libStatGen Software
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This class allows a user to easily read/write a GLF file. More...
#include <GlfFile.h>
Public Types | |
enum | OpenType { READ , WRITE } |
Enum for indicating whether to open the file for read or write. More... | |
Public Member Functions | |
GlfFile () | |
Default Constructor. | |
GlfFile (const char *filename, OpenType mode=READ) | |
Constructor that opens the specified file based on the specified mode (READ/WRITE). More... | |
virtual | ~GlfFile () |
Closes the file if there is one open, adding an end marker record if there is a previous section and one has not already been written. | |
bool | openForRead (const char *filename) |
Open a glf file for reading with the specified filename. More... | |
bool | openForRead (const char *filename, GlfHeader &header) |
Open a glf file for reading with the specified filename and read the header into the specified header. More... | |
bool | openForWrite (const char *filename, bool compressed=true) |
Open a glf file for writing with the specified filename. More... | |
void | close () |
Close the file if there is one open, adding an end marker record if there is a previous section and one has not already been written. | |
bool | isEOF () |
Returns whether or not the end of the file has been reached. More... | |
bool | readHeader (GlfHeader &header) |
Reads the header section from the file and stores it in the passed in header. More... | |
bool | writeHeader (GlfHeader &header) |
Writes the specified header into the file. More... | |
bool | getNextRefSection (GlfRefSection &refSection) |
Gets the next reference section from the file & stores it in the passed in section, consuming records until a new section is found. More... | |
bool | writeRefSection (const GlfRefSection &refSection) |
Write the reference section to the file, adding an end marker record if there is a previous section and one has not already been written. More... | |
bool | getNextRecord (GlfRecord &record) |
Gets the nextrecord from the file & stores it in the passed in record. More... | |
bool | writeRecord (const GlfRecord &record) |
Writes the specified record into the file. More... | |
uint32_t | getCurrentRecordCount () |
Return the number of records that have been read/written so far. More... | |
GlfStatus::Status | getFailure () |
Get the Status of the last call that sets status. More... | |
GlfStatus::Status | getStatus () |
Get the Status of the last call that sets status. More... | |
const char * | getStatusMessage () |
Get the Status of the last call that sets status. More... | |
enum GlfFile::OpenType |
Constructor that opens the specified file based on the specified mode (READ/WRITE).
Default is READ.
filename | name of the file to open. |
mode | mode to use for opening the file (defaults to READ). |
Definition at line 33 of file GlfFile.cpp.
References getStatusMessage(), openForRead(), openForWrite(), and READ.
uint32_t GlfFile::getCurrentRecordCount | ( | ) |
Return the number of records that have been read/written so far.
Definition at line 483 of file GlfFile.cpp.
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Get the Status of the last call that sets status.
To remain backwards compatable - will be removed later.
Definition at line 121 of file GlfFile.h.
References getStatus().
bool GlfFile::getNextRecord | ( | GlfRecord & | record | ) |
Gets the nextrecord from the file & stores it in the passed in record.
record | object to populate with the file's next record. |
Definition at line 368 of file GlfFile.cpp.
References GlfStatus::FAIL_ORDER, GlfRecord::getRecordType(), isEOF(), GlfRecord::read(), GlfStatus::setStatus(), GlfStatus::SUCCESS, and GlfStatus::UNKNOWN.
Referenced by getNextRefSection().
bool GlfFile::getNextRefSection | ( | GlfRefSection & | refSection | ) |
Gets the next reference section from the file & stores it in the passed in section, consuming records until a new section is found.
refSection | object to populate with the file's next reference section. |
Definition at line 240 of file GlfFile.cpp.
References GlfStatus::FAIL_IO, GlfStatus::FAIL_ORDER, getNextRecord(), isEOF(), GlfRefSection::read(), GlfStatus::setStatus(), GlfStatus::SUCCESS, and GlfStatus::UNKNOWN.
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Get the Status of the last call that sets status.
Definition at line 128 of file GlfFile.h.
References GlfStatus::getStatus().
Referenced by getFailure().
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inline |
Get the Status of the last call that sets status.
Definition at line 135 of file GlfFile.h.
References GlfStatus::getStatusMessage().
Referenced by GlfFile(), GlfFileReader::GlfFileReader(), and GlfFileWriter::GlfFileWriter().
bool GlfFile::isEOF | ( | ) |
Returns whether or not the end of the file has been reached.
Definition at line 152 of file GlfFile.cpp.
References ifeof().
Referenced by getNextRecord(), and getNextRefSection().
bool GlfFile::openForRead | ( | const char * | filename | ) |
Open a glf file for reading with the specified filename.
filename | glf file to open for reading. |
Definition at line 66 of file GlfFile.cpp.
References GlfStatus::FAIL_IO, ifopen(), GlfStatus::setStatus(), and GlfStatus::SUCCESS.
Referenced by GlfFile(), GlfFileReader::GlfFileReader(), and openForRead().
bool GlfFile::openForRead | ( | const char * | filename, |
GlfHeader & | header | ||
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Open a glf file for reading with the specified filename and read the header into the specified header.
filename | glf file to open for reading. |
header | header object to populate with the file's glf header. |
Definition at line 92 of file GlfFile.cpp.
References openForRead(), and readHeader().
bool GlfFile::openForWrite | ( | const char * | filename, |
bool | compressed = true |
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Open a glf file for writing with the specified filename.
filename | glf file to open for writing. |
compressed | whether or not to compress the file, defaults to true |
Definition at line 109 of file GlfFile.cpp.
References InputFile::BGZF, GlfStatus::FAIL_IO, ifopen(), GlfStatus::setStatus(), GlfStatus::SUCCESS, and InputFile::UNCOMPRESSED.
Referenced by GlfFile(), and GlfFileWriter::GlfFileWriter().
bool GlfFile::readHeader | ( | GlfHeader & | header | ) |
Reads the header section from the file and stores it in the passed in header.
header | header object to populate with the file's glf header. |
Definition at line 165 of file GlfFile.cpp.
References GlfStatus::FAIL_ORDER, GlfHeader::read(), GlfStatus::setStatus(), GlfStatus::SUCCESS, and GlfStatus::UNKNOWN.
Referenced by openForRead().
bool GlfFile::writeHeader | ( | GlfHeader & | header | ) |
Writes the specified header into the file.
header | header object to write into the file. |
Definition at line 200 of file GlfFile.cpp.
References GlfStatus::FAIL_ORDER, GlfStatus::setStatus(), GlfStatus::SUCCESS, GlfStatus::UNKNOWN, and GlfHeader::write().
bool GlfFile::writeRecord | ( | const GlfRecord & | record | ) |
Writes the specified record into the file.
record | record to write to the file. |
Definition at line 429 of file GlfFile.cpp.
References GlfStatus::FAIL_ORDER, GlfRecord::getRecordType(), GlfStatus::setStatus(), GlfStatus::SUCCESS, GlfStatus::UNKNOWN, and GlfRecord::write().
Referenced by writeRefSection().
bool GlfFile::writeRefSection | ( | const GlfRefSection & | refSection | ) |
Write the reference section to the file, adding an end marker record if there is a previous section and one has not already been written.
refSection | reference section to write to the file. |
Definition at line 308 of file GlfFile.cpp.
References GlfStatus::FAIL_IO, GlfStatus::FAIL_ORDER, GlfStatus::setStatus(), GlfStatus::SUCCESS, GlfStatus::UNKNOWN, GlfRefSection::write(), and writeRecord().