BamTools::SamProgramChain Class Reference

Sorted container "chain" of SamProgram records. More...

#include <SamProgramChain.h>

List of all members.

Public Member Functions
	SamProgramChain (void)
	constructor
	SamProgramChain (const SamProgramChain &other)
	copy constructor
	~SamProgramChain (void)
	destructor
void	Add (SamProgram &program)
	Appends a program to program chain.
void	Add (std::vector< SamProgram > &programs)
	Appends a batch of programs to the end of the chain.
void	Clear (void)
	Clears all program records.
bool	Contains (const SamProgram &program) const
	Returns true if chains has this program record (matching on ID).
bool	Contains (const std::string &programId) const
	Returns true if chains has a program record with this ID.
SamProgram &	First (void)
	Fetches first (oldest) record in the chain.
const SamProgram &	First (void) const
	Fetches first (oldest) record in the chain.
bool	IsEmpty (void) const
	Returns true if chain contains no records.
SamProgram &	Last (void)
	Fetches last (newest) record in the chain.
const SamProgram &	Last (void) const
	Fetches last (newest) record in the chain.
int	Size (void) const
	Returns number of program records in the chain.
SamProgram &	operator[] (const std::string &programId)
	Retrieves the modifiable SamProgram record that matches programId.
SamProgramIterator	Begin (void)
SamProgramConstIterator	Begin (void) const
SamProgramConstIterator	ConstBegin (void) const
SamProgramIterator	End (void)
SamProgramConstIterator	End (void) const
SamProgramConstIterator	ConstEnd (void) const

---

Detailed Description

Sorted container "chain" of SamProgram records.

Provides methods for operating on a collection of SamProgram records.

Note:

Underlying container is *NOT* ordered by linkage, but by order of appearance in SamHeader and subsequent Add() calls. Using the current iterators will not allow you to step through the header's program history. Instead use First()/Last() to access oldest/newest records, respectively.

---

Constructor & Destructor Documentation

SamProgramChain::SamProgramChain

(

void

)

constructor

SamProgramChain::SamProgramChain

(

const SamProgramChain &

other

)

copy constructor

SamProgramChain::~SamProgramChain

(

void

)

destructor

---

Member Function Documentation

void SamProgramChain::Add

(

std::vector< SamProgram > &

programs

)

Appends a batch of programs to the end of the chain.

This is an overloaded function.

Parameters:

[in]

programs

batch of program records to append

See also:

Add()

void SamProgramChain::Add

(

SamProgram &

program

)

Appends a program to program chain.

Duplicate entries are silently discarded.

Note:

Underlying container is *NOT* ordered by linkage, but by order of appearance in SamHeader and subsequent Add() calls. Using the current iterators will not allow you to step through the header's program history. Instead use First()/Last() to access oldest/newest records, respectively.

Parameters:

[in]

program

entry to be appended

SamProgramConstIterator SamProgramChain::Begin

(

void

)

const

Returns:

an STL const_iterator pointing to the first (oldest) program record

This is an overloaded function.

See also:

ConstBegin(), End(), First()

SamProgramIterator SamProgramChain::Begin

(

void

)

Returns:

an STL iterator pointing to the first (oldest) program record

See also:

ConstBegin(), End(), First()

void SamProgramChain::Clear

(

void

)

Clears all program records.

SamProgramConstIterator SamProgramChain::ConstBegin

(

void

)

const

Returns:

an STL const_iterator pointing to the first (oldest) program record

See also:

Begin(), ConstEnd(), First()

SamProgramConstIterator SamProgramChain::ConstEnd

(

void

)

const

Returns:

an STL const_iterator pointing to the imaginary entry after the last (newest) program record

See also:

ConstBegin(), End(), Last()

bool SamProgramChain::Contains

(

const std::string &

programId

)

const

Returns true if chains has a program record with this ID.

Parameters:

[in]

programId

search for program matching this ID

Returns:

true if chain contains a program record with this ID

bool SamProgramChain::Contains

(

const SamProgram &

program

)

const

Returns true if chains has this program record (matching on ID).

This is an overloaded function.

Parameters:

[in]

program

SamProgram to search for

Returns:

true if chain contains program (matching on ID)

SamProgramConstIterator SamProgramChain::End

(

void

)

const

Returns:

an STL const_iterator pointing to the imaginary entry after the last (newest) program record

This is an overloaded function.

See also:

Begin(), ConstEnd(), Last()

SamProgramIterator SamProgramChain::End

(

void

)

Returns:

an STL iterator pointing to the imaginary entry after the last (newest) program record

See also:

Begin(), ConstEnd(), Last()

const SamProgram & SamProgramChain::First

(

void

)

const

Fetches first (oldest) record in the chain.

This is an overloaded function.

Warning:

This function will fail if the chain is empty. If this is possible, check the result of IsEmpty() before calling this function.

Returns:

a read-only reference to the first (oldest) program entry

See also:

Begin(), ConstBegin(), Last()

SamProgram & SamProgramChain::First

(

void

)

Fetches first (oldest) record in the chain.

Warning:

This function will fail if the chain is empty. If this is possible, check the result of IsEmpty() before calling this function.

Returns:

a modifiable reference to the first (oldest) program entry

See also:

Begin(), Last()

bool SamProgramChain::IsEmpty

(

void

)

const

Returns true if chain contains no records.

See also:

Size()

const SamProgram & SamProgramChain::Last

(

void

)

const

Fetches last (newest) record in the chain.

This is an overloaded function.

Warning:

This function will fail if the chain is empty. If this is possible, check the result of IsEmpty() before calling this function.

Returns:

a read-only reference to the last (newest) program entry

See also:

End(), ConstEnd(), First()

SamProgram & SamProgramChain::Last

(

void

)

Fetches last (newest) record in the chain.

Warning:

This function will fail if the chain is empty. If this is possible, check the result of IsEmpty() before calling this function.

Returns:

a modifiable reference to the last (newest) program entry

See also:

End(), First()

SamProgram & SamProgramChain::operator[]

(

const std::string &

programId

)

Retrieves the modifiable SamProgram record that matches programId.

Warning:

If the chain contains no read group matching this ID, this function will print an error and terminate. Check the return value of Contains() if this may be possible.

Parameters:

[in]

programId

ID of program record to retrieve

Returns:

a modifiable reference to the SamProgram associated with the ID

int SamProgramChain::Size

(

void

)

const

Returns number of program records in the chain.

See also:

IsEmpty()

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

• SamProgramChain.h
• SamProgramChain.cpp