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gnBaseSpec Class Reference

gnBaseSpec is the class which stores genetic information and is best accessed using gnSequence. More...

#include <gnBaseSpec.h>

Inheritance diagram for gnBaseSpec:

List of all members.

Public Member Functions
	gnBaseSpec ()
virtual	~gnBaseSpec ()
	Destructor, frees memory.
virtual gnBaseSpec *	Clone () const=0
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 gnSeqI	GetLength () const=0
	Get the length of all the sequence data covered by this spec.
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	SetReverseComplement (const boolean value)=0
	Sets the reverse complement bit for this spec.
virtual void	SetCircular (const boolean value)
	Sets whether this spec should be read circular.
virtual void	CropStart (gnSeqI cropLen)=0
	Crop the first cropLen bases from the sequence.
virtual void	CropEnd (gnSeqI cropLen)=0
	Crop the last cropLen bases from the sequence.
virtual boolean	SeqRead (const gnSeqI start, gnSeqC *buf, uint32 &bufLen, const uint32 contigI) const=0
	Reads sequence data from this spec.
virtual void	Clear ()
	Clears all data from this spec.
Protected Attributes
boolean	m_reverseComplement
boolean	m_circular
string	m_name
string	m_sourceName

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Detailed Description

gnBaseSpec is the class which stores genetic information and is best accessed using gnSequence.

Definition at line 27 of file gnBaseSpec.h.

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Constructor & Destructor Documentation

gnBaseSpec::gnBaseSpec (    )  [inline]

Definition at line 30 of file gnBaseSpec.h.

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

Destructor, frees memory. Definition at line 34 of file gnBaseSpec.h.

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Member Function Documentation

void gnBaseSpec::Clear (    )  [inline, virtual]

Clears all data from this spec. Reimplemented in gnContigSpec, gnFragmentSpec, gnGenomeSpec, gnMultiSpec, gnSourceSpec, and gnStringSpec. Definition at line 136 of file gnBaseSpec.h. References m_circular, m_name, m_reverseComplement, and m_sourceName. Referenced by gnMultiSpec::Clear(), gnContigSpec::Clear(), gnFragmentSpec::gnFragmentSpec(), and gnGenomeSpec::gnGenomeSpec().

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

Implements gnClone. Implemented in gnContigSpec, gnFragmentSpec, gnGenomeSpec, gnMultiSpec, gnSourceSpec, and gnStringSpec.

virtual gnBaseSpec* gnBaseSpec::CloneRange (  const uint32    startI, const uint32    len )  const [pure virtual]

Implemented in gnContigSpec.

virtual void gnBaseSpec::CropEnd (  gnSeqI    cropLen )  [pure 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. Implemented in gnContigSpec, gnFragmentSpec, and gnMultiSpec. Referenced by gnMultiSpec::CropEnd().

virtual void gnBaseSpec::CropStart (  gnSeqI    cropLen )  [pure 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. Implemented in gnContigSpec, gnFragmentSpec, and gnMultiSpec. Referenced by gnMultiSpec::CropStart().

virtual gnSeqI gnBaseSpec::GetLength (    )  const [pure virtual]

Get the length of all the sequence data covered by this spec. Returns: This spec's length in base pairs. Implemented in gnContigSpec, and gnMultiSpec. Referenced by gnMultiSpec::CropEnd(), gnMultiSpec::CropStart(), gnDNXSource::GetContigSeqLength(), gnMultiSpec::GetLength(), gnMultiSpec::GetSpecEndBase(), gnMultiSpec::GetSpecIndexByBase(), gnMultiSpec::GetSpecStartBase(), and gnMultiSpec::SeqRead().

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

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 m_name. Referenced by gnSequence::contigName(), gnDNXSource::GetContigID(), gnDNXSource::GetContigName(), gnMultiSpec::GetSpecIndexByName(), gnDNXSource::HasContig(), gnGBKSource::Write(), and gnDNXSource::Write().

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

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 m_circular. Referenced by gnSequence::isCircular(), and gnGBKSource::Write().

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

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 m_reverseComplement. Referenced by gnSequence::globalToSource(), gnSequence::isReverseComplement(), gnGenomeSpec::SetReverseComplement(), and gnFragmentSpec::SetReverseComplement().

virtual boolean gnBaseSpec::SeqRead (  const gnSeqI    start, gnSeqC *    buf, uint32 &    bufLen, const uint32    contigI )  const [pure 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. Implemented in gnContigSpec, and gnMultiSpec. Referenced by gnMultiSpec::SeqRead().

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

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 m_circular. Referenced by gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnSequence::setCircular().

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

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 m_name. Referenced by gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnDNXSource::ParseStream(), and gnSequence::setContigName().

virtual void gnBaseSpec::SetReverseComplement (  const boolean    value )  [pure virtual]

Sets the reverse complement bit for this spec. Parameters: value  True for reverse complement, false otherwise. Implemented in gnContigSpec, gnFragmentSpec, and gnGenomeSpec.

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Member Data Documentation

boolean gnBaseSpec::m_circular [protected]

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

string gnBaseSpec::m_name [protected]

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

boolean gnBaseSpec::m_reverseComplement [protected]

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

string gnBaseSpec::m_sourceName [protected]

Reimplemented in gnMultiSpec. Definition at line 111 of file gnBaseSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnContigSpec::GetSourceName(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), and gnContigSpec::SetSourceName().

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

• gnBaseSpec.h

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