Merge pull request #49 from JGI-Bioinformatics/master

Flush close on destroy, CMake and buff_size
Added CMakeLists.txt and included buff_size in the constructor of the i/ofstream classes
Including a close on the underlying I/ofstream on destruction

Author: ferdymercury

.gitignore

@@ -1 +1,4 @@
 /local
+/build*
+/nbproject/
+/.vscode/

CMakeLists.txt

@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
+project(zstr)
+
+if(${CMAKE_VERSION} VERSION_LESS 3.13)
+  message(WARNING "Interface libraries are not well supported before cmake 3.13, you will need to include within the parent CMakeLists.txt: INCLUDE_DIRECTORIES(zstr/src)") 
+endif()
+
+# zlib is required
+find_package(ZLIB 1.2.3 REQUIRED)
+
+add_library(zstr INTERFACE)
+target_include_directories(zstr INTERFACE src ${ZLIB_INCLUDE_DIRS})
+target_link_libraries(zstr INTERFACE ${ZLIB_LIBRARIES})
+
+message(STATUS "Adding zstr and ZLIB for ${PROJECT_NAME}: includes: ${CMAKE_CURRENT_SOURCE_DIR}/src ${ZLIB_INCLUDE_DIRS} and libraries: ${ZLIB_LIBRARIES}")
+

README.org

@@ -10,6 +10,9 @@ For input access (decompression), the compression format is auto-detected, and m
 
 For output access (compression), the only parameter exposed by this API is the compression level.
 
+To add zstr within a CMake project, include this directory within your CMakeLists.txxt: 'add_subdirectory(zstr)' and include zstr for each required target when specifiying target_link_libraries. 
+  For cmake versions < 3.13, you will also need to 'include_directories(zstr/src)'
+
 Alternatives to this library include:
 
 - The original [[http://www.zlib.net/][ZLib]], through its [[http://www.zlib.net/manual.html][C API]]. This does not interact nicely with C++ iostreams.

src/zstr.hpp

@@ -255,7 +255,6 @@ class istreambuf
     bool is_text;
     int window_bits;
 
-    static const std::size_t default_buff_size = static_cast<std::size_t>(1 << 20);
 }; // class istreambuf
 
 class ostreambuf
@@ -354,8 +353,6 @@ class ostreambuf
     std::size_t buff_size;
     bool failed = false;
 
-public:
-    static const std::size_t default_buff_size = static_cast<std::size_t>(1 << 20);
 }; // class ostreambuf
 
 class istream
@@ -420,17 +417,17 @@ class ifstream
       public std::istream
 {
 public:
-    explicit ifstream(const std::string& filename, std::ios_base::openmode mode = std::ios_base::in)
+    explicit ifstream(const std::string filename, std::ios_base::openmode mode = std::ios_base::in, size_t buff_size = default_buff_size)
         : detail::strict_fstream_holder< strict_fstream::ifstream >(filename, mode),
-          std::istream(new istreambuf(_fs.rdbuf()))
+          std::istream(new istreambuf(_fs.rdbuf(), buff_size))
     {
         exceptions(std::ios_base::badbit);
     }
     explicit ifstream(): detail::strict_fstream_holder< strict_fstream::ifstream >(), std::istream(new istreambuf(_fs.rdbuf())){}
     void close() {
         _fs.close();
     }
-    void open(const std::string& filename, std::ios_base::openmode mode = std::ios_base::in) {
+    void open(const std::string filename, std::ios_base::openmode mode = std::ios_base::in) {
         _fs.open(filename, mode);
         std::istream::operator=(std::istream(new istreambuf(_fs.rdbuf())));
     }
@@ -439,6 +436,7 @@ class ifstream
     }
     virtual ~ifstream()
     {
+        if (_fs.is_open()) close();
         if (rdbuf()) delete rdbuf();
     }
 
@@ -454,10 +452,10 @@ class ofstream
       public std::ostream
 {
 public:
-    explicit ofstream(const std::string& filename, std::ios_base::openmode mode = std::ios_base::out,
-                      int level = Z_DEFAULT_COMPRESSION)
+    explicit ofstream(const std::string filename, std::ios_base::openmode mode = std::ios_base::out,
+                      int level = Z_DEFAULT_COMPRESSION, size_t buff_size = default_buff_size)
         : detail::strict_fstream_holder< strict_fstream::ofstream >(filename, mode | std::ios_base::binary),
-          std::ostream(new ostreambuf(_fs.rdbuf(), ostreambuf::default_buff_size, level))
+          std::ostream(new ostreambuf(_fs.rdbuf(), buff_size, level))
     {
         exceptions(std::ios_base::badbit);
     }
@@ -466,10 +464,10 @@ class ofstream
         std::ostream::flush();
         _fs.close();
     }
-    void open(const std::string& filename, std::ios_base::openmode mode = std::ios_base::out, int level = Z_DEFAULT_COMPRESSION) {
+    void open(const std::string filename, std::ios_base::openmode mode = std::ios_base::out, int level = Z_DEFAULT_COMPRESSION) {
         flush();
         _fs.open(filename, mode | std::ios_base::binary);
-        std::ostream::operator=(std::ostream(new ostreambuf(_fs.rdbuf(), ostreambuf::default_buff_size, level)));
+        std::ostream::operator=(std::ostream(new ostreambuf(_fs.rdbuf(), default_buff_size, level)));
     }
     bool is_open() const {
         return _fs.is_open();
@@ -481,6 +479,7 @@ class ofstream
     }
     virtual ~ofstream()
     {
+        if (_fs.is_open()) close();
         if (rdbuf()) delete rdbuf();
     }