MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > Class Template Reference

Inheritance diagram for MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >:

Collaboration diagram for MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >:

List of all members.

Public Member Functions
void	constructorClear ()
const std::string &	getErrorString ()
arrayHeaderClass &	getHeader ()
void	setContentCookie (uint32_t c)
void	setContentVersion (uint32_t v)
elementT	operator[] (indexT i)
void	set (indexT i, elementT v)
int	create (const char *file, indexT elementCount, int optionalHeaderCount=0)
	Create a vector with elementCount memebers.
int	create (indexT elementCount, int optionalHeaderCount=0)
	allow anonymous (malloc) create.
bool	open (const char *file, int flags=O_RDONLY)
	open a previously created mapped vector
bool	close ()
void	debugPrint (FILE *f)
size_t	getElementCount () const
Protected Attributes
arrayHeaderClass *	header
char *	data
std::string	errorStr

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Detailed Description

template<class elementT, typename indexT, unsigned int cookieVal, unsigned int versionVal, elementT accessorFunc, void setterFunc, size_t elementCount2BytesFunc, class arrayHeaderClass>
class MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >

Definition at line 141 of file MemoryMapArray.h.

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Member Function Documentation

template<class elementT , typename indexT , unsigned int cookieVal, unsigned int versionVal, elementT accessorFunc, void setterFunc, size_t elementCount2BytesFunc, class arrayHeaderClass >

int MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >::create	(	const char *	file,
		indexT	elementCount,
		int	optionalHeaderCount = 0
	)		[inline]

Create a vector with elementCount memebers.

Does administrative setup of the header and populating this class members. User will need to finish populating the contents of the metaData and data sections.

If file==NULL, the underlying allocation is done via malloc(), so that the results of write access to this vecor are not saved in a file.

If file!=NULL, a file will be created on disk, and all write accesses done via the method ::set will be persistent in that file.

Definition at line 208 of file MemoryMapArray.h.

Referenced by MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >::create(), and GenomeSequence::loadDBSNP().

    {
        size_t len = elementCount2BytesFunc(elementCount) +
                     header->getHeaderSize(optionalHeaderCount);
        int rc;
        rc = MemoryMap::create(file, len);
        if (rc)
        {
            std::ostringstream buf;
            buf << file << ": failed to create file";
            errorStr = buf.str();
            close();
            return rc;
        }
        header = (arrayHeaderClass *) MemoryMap::data;
        header->constructorClear();
        header->typeCookie = cookieVal;
        header->typeVersion = versionVal;
        header->headerSize = header->getHeaderSize(optionalHeaderCount);
        header->elementCount = elementCount;
        data = (char *)((char *) MemoryMap::data + header->headerSize);

        const char *env;
        char hostname[256];
        env = getenv("USER");
        if (env) header->setCreationUser(env);
        header->creationDate = time(NULL);
#if defined(_WIN32)
        hostname[0] = '\0';
#else
        gethostname(hostname, sizeof(hostname));
#endif
        header->setCreationHost(hostname);
        return 0;
    }

template<class elementT , typename indexT , unsigned int cookieVal, unsigned int versionVal, elementT accessorFunc, void setterFunc, size_t elementCount2BytesFunc, class arrayHeaderClass >

int MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >::create	(	indexT	elementCount,
		int	optionalHeaderCount = 0
	)		[inline]

allow anonymous (malloc) create.

we do this when we don't expect to save the results.

The single use case so far is in GenomeSequence::populateDBSNP.

Definition at line 250 of file MemoryMapArray.h.

References MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >::create().

    {
        return create(NULL, elementCount, optionalHeaderCount);
    }

template<class elementT , typename indexT , unsigned int cookieVal, unsigned int versionVal, elementT accessorFunc, void setterFunc, size_t elementCount2BytesFunc, class arrayHeaderClass >

bool MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >::open	(	const char *	file,
		int	flags = O_RDONLY
	)		[inline, virtual]

open a previously created mapped vector

useMemoryMapFlag will determine whether it uses mmap() or malloc()/read() to populate the memory

Reimplemented from MemoryMap.

Reimplemented in GenomeSequence.

Definition at line 269 of file MemoryMapArray.h.

Referenced by GenomeSequence::loadDBSNP().

    {
        int rc = MemoryMap::open(file, flags);
        if (rc)
        {
            std::ostringstream buf;
            buf << file << ": open() failed (error=" << strerror(errno) << ").";
            errorStr = buf.str();
            return true;
        }
        header = (arrayHeaderClass *) MemoryMap::data;
        data = (char *)((char *) MemoryMap::data + header->headerSize);
        if (header->typeCookie!=cookieVal)
        {
            std::ostringstream buf;
            buf << file << ": wrong type of file (expected type "
            << cookieVal << " but got " << header->typeCookie << ")";
            errorStr = buf.str();
            // XXX insert better error handling
            close();
            return true;
        }
        if (header->typeVersion!=versionVal)
        {
            std::ostringstream buf;
            buf << file << ": wrong version of file (expected version "
            << versionVal << " but got " << header->typeVersion << ")";
            errorStr = buf.str();
            // XXX insert better error handling
            close();
            return true;
        }
        return false;
    }

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

• general/MemoryMapArray.h