This class allows a user to easily read/write a GLF file. More...

#include <GlfFile.h>

Inheritance diagram for GlfFile:

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).
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.
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.
bool	openForWrite (const char *filename, bool compressed=true)
	Open a glf file for writing with the specified filename.
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.
bool	readHeader (GlfHeader &header)
	Reads the header section from the file and stores it in the passed in header.
bool	writeHeader (GlfHeader &header)
	Writes the specified header into the file.
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.
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.
bool	getNextRecord (GlfRecord &record)
	Gets the nextrecord from the file & stores it in the passed in record.
bool	writeRecord (const GlfRecord &record)
	Writes the specified record into the file.
uint32_t	getCurrentRecordCount ()
	Return the number of records that have been read/written so far.
GlfStatus::Status	getFailure ()
	Get the Status of the last call that sets status.
GlfStatus::Status	getStatus ()
	Get the Status of the last call that sets status.
const char *	getStatusMessage ()
	Get the Status of the last call that sets status.

Detailed Description

This class allows a user to easily read/write a GLF file.

Definition at line 28 of file GlfFile.h.

Member Enumeration Documentation

enum GlfFile::OpenType

Enum for indicating whether to open the file for read or write.

Enumerator:

READ	open for reading.
WRITE	open for writing.

Definition at line 32 of file GlfFile.h.

        {
            READ, ///< open for reading.
            WRITE ///< open for writing.
        };

Constructor & Destructor Documentation

GlfFile::GlfFile	(	const char *	filename,
		OpenType	mode = `READ`
	)

Constructor that opens the specified file based on the specified mode (READ/WRITE).

Default is READ.

Parameters:

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.

    : myFilePtr(NULL),
      myEndMarker()
{
    resetFile();

    bool openStatus = true;
    if(mode == READ)
    {
        // open the file for read.
        openStatus = openForRead(filename);
    }
    else
    {
        // open the file for write.
        openStatus = openForWrite(filename);
    }
    if(!openStatus)
    {
        // Failed to open the file - print error and abort.
        fprintf(stderr, "%s\n", getStatusMessage());
        std::cerr << "FAILURE - EXITING!!!" << std::endl;
        exit(-1);
    }
}

GlfFile::~GlfFile ( ) [virtual]

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.

Definition at line 59 of file GlfFile.cpp.

{
    resetFile();
}

Member Function Documentation

void GlfFile::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.

Definition at line 142 of file GlfFile.cpp.

{
    // Resetting the file will close it if it is open, and
    // will reset all other variables.
    resetFile();
}

uint32_t GlfFile::getCurrentRecordCount ( )

Return the number of records that have been read/written so far.

Returns:: number of records that have been read/written so far.

Definition at line 483 of file GlfFile.cpp.

{
    return(myRecordCount);
}

GlfStatus::Status GlfFile::getFailure ( ) [inline]

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().

    {
        return(getStatus());
    }

bool GlfFile::getNextRecord ( GlfRecord & record )

Gets the nextrecord from the file & stores it in the passed in record.

Parameters:

record object to populate with the file's next record.

Returns:: true = record was successfully set. false = record not successfully set or for the endMarker 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().

{
    if(myIsOpenForRead == false)
    {
        // File is not open for read
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read reference section since the file is not open for reading");
        throw(GlfException(myStatus));
        return(false);
    }

    if(myNextSection == HEADER)
    {
        // The header has not yet been read.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read reference section since the header has not been read.");
        throw(GlfException(myStatus));
        return(false);
    }
    
    if(myNextSection == REF_SECTION)
    {
        // The reference section has not yet been read.
        // TODO - maybe just read the reference section.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read record since a reference section has not been read.");
        throw(GlfException(myStatus));
        return(false);
    }

    // Check for end of file.  If end of file, return false.
    if(isEOF())
    {
        return(false);
    }

    // Read the record.
    if(record.read(myFilePtr))
    {
        myStatus = GlfStatus::SUCCESS;
        if(record.getRecordType() != 0)
        {
            return(true);
        }
        else
        {
            // Not an error, so no exception thrown, but no more records.
            // The next thing is a reference section.
            myNextSection = REF_SECTION;
            return(false);
        }
    }
    
    myStatus.setStatus(GlfStatus::UNKNOWN, 
                       "Failed reading a record from the file.");
    throw(GlfException(myStatus));
    return(false);
}

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.

Parameters:

refSection object to populate with the file's next reference section.

Returns:: true = section was successfully set. false = section was not successfully set.

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.

{
    if(myIsOpenForRead == false)
    {
        // File is not open for read
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read reference section since the file is not open for reading");
        throw(GlfException(myStatus));
        return(false);
    }

    if(myNextSection == HEADER)
    {
        // The header has not yet been read.
        // TODO - maybe just read the header.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read reference section since the header has not been read.");
        throw(GlfException(myStatus));
        return(false);
    }

    // Keep reading until the next section is found.
    if(myNextSection == RECORD)
    {
        GlfRecord record;
        while(getNextRecord(record))
        {
            // Nothing to do, with the record.
        }
    }

    // Check for end of file.  If end of file, return false.
    if(isEOF())
    {
        return(false);
    }

    if(myNextSection != REF_SECTION)
    {
        // Failed reading all the records, so throw exception.
        myStatus.setStatus(GlfStatus::FAIL_IO, 
                           "Failed to get to a reference section.");
        throw(GlfException(myStatus));
        return(false);
    }

    // Ready to read the section:
    if(refSection.read(myFilePtr))
    {
        myStatus = GlfStatus::SUCCESS;
        // Next a record should be read.
        myNextSection = RECORD;
        return(true);
    }

    // If it is the EOF, just return false.
    if(isEOF())
    {
        return(false);
    }
    myStatus.setStatus(GlfStatus::UNKNOWN, 
                       "Failed reading a reference section from the file.");
    throw(GlfException(myStatus));
    return(false);
}

GlfStatus::Status GlfFile::getStatus ( ) [inline]

Get the Status of the last call that sets status.

Returns:: status of the last method that sets a status.

Definition at line 128 of file GlfFile.h.

References GlfStatus::getStatus().

Referenced by getFailure().

    {
        return(myStatus.getStatus());
    }

const char* GlfFile::getStatusMessage ( ) [inline]

Get the Status of the last call that sets status.

Returns:: status message of the last method that sets a status.

Definition at line 135 of file GlfFile.h.

References GlfStatus::getStatusMessage().

Referenced by GlfFile(), GlfFileReader::GlfFileReader(), and GlfFileWriter::GlfFileWriter().

    {
        return(myStatus.getStatusMessage());
    }

bool GlfFile::isEOF ( )

Returns whether or not the end of the file has been reached.

Returns:: true = EOF; false = not eof. If the file is not open, true is returned.

Definition at line 152 of file GlfFile.cpp.

References ifeof().

Referenced by getNextRecord(), and getNextRefSection().

{
    if (myFilePtr != NULL)
    {
        // File Pointer is set, so return if eof.
        return(ifeof(myFilePtr));
    }
    // File pointer is not set, so return true, eof.
    return true;
}

bool GlfFile::openForRead ( const char * filename )

Open a glf file for reading with the specified filename.

Parameters:

filename glf file to open for reading.

Returns:: true = success; false = failure.

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().

{
    // Reset for any previously operated on files.
    resetFile();

    myFilePtr = ifopen(filename, "rb");
   
    if (myFilePtr == NULL)
    {
        std::string errorMessage = "Failed to Open ";
        errorMessage += filename;
        errorMessage += " for reading";
        myStatus.setStatus(GlfStatus::FAIL_IO, errorMessage.c_str());
        throw(GlfException(myStatus));
        return(false);
    }

    myIsOpenForRead = true;
    // Successfully opened the file.
    myStatus = GlfStatus::SUCCESS;
    return(true);
}

bool GlfFile::openForRead	(	const char *	filename,
		GlfHeader &	header
	)

Open a glf file for reading with the specified filename and read the header into the specified header.

Parameters:

filename	glf file to open for reading.
header	header object to populate with the file's glf header.

Returns:: true = success; false = failure.

Definition at line 92 of file GlfFile.cpp.

References openForRead(), and readHeader().

{
    if(!openForRead(filename))
    {
        return(false);
    }

    // Read the header
    if(!readHeader(header))
    {
        return(false);
    }
    return(true);
}

bool GlfFile::openForWrite	(	const char *	filename,
		bool	compressed = `true`
	)

Open a glf file for writing with the specified filename.

Parameters:

filename	glf file to open for writing.
compressed	whether or not to compress the file, defaults to true

Returns:: true = success; false = failure.

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().

{
    // Reset for any previously operated on files.
    resetFile();

    if(compressed)
    {
        myFilePtr = ifopen(filename, "wb", InputFile::BGZF);
    }
    else
    {
        myFilePtr = ifopen(filename, "wb", InputFile::UNCOMPRESSED);
    }

    if (myFilePtr == NULL)
    {
        std::string errorMessage = "Failed to Open ";
        errorMessage += filename;
        errorMessage += " for writing";
        myStatus.setStatus(GlfStatus::FAIL_IO, errorMessage.c_str());
        throw(GlfException(myStatus));
        return(false);
    }
   
    myIsOpenForWrite = true;

    // Successfully opened the file.
    myStatus = GlfStatus::SUCCESS;
    return(true);
}

bool GlfFile::readHeader ( GlfHeader & header )

Reads the header section from the file and stores it in the passed in header.

Parameters:

header header object to populate with the file's glf header.

Returns:: true = success; false = failure.

Definition at line 165 of file GlfFile.cpp.

References GlfStatus::FAIL_ORDER, GlfHeader::read(), GlfStatus::setStatus(), GlfStatus::SUCCESS, and GlfStatus::UNKNOWN.

Referenced by openForRead().

{
    if(myIsOpenForRead == false)
    {
        // File is not open for read
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read header since the file is not open for reading");
        throw(GlfException(myStatus));
        return(false);
    }

    if(myNextSection != HEADER)
    {
        // The header has already been read.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot read header since it has already been read.");
        throw(GlfException(myStatus));
        return(false);
    }

    if(header.read(myFilePtr))
    {
        // The header has now been successfully read.
        myNextSection = REF_SECTION;
        myStatus = GlfStatus::SUCCESS;
        return(true);
    }
    myStatus.setStatus(GlfStatus::UNKNOWN, 
                       "Failed to read the header.");
    throw(GlfException(myStatus));
    return(false);
}

bool GlfFile::writeHeader ( GlfHeader & header )

Writes the specified header into the file.

Parameters:

header header object to write into the file.

Returns:: true = success; false = failure.

Definition at line 200 of file GlfFile.cpp.

References GlfStatus::FAIL_ORDER, GlfStatus::setStatus(), GlfStatus::SUCCESS, GlfStatus::UNKNOWN, and GlfHeader::write().

{
    if(myIsOpenForWrite == false)
    {
        // File is not open for write
        // -OR-
        // The header has already been written.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write header since the file is not open for writing");
        throw(GlfException(myStatus));
        return(false);
    }

    if(myNextSection != HEADER)
    {
        // The header has already been written.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write header since it has already been written");
        throw(GlfException(myStatus));
        return(false);
    }

    if(header.write(myFilePtr))
    {
        // The header has now been successfully written.
        myNextSection = REF_SECTION;
        myStatus = GlfStatus::SUCCESS;
        return(true);
    }

    // return the status.
    myStatus.setStatus(GlfStatus::UNKNOWN, 
                       "Failed to write the header.");
    throw(GlfException(myStatus));
    return(false);
}

bool GlfFile::writeRecord ( const GlfRecord & record )

Writes the specified record into the file.

Parameters:

record record to write to the file.

Returns:: true = success; false = failure.

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().

{
    if(myIsOpenForWrite == false)
    {
        // File is not open for write
        // -OR-
        // The header has already been written.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write record since the file is not open for writing");
        throw(GlfException(myStatus));
       return(false);
    }

    if(myNextSection == HEADER)
    {
        // The header has not been written.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write record since the header has not been written");
        throw(GlfException(myStatus));
        return(false);
    }

    if(myNextSection != RECORD)
    {
        // The header has not been written.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write record since a reference section has not been written");
        throw(GlfException(myStatus));
        return(false);
    }

    if(record.write(myFilePtr))
    {
        myStatus = GlfStatus::SUCCESS;
        // The record has now been successfully written.

        // Check if it was the end marker - if so, set that next a 
        // reference section is expected.
        if(record.getRecordType() == 0)
        {
            myNextSection = REF_SECTION;
        }
        return(true);
    }

    // return the status.
    myStatus.setStatus(GlfStatus::UNKNOWN, 
                       "Failed writing a record to the file.");
    throw(GlfException(myStatus));
    return(false);    
}

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.

Parameters:

refSection reference section to write to the file.

Returns:: true = succes; false = failure.

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().

{
    if(myIsOpenForWrite == false)
    {
        // File is not open for write
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write reference section since the file is not open for writing");
        throw(GlfException(myStatus));
        return(false);
    }

    if(myNextSection == HEADER)
    {
        // The header has not been written.
        myStatus.setStatus(GlfStatus::FAIL_ORDER, 
                           "Cannot write reference section since the header has not been written");
        throw(GlfException(myStatus));
       return(false);
    }

    if(myNextSection == RECORD)
    {
        // did not write a end marker record, so write one now.
        if(!writeRecord(myEndMarker))
        {
            // Failed to write the end marker record.
            myStatus.setStatus(GlfStatus::FAIL_IO,
                               "Failed to write end of chromosome/section marker.");
            throw(GlfException(myStatus));
            return(false);
        }
    }

    if(myNextSection != REF_SECTION)
    {
        // Not ready to write a reference section.
        myStatus.setStatus(GlfStatus::FAIL_IO,
                           "Not ready for a chromosome/section header.");
        throw(GlfException(myStatus));
        return(false);
    }

    if(refSection.write(myFilePtr))
    {
        myStatus = GlfStatus::SUCCESS;
        // A reference section has now been successfully written.
        myNextSection = RECORD;
        return(true);
    }

    // return the status.
    myStatus.setStatus(GlfStatus::UNKNOWN, 
                       "Failed writing a reference section to the file.");
    throw(GlfException(myStatus));
    return(false);    
}

The documentation for this class was generated from the following files:

glf/GlfFile.h
glf/GlfFile.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation