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gnContigSpec Class Reference

gnContigSpec is an interface for classes which store contigs, or reads, of DNA or protein sequence More...

#include <gnContigSpec.h>

Inheritance diagram for gnContigSpec:


Public Member Functions
	gnContigSpec ()
virtual	~gnContigSpec ()
	Destructor, frees memory.
virtual gnContigSpec *	Clone () const=0
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 gnSeqI	GetSourceLength () const=0
	Get the length of the source for this spec.
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 void	Clear ()
	Clears all 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=0
	all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement.
Protected Attributes
gnSeqI	m_start
gnSeqI	m_length
uint32	m_SourceContigIndex
boolean	m_reverseComplement
boolean	m_circular
string	m_name
string	m_sourceName

Detailed Description

gnContigSpec is an interface for classes which store contigs, or reads, of DNA or protein sequence

Definition at line 27 of file gnContigSpec.h.

Constructor & Destructor Documentation

gnContigSpec::gnContigSpec ( ) [inline]

Definition at line 30 of file gnContigSpec.h.

virtual gnContigSpec::~gnContigSpec ( ) [inline, virtual]

Destructor, frees memory.

Definition at line 34 of file gnContigSpec.h.

Member Function Documentation

void gnContigSpec::Clear ( ) [virtual]

Clears all data from this spec.

Reimplemented from gnBaseSpec.
Reimplemented in gnSourceSpec, and gnStringSpec.
Definition at line 60 of file gnContigSpec.cpp.
References gnBaseSpec::Clear(), m_length, m_SourceContigIndex, and m_start.
Referenced by gnStringSpec::Clear(), gnSourceSpec::Clear(), and gnStringSpec::gnStringSpec().

virtual gnContigSpec* gnContigSpec::Clone ( ) const [pure virtual]

Implements gnBaseSpec.
Implemented in gnSourceSpec, and gnStringSpec.
Referenced by gnSequence::gnSequence().

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

const uint32 len

) const [pure virtual]

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

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

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 m_length.

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

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 GetSourceLength(), m_length, gnBaseSpec::m_reverseComplement, and m_start.

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

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 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().

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

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 m_SourceContigIndex, and uint32.
Referenced by gnSequence::globalToSource().

virtual gnSeqI gnContigSpec::GetSourceLength ( ) const [pure virtual]

Get the length of the source for this spec.

Returns:
The source length.

Implemented in gnSourceSpec, and gnStringSpec.
Referenced by CropStart(), gnSequence::globalToSource(), SeqRead(), and SetReverseComplement().

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

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]

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 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().

virtual boolean gnContigSpec::Read ( const gnSeqI start,

gnSeqC * buf,

uint32 & bufLen

) const [protected, pure virtual]

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

Implemented in gnSourceSpec, and gnStringSpec.
Referenced by SeqRead().

boolean gnContigSpec::SeqRead ( const gnSeqI start,

gnSeqC * buf,

uint32 & bufLen,

const uint32 contigI

) const [virtual]

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(), GetSourceLength(), gnSeqI, m_length, gnBaseSpec::m_reverseComplement, m_start, 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]

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 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]

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 GetSourceLength(), m_length, gnBaseSpec::m_reverseComplement, and m_start.
Referenced by gnFragmentSpec::SetReverseComplement().

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

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 m_SourceContigIndex.

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

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]

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 m_start.