Organized api/internal into subdirs

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

diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h
deleted file mode 100644 (file)
index 88d7472..0000000
--- a/src/api/internal/BgzfStream_p.h
+++ /dev/null
@@ -1,97 +0,0 @@
-// ***************************************************************************
-// BgzfStream_p.h (c) 2011 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011(DB)
-// ---------------------------------------------------------------------------
-// Based on BGZF routines developed at the Broad Institute.
-// Provides the basic functionality for reading & writing BGZF files
-// Replaces the old BGZF.* files to avoid clashing with other toolkits
-// ***************************************************************************
-
-#ifndef BGZFSTREAM_P_H
-#define BGZFSTREAM_P_H
-
-//  -------------
-//  W A R N I N G
-//  -------------
-//
-// This file is not part of the BamTools API.  It exists purely as an
-// implementation detail. This header file may change from version to version
-// without notice, or even be removed.
-//
-// We mean it.
-
-#include "api/api_global.h"
-#include "api/IBamIODevice.h"
-#include <string>
-
-namespace BamTools {
-namespace Internal {
-
-class BgzfStream {
-
-    // constructor & destructor
-    public:
-        BgzfStream(void);
-        ~BgzfStream(void);
-
-    // main interface methods
-    public:
-        // closes BGZF file
-        void Close(void);
-        // 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
-        size_t Read(char* data, const size_t dataLength);
-        // seek to position in BGZF file
-        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
-        size_t Write(const char* data, const size_t dataLength);
-
-    // internal methods
-    private:
-        // compresses the current block
-        size_t DeflateBlock(void);
-        // flushes the data in the BGZF block
-        void FlushBlock(void);
-        // de-compresses the current block
-        size_t InflateBlock(const size_t& blockLength);
-        // reads a BGZF block
-        void ReadBlock(void);
-
-    // static 'utility' methods
-    public:
-        // checks BGZF block header
-        static bool CheckBlockHeader(char* header);
-
-    // data members
-    public:
-        unsigned int m_blockLength;
-        unsigned int m_blockOffset;
-        uint64_t     m_blockAddress;
-
-        bool m_isWriteCompressed;
-        IBamIODevice* m_device;
-
-        struct RaiiWrapper {
-            RaiiWrapper(void);
-            ~RaiiWrapper(void);
-            char* UncompressedBlock;
-            char* CompressedBlock;
-        };
-        RaiiWrapper Resources;
-};
-
-} // namespace Internal
-} // namespace BamTools
-
-#endif // BGZFSTREAM_P_H