BamTools::SamSequenceDictionary Class Reference

Container of SamSequence entries. More...

#include <SamSequenceDictionary.h>

List of all members.

Public Member Functions
	SamSequenceDictionary (void)
	constructor
	SamSequenceDictionary (const SamSequenceDictionary &other)
	copy constructor
	~SamSequenceDictionary (void)
	destructor
void	Add (const SamSequence &sequence)
	Appends a sequence to the dictionary.
void	Add (const std::string &name, const int &length)
	Appends a sequence to the dictionary.
void	Add (const SamSequenceDictionary &sequences)
	Appends another sequence dictionary to this one.
void	Add (const std::vector< SamSequence > &sequences)
	Appends multiple sequences to the dictionary.
void	Add (const std::map< std::string, int > &sequenceMap)
	Appends multiple sequences to the dictionary.
void	Clear (void)
	Clears all sequence entries.
bool	Contains (const SamSequence &sequence) const
	Returns true if dictionary contains sequence (matches on name).
bool	Contains (const std::string &sequenceName) const
	Returns true if dictionary contains sequence.
bool	IsEmpty (void) const
	Returns true if dictionary contains no sequences.
void	Remove (const SamSequence &sequence)
	Removes sequence from dictionary, if found (matches on name).
void	Remove (const std::string &sequenceName)
	Removes sequence from dictionary, if found.
void	Remove (const std::vector< SamSequence > &sequences)
	Removes multiple sequences from dictionary.
void	Remove (const std::vector< std::string > &sequenceNames)
	Removes multiple sequences from dictionary.
int	Size (void) const
	Returns number of sequences in dictionary.
SamSequence &	operator[] (const std::string &sequenceName)
	Retrieves the modifiable SamSequence that matches sequenceName.
SamSequenceIterator	Begin (void)
SamSequenceConstIterator	Begin (void) const
SamSequenceConstIterator	ConstBegin (void) const
SamSequenceIterator	End (void)
SamSequenceConstIterator	End (void) const
SamSequenceConstIterator	ConstEnd (void) const

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Detailed Description

Container of SamSequence entries.

Provides methods for operating on a collection of SamSequence entries.

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Constructor & Destructor Documentation

SamSequenceDictionary::SamSequenceDictionary

(

void

)

constructor

SamSequenceDictionary::SamSequenceDictionary

(

const SamSequenceDictionary &

other

)

copy constructor

SamSequenceDictionary::~SamSequenceDictionary

(

void

)

destructor

---

Member Function Documentation

void SamSequenceDictionary::Add

(

const std::map< std::string, int > &

sequenceMap

)

Appends multiple sequences to the dictionary.

This is an overloaded function.

Parameters:

[in]

sequenceMap

map of sequence entries (name => length) to be added

See also:

Add()

void SamSequenceDictionary::Add

(

const std::vector< SamSequence > &

sequences

)

Appends multiple sequences to the dictionary.

This is an overloaded function.

Parameters:

[in]

sequences

entries to be added

See also:

Add()

void SamSequenceDictionary::Add

(

const SamSequenceDictionary &

sequences

)

Appends another sequence dictionary to this one.

This is an overloaded function.

Parameters:

[in]

sequences

sequence dictionary to be appended

See also:

Add()

void SamSequenceDictionary::Add	(	const std::string &	name,
		const int &	length
	)

Appends a sequence to the dictionary.

This is an overloaded function.

Parameters:

[in]	name	name of sequence entry to be added
[in]	length	length of sequence entry to be added

See also:

Add()

void SamSequenceDictionary::Add

(

const SamSequence &

sequence

)

Appends a sequence to the dictionary.

Duplicate entries are silently discarded.

Parameters:

[in]

sequence

entry to be added

SamSequenceConstIterator SamSequenceDictionary::Begin

(

void

)

const

Returns:

an STL const_iterator pointing to the first sequence

This is an overloaded function.

See also:

ConstBegin(), End()

SamSequenceIterator SamSequenceDictionary::Begin

(

void

)

Returns:

an STL iterator pointing to the first sequence

See also:

ConstBegin(), End()

void SamSequenceDictionary::Clear

(

void

)

Clears all sequence entries.

SamSequenceConstIterator SamSequenceDictionary::ConstBegin

(

void

)

const

Returns:

an STL const_iterator pointing to the first sequence

See also:

Begin(), ConstEnd()

SamSequenceConstIterator SamSequenceDictionary::ConstEnd

(

void

)

const

Returns:

an STL const_iterator pointing to the imaginary entry after the last sequence

See also:

End(), ConstBegin()

bool SamSequenceDictionary::Contains

(

const std::string &

sequenceName

)

const

Returns true if dictionary contains sequence.

Parameters:

[in]

sequenceName

search for sequence matching this name

Returns:

true if dictionary contains a sequence with this name

bool SamSequenceDictionary::Contains

(

const SamSequence &

sequence

)

const

Returns true if dictionary contains sequence (matches on name).

This is an overloaded function.

Parameters:

[in]

sequence

search for this sequence

Returns:

true if dictionary contains sequence (matching on name)

SamSequenceConstIterator SamSequenceDictionary::End

(

void

)

const

Returns:

an STL const_iterator pointing to the imaginary entry after the last sequence

This is an overloaded function.

See also:

Begin(), ConstEnd()

SamSequenceIterator SamSequenceDictionary::End

(

void

)

Returns:

an STL iterator pointing to the imaginary entry after the last sequence

See also:

Begin(), ConstEnd()

bool SamSequenceDictionary::IsEmpty

(

void

)

const

Returns true if dictionary contains no sequences.

See also:

Size()

SamSequence & SamSequenceDictionary::operator[]

(

const std::string &

sequenceName

)

Retrieves the modifiable SamSequence that matches sequenceName.

Note:

If the dictionary contains no sequence matching this name, this function inserts a new one with this name (length:0), 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]

sequenceName

name of sequence to retrieve

Returns:

a modifiable reference to the SamSequence associated with the name

void SamSequenceDictionary::Remove

(

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

sequenceNames

)

Removes multiple sequences from dictionary.

This is an overloaded function.

Parameters:

[in]

sequenceNames

names of the sequences to remove

See also:

Remove()

void SamSequenceDictionary::Remove

(

const std::vector< SamSequence > &

sequences

)

Removes multiple sequences from dictionary.

This is an overloaded function.

Parameters:

[in]

sequences

sequences to remove

See also:

Remove()

void SamSequenceDictionary::Remove

(

const std::string &

sequenceName

)

Removes sequence from dictionary, if found.

Parameters:

[in]

sequenceName

name of sequence to remove

See also:

Remove()

void SamSequenceDictionary::Remove

(

const SamSequence &

sequence

)

Removes sequence from dictionary, if found (matches on name).

This is an overloaded function.

Parameters:

[in]

sequence

SamSequence to remove (matching on name)

int SamSequenceDictionary::Size

(

void

)

const

Returns number of sequences in dictionary.

See also:

IsEmpty()

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

• SamSequenceDictionary.h
• SamSequenceDictionary.cpp