BamTools::SamReadGroupDictionary Class Reference

Container of SamReadGroup entries. More...

#include <SamReadGroupDictionary.h>

List of all members.

Public Member Functions
	SamReadGroupDictionary (void)
	constructor
	SamReadGroupDictionary (const SamReadGroupDictionary &other)
	copy constructor
	~SamReadGroupDictionary (void)
	destructor
void	Add (const SamReadGroup &readGroup)
	Appends a read group to the dictionary.
void	Add (const std::string &readGroupId)
	Appends a read group to the dictionary.
void	Add (const SamReadGroupDictionary &readGroups)
	Appends another read group dictionary to this one.
void	Add (const std::vector< SamReadGroup > &readGroups)
	Appends multiple read groups to the dictionary.
void	Add (const std::vector< std::string > &readGroupIds)
	Appends multiple read groups to the dictionary.
void	Clear (void)
	Clears all read group entries.
bool	Contains (const SamReadGroup &readGroup) const
	Returns true if dictionary contains read group (matching on ID).
bool	Contains (const std::string &readGroupId) const
	Returns true if dictionary contains read group.
bool	IsEmpty (void) const
	Returns true if dictionary contains no read groups.
void	Remove (const SamReadGroup &readGroup)
	Removes read group from dictionary, if found (matching on ID).
void	Remove (const std::string &readGroupId)
	Removes read group from dictionary, if found.
void	Remove (const std::vector< SamReadGroup > &readGroups)
	Removes multiple read groups from dictionary (matching on ID).
void	Remove (const std::vector< std::string > &readGroupIds)
	Removes multiple read groups from dictionary.
int	Size (void) const
	Returns number of read groups in dictionary.
SamReadGroup &	operator[] (const std::string &readGroupId)
	Retrieves the modifiable SamReadGroup that matches readGroupId.
SamReadGroupIterator	Begin (void)
SamReadGroupConstIterator	Begin (void) const
SamReadGroupConstIterator	ConstBegin (void) const
SamReadGroupIterator	End (void)
SamReadGroupConstIterator	End (void) const
SamReadGroupConstIterator	ConstEnd (void) const

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Detailed Description

Container of SamReadGroup entries.

Provides methods for operating on a collection of SamReadGroup entries.

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Constructor & Destructor Documentation

SamReadGroupDictionary::SamReadGroupDictionary

(

void

)

constructor

SamReadGroupDictionary::SamReadGroupDictionary

(

const SamReadGroupDictionary &

other

)

copy constructor

SamReadGroupDictionary::~SamReadGroupDictionary

(

void

)

destructor

---

Member Function Documentation

void SamReadGroupDictionary::Add

(

const std::vector< std::string > &

readGroupIds

)

Appends multiple read groups to the dictionary.

This is an overloaded function.

Parameters:

[in]

readGroupIds

IDs of read groups to be added

See also:

Add()

void SamReadGroupDictionary::Add

(

const std::vector< SamReadGroup > &

readGroups

)

Appends multiple read groups to the dictionary.

This is an overloaded function.

Parameters:

[in]

readGroups

entries to be added

See also:

Add()

void SamReadGroupDictionary::Add

(

const SamReadGroupDictionary &

readGroups

)

Appends another read group dictionary to this one.

This is an overloaded function.

Parameters:

[in]

readGroups

entries to be added

See also:

Add()

void SamReadGroupDictionary::Add

(

const std::string &

readGroupId

)

Appends a read group to the dictionary.

This is an overloaded function.

Parameters:

[in]

readGroupId

ID of read group to be added

See also:

Add()

void SamReadGroupDictionary::Add

(

const SamReadGroup &

readGroup

)

Appends a read group to the dictionary.

Duplicate entries are silently discarded.

Parameters:

[in]

readGroup

entry to be added

SamReadGroupConstIterator SamReadGroupDictionary::Begin

(

void

)

const

Returns:

an STL const_iterator pointing to the first read group

This is an overloaded function.

See also:

ConstBegin(), End()

SamReadGroupIterator SamReadGroupDictionary::Begin

(

void

)

Returns:

an STL iterator pointing to the first read group

See also:

ConstBegin(), End()

void SamReadGroupDictionary::Clear

(

void

)

Clears all read group entries.

SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin

(

void

)

const

Returns:

an STL const_iterator pointing to the first read group

See also:

Begin(), ConstEnd()

SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd

(

void

)

const

Returns:

an STL const_iterator pointing to the imaginary entry after the last read group

See also:

ConstBegin(), End()

bool SamReadGroupDictionary::Contains

(

const std::string &

readGroupId

)

const

Returns true if dictionary contains read group.

Parameters:

[in]

readGroupId

search for read group matching this ID

Returns:

true if dictionary contains a read group with this ID

bool SamReadGroupDictionary::Contains

(

const SamReadGroup &

readGroup

)

const

Returns true if dictionary contains read group (matching on ID).

This is an overloaded function.

Parameters:

[in]

readGroup

search for this read group

Returns:

true if dictionary contains read group (matching on ID).

SamReadGroupConstIterator SamReadGroupDictionary::End

(

void

)

const

Returns:

an STL const_iterator pointing to the imaginary entry after the last read group

This is an overloaded function.

See also:

Begin(), ConstEnd()

SamReadGroupIterator SamReadGroupDictionary::End

(

void

)

Returns:

an STL iterator pointing to the imaginary entry after the last read group

See also:

Begin(), ConstEnd()

bool SamReadGroupDictionary::IsEmpty

(

void

)

const

Returns true if dictionary contains no read groups.

See also:

Size()

SamReadGroup & SamReadGroupDictionary::operator[]

(

const std::string &

readGroupId

)

Retrieves the modifiable SamReadGroup that matches readGroupId.

Note:

If the dictionary contains no read group matching this ID, this function inserts a new one with this ID, and returns a reference to it. If you want to avoid this insertion behavior, check the result of Contains() before using this operator.

Parameters:

[in]

readGroupId

ID of read group to retrieve

Returns:

a modifiable reference to the SamReadGroup associated with the ID

void SamReadGroupDictionary::Remove

(

const std::vector< std::string > &

readGroupIds

)

Removes multiple read groups from dictionary.

This is an overloaded function.

Parameters:

[in]

readGroupIds

IDs of the read groups to remove

See also:

Remove()

void SamReadGroupDictionary::Remove

(

const std::vector< SamReadGroup > &

readGroups

)

Removes multiple read groups from dictionary (matching on ID).

This is an overloaded function.

Parameters:

[in]

readGroups

read groups to remove

See also:

Remove()

void SamReadGroupDictionary::Remove

(

const std::string &

readGroupId

)

Removes read group from dictionary, if found.

Parameters:

[in]

readGroupId

ID of read group to remove

See also:

Remove()

void SamReadGroupDictionary::Remove

(

const SamReadGroup &

readGroup

)

Removes read group from dictionary, if found (matching on ID).

This is an overloaded function.

Parameters:

[in]

readGroup

read group to remove (matches on ID)

int SamReadGroupDictionary::Size

(

void

)

const

Returns number of read groups in dictionary.

See also:

IsEmpty()

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

• SamReadGroupDictionary.h
• SamReadGroupDictionary.cpp