Cleaned up intra-API includes & moved version numbers to 2.0.0

[bamtools.git] / src / api / internal / BgzfStream_p.h

diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h
index 838f30cde3f2f2a163fa72cd2852ea00315a4887..88d7472eeebfa81bed6cd2021841a2534877b7ac 100644 (file)
--- a/src/api/internal/BgzfStream_p.h
+++ b/src/api/internal/BgzfStream_p.h
@@ -2,7 +2,7 @@
 // BgzfStream_p.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 5 April 2011(DB)
+// Last modified: 10 October 2011(DB)
 // ---------------------------------------------------------------------------
 // Based on BGZF routines developed at the Broad Institute.
 // Provides the basic functionality for reading & writing BGZF files
@@ -22,10 +22,8 @@
 //
 // We mean it.
 
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
-#include "zlib.h"
-#include <cstdio>
+#include "api/api_global.h"
+#include "api/IBamIODevice.h"
 #include <string>
 
 namespace BamTools {
@@ -42,65 +40,56 @@ class BgzfStream {
     public:
         // closes BGZF file
         void Close(void);
-        // opens the BGZF file (mode is either "rb" for reading, or "wb" for writing)
-        bool Open(const std::string& filename, const char* mode);
+        // returns true if BgzfStream open for IO
+        bool IsOpen(void) const;
+        // opens the BGZF file
+        void Open(const std::string& filename, const IBamIODevice::OpenMode mode);
         // reads BGZF data into a byte buffer
-        int Read(char* data, const unsigned int dataLength);
+        size_t Read(char* data, const size_t dataLength);
         // seek to position in BGZF file
-        bool Seek(const int64_t& position);
+        void Seek(const int64_t& position);
+        // sets IO device (closes previous, if any, but does not attempt to open)
+        void SetIODevice(IBamIODevice* device);
         // enable/disable compressed output
         void SetWriteCompressed(bool ok);
         // get file position in BGZF file
         int64_t Tell(void) const;
         // writes the supplied data into the BGZF buffer
-        unsigned int Write(const char* data, const unsigned int dataLen);
+        size_t Write(const char* data, const size_t dataLength);
 
     // internal methods
     private:
         // compresses the current block
-        int DeflateBlock(void);
+        size_t DeflateBlock(void);
         // flushes the data in the BGZF block
         void FlushBlock(void);
         // de-compresses the current block
-        int InflateBlock(const int& blockLength);
+        size_t InflateBlock(const size_t& blockLength);
         // reads a BGZF block
-        bool ReadBlock(void);
+        void ReadBlock(void);
 
     // static 'utility' methods
     public:
         // checks BGZF block header
-        static inline bool CheckBlockHeader(char* header);
+        static bool CheckBlockHeader(char* header);
 
     // data members
     public:
-        unsigned int UncompressedBlockSize;
-        unsigned int CompressedBlockSize;
-        unsigned int BlockLength;
-        unsigned int BlockOffset;
-        uint64_t BlockAddress;
-        bool IsOpen;
-        bool IsWriteOnly;
-        bool IsWriteCompressed;
-        FILE* Stream;
-        char* UncompressedBlock;
-        char* CompressedBlock;
-};
+        unsigned int m_blockLength;
+        unsigned int m_blockOffset;
+        uint64_t     m_blockAddress;
 
-// -------------------------------------------------------------
-// static 'utility' method implementations
+        bool m_isWriteCompressed;
+        IBamIODevice* m_device;
 
-// checks BGZF block header
-inline
-bool BgzfStream::CheckBlockHeader(char* header) {
-    return (header[0] == Constants::GZIP_ID1 &&
-            header[1] == (char)Constants::GZIP_ID2 &&
-            header[2] == Z_DEFLATED &&
-            (header[3] & Constants::FLG_FEXTRA) != 0 &&
-            BamTools::UnpackUnsignedShort(&header[10]) == Constants::BGZF_XLEN &&
-            header[12] == Constants::BGZF_ID1 &&
-            header[13] == Constants::BGZF_ID2 &&
-            BamTools::UnpackUnsignedShort(&header[14]) == Constants::BGZF_LEN );
-}
+        struct RaiiWrapper {
+            RaiiWrapper(void);
+            ~RaiiWrapper(void);
+            char* UncompressedBlock;
+            char* CompressedBlock;
+        };
+        RaiiWrapper Resources;
+};
 
 } // namespace Internal
 } // namespace BamTools