNA,	120 } },  //	1	D	 Deuterium         
 	{ He,	"Helium",			"He",	4.0026,	false, {	31,		kNA,	32,		46,		kNA,	kNA,	140 } },  //	2	He	 He­lium           
 	{ Li,	"Lithium",			"Li",	6.94,	true,  {	167,	145,	134,	133,	124,	kNA,	182 } },  //	3	Li	 Lith­ium          
 	{ Be,	"Beryllium",		"Be",	9.0122,	true,  {	112,	105,	90,		102,	90,		85,		kNA } },  //	4	Be	 Beryl­lium        
@@ -134,7 +133,9 @@ const AtomTypeInfo kKnownAtoms[] =
 	{ Mc,	"Moscovium",		"Mc",	290,	true,  {	kNA,	kNA,	kNA,	162,	kNA,	kNA,	kNA } },  //	115	Mc	 Moscov­ium        
 	{ Lv,	"Livermorium",		"Lv",	293,	true,  {	kNA,	kNA,	kNA,	175,	kNA,	kNA,	kNA } },  //	116	Lv	 Liver­morium      
 	{ Ts,	"Tennessine",		"Ts",	294,	true,  {	kNA,	kNA,	kNA,	165,	kNA,	kNA,	kNA } },  //	117	Ts	 Tenness­ine       
-	{ Og,	"Oganesson",		"Og",	294,	true,  {	kNA,	kNA,	kNA,	157,	kNA,	kNA,	kNA } }   //	118	Og	 Oga­nesson        
+	{ Og,	"Oganesson",		"Og",	294,	true,  {	kNA,	kNA,	kNA,	157,	kNA,	kNA,	kNA } },  //	118	Og	 Oga­nesson        
+
+	{ D,	"Deuterium",		"D",	2.014,	false, {	53,		25,		37,		32,		kNA,	kNA,	120 } },  //	1	D	 Deuterium         
 };                                                                                                                                                    
 
 uint32_t kKnownAtomsCount = sizeof(kKnownAtoms) / sizeof(AtomTypeInfo);

src/CifUtils.cpp

@@ -18,9 +18,8 @@
 #endif
 
 #include <boost/algorithm/string.hpp>
-#if BOOST_VERSION >= 104800
 #include <boost/timer/timer.hpp>
-#endif
+#include <boost/date_time/posix_time/posix_time.hpp>
 
 #include "cif++/CifUtils.hpp"
 
@@ -440,9 +439,16 @@ struct ProgressImpl
 {
 					ProgressImpl(int64_t inMax, const string& inAction)
 						: mMax(inMax), mConsumed(0), mAction(inAction), mMessage(inAction)
-						, mThread(std::bind(&ProgressImpl::Run, this)) {}
+						, mThread(std::bind(&ProgressImpl::Run, this))
+						, mStart(boost::posix_time::second_clock::local_time()) {}
 
 	void			Run();
+	void			Stop()
+	{
+		mStop = true;
+		if (mThread.joinable())
+			mThread.join();
+	}
 	
 	void			PrintProgress();
 	void			PrintDone();
@@ -454,29 +460,35 @@ struct ProgressImpl
 	string			mAction, mMessage;
 	std::mutex		mMutex;
 	std::thread		mThread;
-	boost::timer::cpu_timer
-					mTimer;
+	boost::timer::cpu_timer mTimer;
+	boost::posix_time::ptime mStart;
+	bool			mStop = false;
 };
 
 void ProgressImpl::Run()
 {
+	using namespace boost::posix_time;
+	// using namespace boost::local_time;
+
 	bool printedAny = false;
 	
 	try
 	{
-		std::this_thread::sleep_for(std::chrono::seconds(5));
-			
 		for (;;)
 		{
+			std::this_thread::sleep_for(std::chrono::milliseconds(100));
+
 			std::unique_lock lock(mMutex);
 			
-			if (mConsumed == mMax)
+			if (mStop or mConsumed == mMax)
 				break;
-			
+
+			if (second_clock::local_time() - mStart < seconds(5))
+				continue;
+
 			PrintProgress();
 			printedAny = true;
 
-			std::this_thread::sleep_for(std::chrono::milliseconds(100));
 		}
 	}
 	catch (...) {}
@@ -593,11 +605,8 @@ Progress::Progress(int64_t inMax, const string& inAction)
 
 Progress::~Progress()
 {
-	if (mImpl != nullptr and mImpl->mThread.joinable())
-	{
-		// mImpl->mThread.interrupt();
-		mImpl->mThread.join();
-	}
+	if (mImpl != nullptr)
+		mImpl->Stop();
 
 	delete mImpl;
 }
@@ -605,22 +614,18 @@ Progress::~Progress()
 void Progress::consumed(int64_t inConsumed)
 {
 	if (mImpl != nullptr and 
-		(mImpl->mConsumed += inConsumed) >= mImpl->mMax and
-		mImpl->mThread.joinable())
+		(mImpl->mConsumed += inConsumed) >= mImpl->mMax)
 	{
-		// mImpl->mThread.interrupt();
-		mImpl->mThread.join();
+		mImpl->Stop();
 	}
 }
 
 void Progress::progress(int64_t inProgress)
 {
 	if (mImpl != nullptr and 
-		(mImpl->mConsumed = inProgress) >= mImpl->mMax and
-		mImpl->mThread.joinable())
+		(mImpl->mConsumed = inProgress) >= mImpl->mMax)
 	{
-		// mImpl->mThread.interrupt();
-		mImpl->mThread.join();
+		mImpl->Stop();
 	}
 }