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gnStringSpec Class Reference

gnStringSpec stores a sequence and annotation data in memory. More...

#include <gnStringSpec.h>

Inheritance diagram for gnStringSpec:


Public Member Functions
	gnStringSpec ()
	Empty constructor.
	gnStringSpec (const string &m_string, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp=false)
	Constructor, creates a gnStringSpec using sequence data in the given string.
	gnStringSpec (const gnStringSpec &s)
	Copy constructor.
	~gnStringSpec ()
gnStringSpec *	Clone () const
virtual void	Clear ()
	Clears all data from this spec.
virtual gnSeqI	GetSourceLength () const
	Get the length of the source for this spec.
virtual gnBaseSource *	GetSource () const
virtual gnStringSpec *	CloneRange (const gnSeqI startI, const gnSeqI len) const
	Copies a specified range of bases and returns a pointer to the resulting gnStringSpec.
virtual gnContigSpec *	CloneRange (const uint32 startI, const uint32 len) const=0
virtual string	GetSourceName () const
	Get the name of the source associated with this spec.
virtual gnSeqI	GetStart () const
	Get the base pair index where this contig starts inside of the sequence data.
virtual gnSeqI	GetLength () const
	Get the length of this contig inside of the sequence data.
virtual uint32	GetSourceContigIndex () const
	Returns this contig's index in its source sequence.
virtual void	SetSourceName (const string &sourceName)
	Sets the name of the source associated with this contig.
virtual void	SetStart (const gnSeqI start)
	Sets the starting base pair to read from in the contig's sequence.
virtual void	SetLength (const gnSeqI len)
	Sets the length of reads into this sequence.
virtual void	SetSourceContigIndex (const uint32 contigI)
	Sets this contig's index in its source sequence.
virtual void	SetReverseComplement (const boolean value)
	Sets the reverse complement bit for this contig.
virtual void	CropStart (gnSeqI cropLen)
	Crop the first cropLen bases from the sequence.
virtual void	CropEnd (gnSeqI cropLen)
	Crop the last cropLen bases from the sequence.
virtual boolean	SeqRead (const gnSeqI start, gnSeqC *buf, uint32 &bufLen, const uint32 contigI) const
	Reads sequence data from this spec.
virtual string	GetName () const
	Get the name of the contig associated with this spec.
virtual void	SetName (const string &name)
	Sets the name for this contig.
virtual boolean	IsReverseComplement () const
	Returns true if this spec is read reverse complement.
virtual boolean	IsCircular () const
	Returns true if this spec's sequence is circular.
virtual void	SetCircular (const boolean value)
	Sets whether this spec should be read circular.
Protected Member Functions
virtual boolean	Read (const gnSeqI start, gnSeqC *buf, uint32 &bufLen) const
	all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement.
Protected Attributes
string	m_seqString
gnSeqI	m_start
gnSeqI	m_length
uint32	m_SourceContigIndex
boolean	m_reverseComplement
boolean	m_circular
string	m_name
string	m_sourceName

Detailed Description

gnStringSpec stores a sequence and annotation data in memory.

For a more complete description see the gnBaseSpec documentation.

Definition at line 25 of file gnStringSpec.h.

Constructor & Destructor Documentation

gnStringSpec::gnStringSpec ( )

Empty constructor.

Definition at line 16 of file gnStringSpec.cpp.
References gnContigSpec::Clear().
Referenced by Clone(), and CloneRange().

gnStringSpec::gnStringSpec ( const string & m_string,

const gnSeqI startI = 0,

const gnSeqI endI = GNSEQI_END,

const boolean revComp = false

)

Constructor, creates a gnStringSpec using sequence data in the given string.
A circular spec will be created if the end index is greater than the start.
Parameters:

m_string The string to read base pairs from.

startI The index to start reading base pairs from the string.

endI The index to stop reading base pairs from the string.

revComp True if the sequence is read reverse complement.

Definition at line 21 of file gnStringSpec.cpp.
References gnSeqI, gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_reverseComplement, m_seqString, gnContigSpec::m_SourceContigIndex, and gnContigSpec::m_start.

gnStringSpec::gnStringSpec ( const gnStringSpec & s )

Copy constructor.

Parameters:

s the gnStringSpec to copy.

Definition at line 44 of file gnStringSpec.cpp.
References gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, m_seqString, gnContigSpec::m_SourceContigIndex, gnBaseSpec::m_sourceName, and gnContigSpec::m_start.

gnStringSpec::~gnStringSpec ( )

Definition at line 55 of file gnStringSpec.cpp.
References Clear().

Member Function Documentation

void gnStringSpec::Clear ( ) [virtual]

Clears all data from this spec.

Reimplemented from gnContigSpec.
Definition at line 59 of file gnStringSpec.cpp.
References gnContigSpec::Clear(), and m_seqString.
Referenced by ~gnStringSpec().

gnStringSpec * gnStringSpec::Clone ( ) const [inline, virtual]

Implements gnContigSpec.
Definition at line 75 of file gnStringSpec.h.
References gnStringSpec().

virtual gnContigSpec* gnContigSpec::CloneRange ( const uint32 startI,

const uint32 len

) const [pure virtual, inherited]

Implements gnBaseSpec.
Referenced by gnFragmentSpec::CloneRange().

gnStringSpec * gnStringSpec::CloneRange ( const gnSeqI startI,

const gnSeqI len

) const [virtual]

Copies a specified range of bases and returns a pointer to the resulting gnStringSpec.
You must delete the copy when you are finished with it.
Parameters:

startI The first base pair to copy

len The length of the piece to copy

Returns:
A copy of the gnStringSpec containing only the specified bases

Definition at line 65 of file gnStringSpec.cpp.
References gnStringSpec(), gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, m_seqString, gnContigSpec::m_SourceContigIndex, gnBaseSpec::m_sourceName, and gnContigSpec::m_start.

void gnContigSpec::CropEnd ( gnSeqI cropLen ) [virtual, inherited]

Crop the last cropLen bases from the sequence.
CropEnd will delete features and headers associated with the cropped bases.
Parameters:

cropLen The number of base pairs to delete from the end.

Implements gnBaseSpec.
Definition at line 22 of file gnContigSpec.cpp.
References gnContigSpec::m_length.

void gnContigSpec::CropStart ( gnSeqI cropLen ) [virtual, inherited]

Crop the first cropLen bases from the sequence.
CropStart will delete features and headers associated with the cropped bases.
Parameters:

cropLen The number of base pairs to delete from the beginning.

Implements gnBaseSpec.
Definition at line 16 of file gnContigSpec.cpp.
References gnContigSpec::GetSourceLength(), gnContigSpec::m_length, gnBaseSpec::m_reverseComplement, and gnContigSpec::m_start.

gnSeqI gnContigSpec::GetLength ( ) const [inline, virtual, inherited]

Get the length of this contig inside of the sequence data.

Returns:
This contigs length.

Implements gnBaseSpec.
Definition at line 133 of file gnContigSpec.h.
References gnSeqI, and gnContigSpec::m_length.
Referenced by gnFragmentSpec::CloneRange(), gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

string gnBaseSpec::GetName ( ) const [inline, virtual, inherited]

Get the name of the contig associated with this spec.

Returns:
The contig name or an empty string if none exists.

Definition at line 116 of file gnBaseSpec.h.
References gnBaseSpec::m_name.
Referenced by gnSequence::contigName(), gnDNXSource::GetContigID(), gnDNXSource::GetContigName(), gnMultiSpec::GetSpecIndexByName(), gnDNXSource::HasContig(), gnGBKSource::Write(), and gnDNXSource::Write().

gnBaseSource * gnStringSpec::GetSource ( ) const [inline, virtual]

Definition at line 84 of file gnStringSpec.h.

uint32 gnContigSpec::GetSourceContigIndex ( ) const [inline, virtual, inherited]

Returns this contig's index in its source sequence.

Returns:
This contig's index in the source sequence.

Definition at line 149 of file gnContigSpec.h.
References gnContigSpec::m_SourceContigIndex, and uint32.
Referenced by gnSequence::globalToSource().

gnSeqI gnStringSpec::GetSourceLength ( ) const [inline, virtual]

Get the length of the source for this spec.

Returns:
The source length.

Implements gnContigSpec.
Definition at line 80 of file gnStringSpec.h.
References gnSeqI, and m_seqString.

string gnContigSpec::GetSourceName ( ) const [inline, virtual, inherited]

Get the name of the source associated with this spec.

Returns:
The source name or an empty string if none exists.

Definition at line 119 of file gnContigSpec.h.
References gnBaseSpec::m_sourceName.

gnSeqI gnContigSpec::GetStart ( ) const [inline, virtual, inherited]

Get the base pair index where this contig starts inside of the sequence data.

Returns:
The starting base pair.

Definition at line 128 of file gnContigSpec.h.
References gnSeqI, and gnContigSpec::m_start.
Referenced by gnSequence::globalToSource().

boolean gnBaseSpec::IsCircular ( ) const [inline, virtual, inherited]

Returns true if this spec's sequence is circular.

Returns:
True if this spec's sequence is circular.

Definition at line 128 of file gnBaseSpec.h.
References gnBaseSpec::m_circular.
Referenced by gnSequence::isCircular(), and gnGBKSource::Write().

boolean gnBaseSpec::IsReverseComplement ( ) const [inline, virtual, inherited]

Returns true if this spec is read reverse complement.

Returns:
True if this spec is read reverse complement.

Definition at line 124 of file gnBaseSpec.h.
References gnBaseSpec::m_reverseComplement.
Referenced by gnSequence::globalToSource(), gnSequence::isReverseComplement(), gnGenomeSpec::SetReverseComplement(), and gnFragmentSpec::SetReverseComplement().

boolean gnStringSpec::Read ( const gnSeqI start,

gnSeqC * buf,

uint32 & bufLen

) const [inline, protected, virtual]

all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement.

Implements gnContigSpec.
Definition at line 90 of file gnStringSpec.h.
References m_seqString.

boolean gnContigSpec::SeqRead ( const gnSeqI start,

gnSeqC * buf,

uint32 & bufLen,

const uint32 contigI

) const [virtual, inherited]

Reads sequence data from this spec.
SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence. Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with a valid contig index. SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen". SeqRead will return false if a serious error occurs.
Parameters:

start The base pair to start reading at.

buf The character array to store base pairs into.

bufLen The number of base pairs to read. This will be modified to reflect the actual number of bases read.

contigI The index of the subspec to read or ALL_CONTIGS by default.

Returns:
True if the operation was successful.

Implements gnBaseSpec.
Definition at line 34 of file gnContigSpec.cpp.
References gnFilter::DNAComplementFilter(), gnContigSpec::GetSourceLength(), gnSeqI, gnContigSpec::m_length, gnBaseSpec::m_reverseComplement, gnContigSpec::m_start, gnContigSpec::Read(), and gnFilter::ReverseFilter().

void gnBaseSpec::SetCircular ( const boolean value ) [inline, virtual, inherited]

Sets whether this spec should be read circular.
If circular is set, reads beyond the end of this spec will pick up at the beginning and read up to the start index.
Parameters:

value True for circular, false otherwise.

Definition at line 132 of file gnBaseSpec.h.
References gnBaseSpec::m_circular.
Referenced by gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnSequence::setCircular().

void gnContigSpec::SetLength ( const gnSeqI len ) [inline, virtual, inherited]

Sets the length of reads into this sequence.
This does not affect the actual sequence data but only how much of it is used in this contig.
Parameters:

len The new sequence length.

Returns:
True if successful.

Definition at line 144 of file gnContigSpec.h.
References gnContigSpec::m_length.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

void gnBaseSpec::SetName ( const string & name ) [inline, virtual, inherited]

Sets the name for this contig.

Parameters:

name The new name.

Returns:
True if successful. Honestly, I don't know how this could be unsuccessful...

Definition at line 120 of file gnBaseSpec.h.
References gnBaseSpec::m_name.
Referenced by gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnDNXSource::ParseStream(), and gnSequence::setContigName().

void gnContigSpec::SetReverseComplement ( const boolean value ) [virtual, inherited]

Sets the reverse complement bit for this contig.
This routine will translate the start index to the reverse base pair.
Parameters:

value True for reverse complement, false otherwise.

Returns:
True if successful.

Implements gnBaseSpec.
Definition at line 26 of file gnContigSpec.cpp.
References gnContigSpec::GetSourceLength(), gnContigSpec::m_length, gnBaseSpec::m_reverseComplement, and gnContigSpec::m_start.
Referenced by gnFragmentSpec::SetReverseComplement().

void gnContigSpec::SetSourceContigIndex ( const uint32 contigI ) [inline, virtual, inherited]

Sets this contig's index in its source sequence.

Parameters:

contigI This contig's index in the source sequence.

Definition at line 153 of file gnContigSpec.h.
References gnContigSpec::m_SourceContigIndex.

void gnContigSpec::SetSourceName ( const string & sourceName ) [inline, virtual, inherited]

Sets the name of the source associated with this contig.

Parameters:

sourceName The new name.

Returns:
True if successful.

Definition at line 123 of file gnContigSpec.h.
References gnBaseSpec::m_sourceName.
Referenced by gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnDNXSource::ParseStream().

void gnContigSpec::SetStart ( const gnSeqI start ) [inline, virtual, inherited]

Sets the starting base pair to read from in the contig's sequence.
This does not affect the actual sequence data but only where to begin using it in this contig.
Parameters:

start The new starting base pair.

Returns:
True if successful.

Definition at line 139 of file gnContigSpec.h.
References gnContigSpec::m_start.