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gnGenomeSpec Class Reference

This class contains references to the sequence data, annotation, and other related header data for an organism's genome. More...

#include <gnGenomeSpec.h>

Inheritance diagram for gnGenomeSpec:

List of all members.


Public Member Functions
	gnGenomeSpec ()
	gnGenomeSpec (const gnGenomeSpec &s)
	Copy constructor.
virtual	~gnGenomeSpec ()
	Destructor, frees memory.
virtual gnGenomeSpec *	Clone () const
virtual void	Clear ()
	Clears all data from this spec.
virtual void	SetReverseComplement (const boolean value)
	Sets the reverse complement bit for this spec.
virtual uint32	GetSpecListLength () const
	Returns the number of subspecs this spec contains.
virtual gnFragmentSpec *	GetSpec (const uint32 i) const
	Get the spec at index i in the list of subspecs.
virtual gnFragmentSpec *	GetSpecByBase (const gnSeqI baseI) const
	Get the spec from the list of subspecs which contains the specified base pair.
virtual void	AddSpec (gnBaseSpec *spec, const uint32 i=UINT32_MAX)
	Add a subspec to this spec.
virtual void	RemoveSpec (uint32 i)
	Remove a subspec from this spec.
virtual void	MergeFragments (const uint32 startC, const uint32 endC)
virtual uint32	AddFeature (gnBaseFeature *feat)
	Add a feature to this spec.
virtual uint32	GetFeatureListLength () const
	Returns the number of features this spec contains.
virtual gnBaseFeature *	GetFeature (const uint32 i) const
	Get the feature at index i in the list of features.
virtual void	GetContainedFeatures (const gnLocation &lt, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) const
	Creates a list of all features which are contained by coordinates specified.
virtual void	GetIntersectingFeatures (const gnLocation &lt, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) const
	Creates a list of all features which intersect the coordinates specified.
virtual void	GetBrokenFeatures (const gnLocation &lt, vector< gnBaseFeature * > &feature_vector) const
	Creates a list of features which may have been broken by an edit.
virtual void	RemoveFeature (const uint32 i)
	Remove a feature from this spec.
virtual gnGenomeSpec *	CloneRange (const gnSeqI startI, const gnSeqI len) const
	Copies a specified range of bases and returns a pointer to the resulting gnGenomeSpec.
virtual gnSeqI	GetLength () const
	Get the length of all the sequence data covered by this spec.
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 string	GetSourceName () const
virtual void	SetSourceName (const string &sourceName)
virtual boolean	SeqRead (const gnSeqI start, gnSeqC *buf, uint32 &bufLen, const uint32 contigI) const
	Reads sequence data from this spec.
virtual uint32	GetSpecIndexByBase (const gnSeqI baseI) const
	Get the index of the subspec which contains the specified base pair.
virtual uint32	GetSpecIndexByName (const string &name) const
	Get the index of the spec which has the given name.
virtual gnSeqI	GetSpecStartBase (const uint32 specI) const
	Get the starting base pair, in this spec's sequence, of the given subspec.
virtual gnSeqI	GetSpecEndBase (const uint32 specI) const
	Get the ending base pair, in this spec's sequence, of the given subspec.
virtual uint32	GetHeaderListLength () const
	Returns the number of headers this spec contains.
virtual void	AddHeader (gnBaseHeader *head, const uint32 i=UINT32_MAX)
	Add a header to this spec, adds to the end of the header list by default.
virtual gnBaseHeader *	GetHeader (const uint32 i) const
	Get the headers at index i in the list of headers.
virtual gnBaseHeader *	GetHeader (const string &name, uint32 &i) const
	Find the first header with the specified name, starting at index i.
virtual void	RemoveHeader (uint32 i)
	Remove a header from this spec.
virtual gnBaseSpec *	CloneRange (const uint32 startI, const uint32 len) const=0
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 Attributes
vector< gnFragmentSpec * >	m_SpecList
string	m_sourceName
vector< gnBaseHeader * >	m_headerList
boolean	m_reverseComplement
boolean	m_circular
string	m_name

Detailed Description

This class contains references to the sequence data, annotation, and other related header data for an organism's genome.

The genome is organized into a list of sequence fragments (specs), a list of features, and a list of headers.

Definition at line 33 of file gnGenomeSpec.h.

Constructor & Destructor Documentation

gnGenomeSpec::gnGenomeSpec ( )

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

gnGenomeSpec::gnGenomeSpec ( const gnGenomeSpec & s )

Copy constructor.

Parameters:

s the gnGenomeSpec to copy.

Definition at line 21 of file gnGenomeSpec.cpp.
References gnBaseSpec::m_circular, gnMultiSpec::m_headerList, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, gnMultiSpec::m_sourceName, m_SpecList, and uint32.

gnGenomeSpec::~gnGenomeSpec ( ) [virtual]

Destructor, frees memory.

Definition at line 38 of file gnGenomeSpec.cpp.
References Clear().

Member Function Documentation

uint32 gnGenomeSpec::AddFeature ( gnBaseFeature * feat ) [virtual]

Add a feature to this spec.

Parameters:

feat The feature to add.

Returns:
True if successful

Reimplemented from gnMultiSpec.
Definition at line 128 of file gnGenomeSpec.cpp.
References gnFragmentSpec::AddFeature(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec::GetLength(), GetSpec(), GetSpecListLength(), gnBaseFeature::IsContainedBy(), SeqIndexOutOfBounds(), Throw_gnEx, and uint32.
Referenced by gnSequence::addFeature().

void gnMultiSpec::AddHeader ( gnBaseHeader * head,

const uint32 i = UINT32_MAX

) [virtual, inherited]

Add a header to this spec, adds to the end of the header list by default.

Parameters:

head The header to add.

i The header to insert before. If i is larger than the size of the header list the header will be added to the end of the list.

Definition at line 125 of file gnMultiSpec.cpp.
References gnMultiSpec::m_headerList, uint32, and UINT32_MAX.
Referenced by gnSequence::addHeader(), gnFASSource::GetSpec(), gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

void gnGenomeSpec::AddSpec ( gnBaseSpec * spec,

const uint32 i = UINT32_MAX

) [inline, virtual]

Add a subspec to this spec.
Throws an exception if the insertion index i is out of range
Parameters:

spec The subspec to add.

i The subspec to insert before

Returns:
True if successful

Implements gnMultiSpec.
Definition at line 105 of file gnGenomeSpec.h.
References m_SpecList, uint32, and UINT32_MAX.
Referenced by CloneRange(), gnFASSource::GetSpec(), gnSequence::gnSequence(), gnSequence::insert(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnDNXSource::ParseStream().

void gnGenomeSpec::Clear ( ) [virtual]

Clears all data from this spec.

Reimplemented from gnMultiSpec.
Definition at line 43 of file gnGenomeSpec.cpp.
References gnMultiSpec::Clear(), m_SpecList, and uint32.
Referenced by ~gnGenomeSpec().

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

Implements gnMultiSpec.
Definition at line 83 of file gnGenomeSpec.h.
References gnGenomeSpec().
Referenced by gnSequence::assign(), CloneRange(), gnSEQSource::GetSpec(), gnRAWSource::GetSpec(), gnGBKSource::GetSpec(), gnDNXSource::GetSpec(), gnABISource::GetSpec(), gnDNXSource::gnDNXSource(), gnSequence::gnSequence(), gnSequence::insert(), gnSequence::operator=(), and gnSequence::splitContig().

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

const uint32 len

) const [pure virtual, inherited]

Implemented in gnContigSpec.

gnGenomeSpec * gnGenomeSpec::CloneRange ( const gnSeqI startI,

const gnSeqI len

) const [virtual]

Copies a specified range of bases and returns a pointer to the resulting gnGenomeSpec.
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 gnGenomeSpec containing only the specified bases

Definition at line 67 of file gnGenomeSpec.cpp.
References AddSpec(), Clone(), gnFragmentSpec::CloneRange(), gnMultiSpec::GetLength(), GetSpec(), gnMultiSpec::GetSpecIndexByBase(), GetSpecListLength(), gnMultiSpec::GetSpecStartBase(), gnGenomeSpec(), gnSeqI, GNSEQI_END, m_SpecList, and uint32.
Referenced by gnSequence::erase(), and gnSequence::subseq().

void gnMultiSpec::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.
Reimplemented in gnFragmentSpec.
Definition at line 104 of file gnMultiSpec.cpp.
References gnBaseSpec::CropEnd(), gnBaseSpec::GetLength(), gnMultiSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, gnMultiSpec::RemoveSpec(), and uint32.
Referenced by gnFragmentSpec::CropEnd(), gnSequence::erase(), gnSequence::insert(), and gnSequence::splitContig().

void gnMultiSpec::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.
Reimplemented in gnFragmentSpec.
Definition at line 85 of file gnMultiSpec.cpp.
References gnBaseSpec::CropStart(), gnBaseSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, gnMultiSpec::RemoveSpec(), and uint32.
Referenced by gnFragmentSpec::CropStart(), gnSequence::insert(), and gnSequence::splitContig().

void gnGenomeSpec::GetBrokenFeatures ( const gnLocation & lt,

vector< gnBaseFeature * > & feature_vector

) const [virtual]

Creates a list of features which may have been broken by an edit.

Parameters:

lt The coordinates containing the features to return.

feature_vector The vector to store features in.

Implements gnMultiSpec.
Definition at line 214 of file gnGenomeSpec.cpp.
References gnLocation::CropEnd(), gnFragmentSpec::GetBrokenFeatures(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec::GetLength(), GetSpec(), GetSpecListLength(), gnSeqI, gnLocation::MoveNegative(), and uint32.
Referenced by gnSequence::getBrokenFeatures().

void gnGenomeSpec::GetContainedFeatures ( const gnLocation & lt,

vector< gnBaseFeature * > & feature_vector,

vector< uint32 > & index_vector

) const [virtual]

Creates a list of all features which are contained by coordinates specified.

Parameters:

lt The coordinates containing the features to return.

feature_vector The vector to store features in.

index_vector A vector of indices which correspond to the features.

Implements gnMultiSpec.
Definition at line 171 of file gnGenomeSpec.cpp.
References gnLocation::CropEnd(), gnFragmentSpec::GetContainedFeatures(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec::GetLength(), GetSpec(), GetSpecListLength(), gnSeqI, gnLocation::MoveNegative(), and uint32.
Referenced by gnSequence::getContainedFeatures().

gnBaseFeature * gnGenomeSpec::GetFeature ( const uint32 i ) const [virtual]

Get the feature at index i in the list of features.

Parameters:

i The index of the feature

Returns:
The feature.

Implements gnMultiSpec.
Definition at line 155 of file gnGenomeSpec.cpp.
References FeatureIndexOutOfBounds(), gnFragmentSpec::GetFeature(), gnFragmentSpec::GetFeatureListLength(), GetSpec(), GetSpecListLength(), gnMultiSpec::GetSpecStartBase(), gnBaseFeature::MovePositive(), Throw_gnEx, and uint32.
Referenced by gnSequence::getFeature().

uint32 gnGenomeSpec::GetFeatureListLength ( ) const [virtual]

Returns the number of features this spec contains.

Returns:
The number of features this spec contains.

Implements gnMultiSpec.
Definition at line 147 of file gnGenomeSpec.cpp.
References gnFragmentSpec::GetFeatureListLength(), GetSpec(), GetSpecListLength(), and uint32.
Referenced by gnSequence::getFeatureListLength().

gnBaseHeader * gnMultiSpec::GetHeader ( const string & name,

uint32 & i

) const [virtual, inherited]

Find the first header with the specified name, starting at index i.

Parameters:

name The name of the header to find.

i The index to start looking at.

Returns:
The header or NULL if none was found.

Definition at line 131 of file gnMultiSpec.cpp.
References HeaderIndexOutOfBounds(), gnMultiSpec::m_headerList, and Throw_gnEx.

gnBaseHeader * gnMultiSpec::GetHeader ( const uint32 i ) const [inline, virtual, inherited]

Get the headers at index i in the list of headers.
Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced
Parameters:

i The index of the header

Returns:
The header.

Definition at line 197 of file gnMultiSpec.h.
References gnMultiSpec::m_headerList.
Referenced by gnSequence::getHeader(), gnGBKSource::Write(), gnFASSource::Write(), gnDNXSource::Write(), and gnGBKSource::WriteHeader().

uint32 gnMultiSpec::GetHeaderListLength ( ) const [inline, virtual, inherited]

Returns the number of headers this spec contains.

Returns:
The number of headers this spec contains.

Definition at line 192 of file gnMultiSpec.h.
References gnMultiSpec::m_headerList, and uint32.
Referenced by gnSequence::getHeaderListLength(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnGBKSource::Write().

void gnGenomeSpec::GetIntersectingFeatures ( const gnLocation & lt,

vector< gnBaseFeature * > & feature_vector,

vector< uint32 > & index_vector

) const [virtual]

Creates a list of all features which intersect the coordinates specified.

Parameters:

lt The coordinates intersecting the features to return.

feature_vector The vector to store features in.

index_vector A vector of indices which correspond to the features.

Implements gnMultiSpec.
Definition at line 193 of file gnGenomeSpec.cpp.
References gnLocation::CropEnd(), gnFragmentSpec::GetFeatureListLength(), gnFragmentSpec::GetIntersectingFeatures(), gnMultiSpec::GetLength(), GetSpec(), GetSpecListLength(), gnSeqI, gnLocation::MoveNegative(), and uint32.
Referenced by gnSequence::getIntersectingFeatures().

gnSeqI gnMultiSpec::GetLength ( ) const [virtual, inherited]

Get the length of all the sequence data covered by this spec.

Returns:
This spec's length in base pairs.

Implements gnBaseSpec.
Definition at line 32 of file gnMultiSpec.cpp.
References gnBaseSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, and uint32.
Referenced by AddFeature(), CloneRange(), gnFragmentSpec::CloneRange(), gnSequence::contigLength(), gnMultiSpec::CropEnd(), gnSequence::erase(), GetBrokenFeatures(), GetContainedFeatures(), gnSEQSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnDNXSource::GetContigSeqLength(), GetIntersectingFeatures(), gnSequence::insert(), gnSequence::length(), gnSequence::size(), and gnGBKSource::Write().

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().

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

Definition at line 206 of file gnMultiSpec.h.
References gnMultiSpec::m_sourceName.
Referenced by gnDNXSource::Write().

gnFragmentSpec * gnGenomeSpec::GetSpec ( const uint32 i ) const [inline, virtual]

Get the spec at index i in the list of subspecs.

Parameters:

i The index of the spec

Returns:
The spec.

Implements gnMultiSpec.
Definition at line 93 of file gnGenomeSpec.h.
References FragmentIndexOutOfBounds(), m_SpecList, and Throw_gnEx.
Referenced by AddFeature(), gnSequence::addHeader(), CloneRange(), gnSequence::contig(), gnSequence::contigByName(), gnSequence::contigLength(), gnSequence::contigName(), GetBrokenFeatures(), GetContainedFeatures(), gnDNXSource::GetContigID(), gnDNXSource::GetContigName(), gnDNXSource::GetContigSeqLength(), GetFeature(), GetFeatureListLength(), gnSequence::getHeader(), gnSequence::getHeaderListLength(), GetIntersectingFeatures(), gnSequence::globalToSource(), gnDNXSource::HasContig(), gnSequence::insert(), gnSequence::isReverseComplement(), RemoveFeature(), gnSequence::removeHeader(), gnSequence::setContigName(), gnSequence::setReverseComplement(), SetReverseComplement(), gnGBKSource::Write(), gnFASSource::Write(), and gnDNXSource::Write().

gnFragmentSpec * gnGenomeSpec::GetSpecByBase ( const gnSeqI baseI ) const [inline, virtual]

Get the spec from the list of subspecs which contains the specified base pair.

Parameters:

baseI The base pair index.

Returns:
The spec.

Implements gnMultiSpec.
Definition at line 100 of file gnGenomeSpec.h.
References gnMultiSpec::GetSpecIndexByBase(), and m_SpecList.
Referenced by gnSequence::contigByBase().

gnSeqI gnMultiSpec::GetSpecEndBase ( const uint32 specI ) const [virtual, inherited]

Get the ending base pair, in this spec's sequence, of the given subspec.

Parameters:

specI The subspec index.

Returns:
The subspec's ending base pair.

Definition at line 73 of file gnMultiSpec.cpp.
References gnBaseSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, SpecIndexOutOfBounds(), Throw_gnEx, and uint32.

uint32 gnMultiSpec::GetSpecIndexByBase ( const gnSeqI baseI ) const [virtual, inherited]

Get the index of the subspec which contains the specified base pair.

Parameters:

baseI The base pair index.

Returns:
The subspec index.

Definition at line 41 of file gnMultiSpec.cpp.
References gnBaseSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, SeqIndexOutOfBounds(), Throw_gnEx, and uint32.
Referenced by CloneRange(), gnFragmentSpec::CloneRange(), gnSequence::contigIndexByBase(), GetSpecByBase(), gnFragmentSpec::GetSpecByBase(), and gnSequence::globalToSource().

uint32 gnMultiSpec::GetSpecIndexByName ( const string & name ) const [virtual, inherited]

Get the index of the spec which has the given name.

Parameters:

name The name of the spec to find.

Returns:
The spec index.

Definition at line 52 of file gnMultiSpec.cpp.
References gnBaseSpec::GetName(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), SpecIndexOutOfBounds(), Throw_gnEx, and uint32.
Referenced by gnSequence::contigByName(), and gnSequence::contigIndexByName().

uint32 gnGenomeSpec::GetSpecListLength ( ) const [inline, virtual]

Returns the number of subspecs this spec contains.

Returns:
The number of subspecs this spec contains.

Implements gnMultiSpec.
Definition at line 88 of file gnGenomeSpec.h.
References m_SpecList, and uint32.
Referenced by AddFeature(), CloneRange(), gnSequence::contigListLength(), gnSequence::contigListSize(), GetBrokenFeatures(), GetContainedFeatures(), gnDNXSource::GetContigID(), gnDNXSource::GetContigListLength(), gnDNXSource::GetContigName(), gnDNXSource::GetContigSeqLength(), GetFeature(), GetFeatureListLength(), GetIntersectingFeatures(), gnDNXSource::HasContig(), gnSequence::insert(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), RemoveFeature(), RemoveSpec(), SetReverseComplement(), gnGBKSource::Write(), and gnDNXSource::Write().

gnSeqI gnMultiSpec::GetSpecStartBase ( const uint32 specI ) const [virtual, inherited]

Get the starting base pair, in this spec's sequence, of the given subspec.

Parameters:

specI The subspec index.

Returns:
The subspec's starting base pair.

Definition at line 61 of file gnMultiSpec.cpp.
References gnBaseSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, SpecIndexOutOfBounds(), Throw_gnEx, and uint32.
Referenced by CloneRange(), gnFragmentSpec::CloneRange(), gnSequence::contigStart(), GetFeature(), and 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(), SetReverseComplement(), and gnFragmentSpec::SetReverseComplement().

void gnGenomeSpec::MergeFragments ( const uint32 startC,

const uint32 endC

) [virtual]

Definition at line 112 of file gnGenomeSpec.cpp.
References gnFragmentSpec::AddSpec(), FragmentIndexOutOfBounds(), gnFragmentSpec::GetSpec(), gnFragmentSpec::GetSpecListLength(), m_SpecList, Throw_gnEx, and uint32.
Referenced by gnSequence::mergeContigs().

void gnGenomeSpec::RemoveFeature ( const uint32 i ) [virtual]

Remove a feature from this spec.

Parameters:

i The index of the feature to remove.

Returns:
True if successful

Implements gnMultiSpec.
Definition at line 234 of file gnGenomeSpec.cpp.
References FeatureIndexOutOfBounds(), gnFragmentSpec::GetFeatureListLength(), GetSpec(), GetSpecListLength(), gnFragmentSpec::RemoveFeature(), Throw_gnEx, and uint32.
Referenced by gnSequence::removeFeature().

void gnMultiSpec::RemoveHeader ( uint32 i ) [virtual, inherited]

Remove a header from this spec.
Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced
Parameters:

i The index of the header to remove.

Definition at line 139 of file gnMultiSpec.cpp.
References HeaderIndexOutOfBounds(), gnMultiSpec::m_headerList, and Throw_gnEx.
Referenced by gnSequence::removeHeader().

void gnGenomeSpec::RemoveSpec ( uint32 i ) [inline, virtual]

Remove a subspec from this spec.

Parameters:

i The index of the subspec to remove.

Implements gnMultiSpec.
Definition at line 113 of file gnGenomeSpec.h.
References GetSpecListLength(), and m_SpecList.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

boolean gnMultiSpec::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 147 of file gnMultiSpec.cpp.
References gnBaseSpec::GetLength(), gnMultiSpec::GetSpec(), gnMultiSpec::GetSpecListLength(), gnSeqI, SeqIndexOutOfBounds(), gnBaseSpec::SeqRead(), SpecIndexOutOfBounds(), Throw_gnEx, and uint32.
Referenced by gnSequence::GetSeqC(), gnDNXSource::SeqRead(), gnSequence::ToArray(), and gnSequence::ToString().

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 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 gnGenomeSpec::SetReverseComplement ( const boolean value ) [virtual]

Sets the reverse complement bit for this spec.

Parameters:

value True for reverse complement, false otherwise.

Implements gnBaseSpec.
Definition at line 52 of file gnGenomeSpec.cpp.
References GetSpec(), GetSpecListLength(), gnBaseSpec::IsReverseComplement(), gnBaseSpec::m_reverseComplement, m_SpecList, gnFragmentSpec::SetReverseComplement(), and uint32.
Referenced by gnSequence::setReverseComplement().

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

Definition at line 211 of file gnMultiSpec.h.
References gnMultiSpec::m_sourceName.
Referenced by gnFASSource::GetSpec(), and gnDNXSource::ParseStream().

Member Data Documentation

boolean gnBaseSpec::m_circular [protected, inherited]

Definition at line 108 of file gnBaseSpec.h.
Referenced by gnBaseSpec::Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), gnBaseSpec::IsCircular(), and gnBaseSpec::SetCircular().

vector<gnBaseHeader*> gnMultiSpec::m_headerList [protected, inherited]

Definition at line 186 of file gnMultiSpec.h.
Referenced by gnMultiSpec::AddHeader(), gnMultiSpec::Clear(), gnMultiSpec::GetHeader(), gnMultiSpec::GetHeaderListLength(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec(), and gnMultiSpec::RemoveHeader().

string gnBaseSpec::m_name [protected, inherited]

Definition at line 110 of file gnBaseSpec.h.
Referenced by gnBaseSpec::Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnBaseSpec::GetName(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), and gnBaseSpec::SetName().

boolean gnBaseSpec::m_reverseComplement [protected, inherited]

Definition at line 107 of file gnBaseSpec.h.
Referenced by gnBaseSpec::Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnContigSpec::CropStart(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), gnBaseSpec::IsReverseComplement(), gnContigSpec::SeqRead(), SetReverseComplement(), gnFragmentSpec::SetReverseComplement(), and gnContigSpec::SetReverseComplement().

string gnMultiSpec::m_sourceName [protected, inherited]

Reimplemented from gnBaseSpec.
Definition at line 184 of file gnMultiSpec.h.
Referenced by gnMultiSpec::GetSourceName(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec(), and gnMultiSpec::SetSourceName().

vector<gnFragmentSpec*> gnGenomeSpec::m_SpecList [protected]

Definition at line 78 of file gnGenomeSpec.h.
Referenced by AddSpec(), Clear(), CloneRange(), GetSpec(), GetSpecByBase(), GetSpecListLength(), gnGenomeSpec(), MergeFragments(), RemoveSpec(), and SetReverseComplement().

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

Generated on Mon Feb 3 02:34:49 2003 for libGenome by

1.3-rc3

gnGenomeSpec Class Reference

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation