Organized api/internal into subdirs

[bamtools.git] / src / api / internal / BamHeader_p.cpp

diff --git a/src/api/internal/BamHeader_p.cpp b/src/api/internal/BamHeader_p.cpp
deleted file mode 100644 (file)
index dc734bf..0000000
--- a/src/api/internal/BamHeader_p.cpp
+++ /dev/null
@@ -1,120 +0,0 @@
-// ***************************************************************************
-// BamHeader_p.cpp (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for handling BAM headers.
-// ***************************************************************************
-
-#include "api/BamAux.h"
-#include "api/BamConstants.h"
-#include "api/internal/BamException_p.h"
-#include "api/internal/BamHeader_p.h"
-#include "api/internal/BgzfStream_p.h"
-using namespace BamTools;
-using namespace BamTools::Internal;
-
-#include <cstdlib>
-#include <cstring>
-using namespace std;
-
-// ------------------------
-// static utility methods
-// ------------------------
-
-static inline
-bool isValidMagicNumber(const char* buffer) {
-    return ( strncmp(buffer, Constants::BAM_HEADER_MAGIC,
-                     Constants::BAM_HEADER_MAGIC_LENGTH) == 0 );
-}
-
-// --------------------------
-// BamHeader implementation
-// --------------------------
-
-// ctor
-BamHeader::BamHeader(void) { }
-
-// dtor
-BamHeader::~BamHeader(void) { }
-
-// reads magic number from BGZF stream, returns true if valid
-void BamHeader::CheckMagicNumber(BgzfStream* stream) {
-
-    // try to read magic number
-    char buffer[Constants::BAM_HEADER_MAGIC_LENGTH];
-    const size_t numBytesRead = stream->Read(buffer, Constants::BAM_HEADER_MAGIC_LENGTH);
-    if ( numBytesRead != (int)Constants::BAM_HEADER_MAGIC_LENGTH )
-        throw BamException("BamHeader::CheckMagicNumber", "could not read magic number");
-
-    // validate magic number
-    if ( !isValidMagicNumber(buffer) )
-        throw BamException("BamHeader::CheckMagicNumber", "invalid magic number");
-}
-
-// clear SamHeader data
-void BamHeader::Clear(void) {
-    m_header.Clear();
-}
-
-// return true if SamHeader data is valid
-bool BamHeader::IsValid(void) const {
-    return m_header.IsValid();
-}
-
-// load BAM header ('magic number' and SAM header text) from BGZF stream
-void BamHeader::Load(BgzfStream* stream) {
-
-    // read & check magic number
-    CheckMagicNumber(stream);
-
-    // read header (length, then actual text)
-    uint32_t length(0);
-    ReadHeaderLength(stream, length);
-    ReadHeaderText(stream, length);
-}
-
-// reads SAM header text length from BGZF stream, stores it in @length
-void BamHeader::ReadHeaderLength(BgzfStream* stream, uint32_t& length) {
-
-    // read BAM header text length
-    char buffer[sizeof(uint32_t)];
-    const size_t numBytesRead = stream->Read(buffer, sizeof(uint32_t));
-    if ( numBytesRead != sizeof(uint32_t) )
-        throw BamException("BamHeader::ReadHeaderLength", "could not read header length");
-
-    // convert char buffer to length
-    length = BamTools::UnpackUnsignedInt(buffer);
-    if ( BamTools::SystemIsBigEndian() )
-        BamTools::SwapEndian_32(length);
-}
-
-// reads SAM header text from BGZF stream, stores in SamHeader object
-void BamHeader::ReadHeaderText(BgzfStream* stream, const uint32_t& length) {
-
-    // read header text
-    char* headerText = (char*)calloc(length + 1, 1);
-    const size_t bytesRead = stream->Read(headerText, length);
-
-    // if error reading, clean up buffer & throw
-    if ( bytesRead != length ) {
-        free(headerText);
-        throw BamException("BamHeader::ReadHeaderText", "could not read header text");
-    }
-
-    // otherwise, text was read OK
-    // store & cleanup
-    m_header.SetHeaderText( (string)((const char*)headerText) );
-    free(headerText);
-}
-
-// returns *copy* of SamHeader data object
-SamHeader BamHeader::ToSamHeader(void) const {
-    return m_header;
-}
-
-// returns SAM-formatted string of header data
-string BamHeader::ToString(void) const {
-    return m_header.ToString();
-}