libSlice::ReadManager Class Reference
[C++ Interface]

Detailed Description

Manages the information about all of the read data.

Examples:: SliceDataExample.cc.

Definition at line 106 of file ReadData.hh.

Public Member Functions

ReadManager ()

Simple Constructor.

~ReadManager ()

Deletes all of the reads contained in the map.

int size () const

Returns the number of reads stored in the map.

ReadData * addReadData (const char *id, const char *seqname, const char *dir, const char *chem)

Adds a named read and direction and chemistry.

void insertRead (ReadData *rd)

Inserts a read into the read map.

void resetReadId (ReadData *rd, const string &id)

Removes a read from the map under one id, and inserts it as another.

void removeRead (const string &id)

Removes a read from the map, but does not delete the ReadData.

ReadData * getNextRead ()

Iterates through the list of reads.

void resetReadIterator ()

Reset the read Iterator, so that getNextRead can recycle through list.

void printXML (ostream &out, const string &prefix="") const

Prints the ReadCollection in XML with all of the reads.

ReadData * find (const string &readId) const

Finds a read based on a readId.

Member Function Documentation

ReadData * libSlice::ReadManager::addReadData ( const char * id,

const char * seqname,

const char * dir,

const char * chem

)

Adds a named read and direction and chemistry.
Creates the new read, and stores it in the lookup map
See also:
ReadData
insertRead

Return values:

Pointer to the ReadData object just created

Examples:
SliceDataExample.cc.

Definition at line 429 of file ReadData.cc.

ReadData * libSlice::ReadManager::find ( const string & readId ) const

Finds a read based on a readId.

Returns:
Pointer to ReadData of requested name or NULL if not found

Definition at line 465 of file ReadData.cc.

void libSlice::ReadManager::insertRead ( ReadData * rd )

Inserts a read into the read map.

Exceptions:

Exception If there is already a read with id in the map

Definition at line 494 of file ReadData.cc.

void libSlice::ReadManager::resetReadId ( ReadData * rd,

const string & id

)

Removes a read from the map under one id, and inserts it as another.

See also:
removeRead
insertRead

Definition at line 512 of file ReadData.cc.

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

libSlice::ReadManager Class Reference [C++ Interface]

Detailed Description

Public Member Functions

Member Function Documentation

libSlice::ReadManager Class Reference
[C++ Interface]