Organized api/internal into subdirs

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

diff --git a/src/api/internal/io/BgzfStream_p.h b/src/api/internal/io/BgzfStream_p.h
new file mode 100644 (file)
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+++ b/src/api/internal/io/BgzfStream_p.h
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+// ***************************************************************************
+// 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