backup

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@176 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Cif++.h

@@ -11,6 +11,7 @@
 
 
 #include <boost/lexical_cast.hpp>
 #include <boost/lexical_cast.hpp>
 #include <boost/any.hpp>
 #include <boost/any.hpp>
+#include <boost/filesystem/path.hpp>
 
 
 #include "cif++/CifUtils.h"
 #include "cif++/CifUtils.h"
 
 
@@ -1008,12 +1009,16 @@ class File
 
 
 	File();
 	File();
 	File(std::istream& is, bool validate = false);
 	File(std::istream& is, bool validate = false);
+	File(boost::filesystem::path p, bool validate = false);
 	File(File&& rhs);
 	File(File&& rhs);
 	File(const File& rhs) = delete;
 	File(const File& rhs) = delete;
 	File& operator=(const File& rhs) = delete;
 	File& operator=(const File& rhs) = delete;
 	
 	
 	~File();
 	~File();
 
 
+	void load(boost::filesystem::path p);
+	void save(boost::filesystem::path p);
+
 	void load(std::istream& is);
 	void load(std::istream& is);
 	void save(std::ostream& os);
 	void save(std::ostream& os);
 
 

src/Cif++.cpp

@@ -11,6 +11,9 @@
 #include <boost/algorithm/string.hpp>
 #include <boost/algorithm/string.hpp>
 #include <boost/filesystem/operations.hpp>
 #include <boost/filesystem/operations.hpp>
 #include <boost/filesystem/fstream.hpp>
 #include <boost/filesystem/fstream.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
+#include <boost/iostreams/filter/bzip2.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
 
 
 #if defined(USE_RSRC)
 #if defined(USE_RSRC)
 #include "cif++/mrsrc.h"
 #include "cif++/mrsrc.h"
@@ -24,6 +27,7 @@
 using namespace std;
 using namespace std;
 namespace ba = boost::algorithm;
 namespace ba = boost::algorithm;
 namespace fs = boost::filesystem;
 namespace fs = boost::filesystem;
+namespace io = boost::iostreams;
 
 
 extern int VERBOSE;
 extern int VERBOSE;
 
 
@@ -1950,6 +1954,12 @@ File::File(istream& is, bool validate)
 	load(is);
 	load(is);
 }
 }
 
 
+File::File(boost::filesystem::path p, bool validate)
+	: File()
+{
+	load(p);
+}
+
 File::File(File&& rhs)
 File::File(File&& rhs)
 	: mHead(nullptr), mValidator(nullptr)
 	: mHead(nullptr), mValidator(nullptr)
 {
 {
@@ -1988,6 +1998,51 @@ void File::append(Datablock* e)
 	}
 	}
 }
 }
 
 
+void File::load(fs::path p)
+{
+	fs::ifstream inFile(p, ios_base::in | ios_base::binary);
+	if (not inFile.is_open())
+		throw runtime_error("Could not open file: " + p.string());
+	
+	io::filtering_stream<io::input> in;
+	string ext;
+	
+	if (p.extension() == ".bz2")
+	{
+		in.push(io::bzip2_decompressor());
+		ext = p.stem().extension().string();
+	}
+	else if (p.extension() == ".gz")
+	{
+		in.push(io::gzip_decompressor());
+		ext = p.stem().extension().string();
+	}
+	
+	in.push(inFile);
+
+	load(in);
+}
+
+void File::save(fs::path p)
+{
+	fs::ofstream outFile(p, ios_base::out | ios_base::binary);
+	io::filtering_stream<io::output> out;
+	
+	if (p.extension() == ".gz")
+	{
+		out.push(io::gzip_compressor());
+		p = p.stem();
+	}
+	else if (p.extension() == ".bz2")
+	{
+		out.push(io::bzip2_compressor());
+		p = p.stem();
+	}
+	
+	out.push(outFile);
+	save(out);
+}
+
 void File::load(istream& is)
 void File::load(istream& is)
 {
 {
 	Validator* saved = mValidator;
 	Validator* saved = mValidator;

src/PDB2Cif.cpp

@@ -2621,7 +2621,7 @@ void PDBFileParser::ParseRemark200()
 	{
 	{
 		getCategory("diffrn_radiation_wavelength")->emplace({
 		getCategory("diffrn_radiation_wavelength")->emplace({
 			{ "id", wavelengthNr++ },
 			{ "id", wavelengthNr++ },
-			{ "wavelength", wl },
+			{ "wavelength", wl.empty() ? "." : wl },
 			{ "wt", "1.0" }
 			{ "wt", "1.0" }
 		});
 		});
 	}
 	}