X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBgzfStream_p.h;h=88d7472eeebfa81bed6cd2021841a2534877b7ac;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=04b6c34b88c0d122e3bc43f966b1cbafc4d39108;hpb=243a21d278e81d0a05997ad8bef109153443fb75;p=bamtools.git

diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h
index 04b6c34..88d7472 100644
--- a/src/api/internal/BgzfStream_p.h
+++ b/src/api/internal/BgzfStream_p.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BgzfStream_p.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// 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
@@ -23,11 +22,8 @@
 //
 // We mean it.
 
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
-#include <api/IBamIODevice.h>
-#include "zlib.h"
-#include <cstdio>
+#include "api/api_global.h"
+#include "api/IBamIODevice.h"
 #include <string>
 
 namespace BamTools {
@@ -44,14 +40,14 @@ class BgzfStream {
     public:
         // closes BGZF file
         void Close(void);
+        // returns true if BgzfStream open for IO
         bool IsOpen(void) const;
-        // opens the BGZF stream in requested mode
-        bool Open(const std::string& filename, const char* mode);
-        bool Open(const std::string& filename, const IBamIODevice::OpenMode mode);
+        // opens the BGZF file
+        void Open(const std::string& filename, const IBamIODevice::OpenMode mode);
         // reads BGZF data into a byte buffer
-        unsigned 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
@@ -59,58 +55,41 @@ class BgzfStream {
         // 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 dataLength);
+        size_t Write(const char* data, const size_t dataLength);
 
     // internal methods
     private:
         // compresses the current block
-        unsigned 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 m_uncompressedBlockSize;
-        unsigned int m_compressedBlockSize;
         unsigned int m_blockLength;
         unsigned int m_blockOffset;
         uint64_t     m_blockAddress;
 
-        char* m_uncompressedBlock;
-        char* m_compressedBlock;
-
-        bool m_isOpen;
-        bool m_isWriteOnly;
         bool m_isWriteCompressed;
-
         IBamIODevice* m_device;
-        FILE* m_stream;
-};
 
-// -------------------------------------------------------------
-// static 'utility' method implementations
-
-// 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