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gnSourceSpec Class Reference

gnSourceSpec stores sequence and annotation data from another source. More...

#include <gnSourceSpec.h>

Inheritance diagram for gnSourceSpec::

List of all members.

Public Methods
	gnSourceSpec ()
	Empty constructor. More...
	gnSourceSpec (gnBaseSource *m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI start=0, const gnSeqI endI=GNSEQI_END, const boolean revComp=false)
	Constructor, creates a gnSourceSpec using sequence data in the given source. More...
	gnSourceSpec (const gnSourceSpec &s)
	Copy constructor. More...
	~gnSourceSpec ()
gnSourceSpec*	Clone () const
virtual void	Clear ()
	Clears all data from this spec. More...
virtual gnSeqI	GetSourceLength () const
	Get the length of the source for this spec. More...
virtual gnBaseSource*	GetSource () const
virtual gnSourceSpec*	CloneRange (const gnSeqI startI, const gnSeqI len) const
	Copies a specified range of bases and returns a pointer to the resulting gnSourceSpec. More...
Protected Methods
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. More...
Protected Attributes
gnBaseSource*	m_pSource

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Detailed Description

gnSourceSpec stores sequence and annotation data from another source.

See also:

gnContigSpec , gnBaseSpec

Definition at line 27 of file gnSourceSpec.h.

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Constructor & Destructor Documentation

gnSourceSpec::gnSourceSpec ( )

Empty constructor. Definition at line 16 of file gnSourceSpec.cpp. Referenced by Clone(), and CloneRange().

gnSourceSpec::gnSourceSpec ( gnBaseSource * m_pSource, const uint32 m_ContigIndex = ALL_CONTIGS, const gnSeqI start = 0, const gnSeqI endI = GNSEQI_END, const boolean revComp = false )

Constructor, creates a gnSourceSpec using sequence data in the given source. A circular spec will be created if the end index is greater than the start. Parameters: m_pSource   The source to read base pairs from. m_ContigIndex   The index of the contig in the source, ALL_CONTIGS by default. startI   The index to start reading base pairs from the source. endI   The index to stop reading base pairs from the source. revComp   True if the sequence is read reverse complement. Definition at line 33 of file gnSourceSpec.cpp.

gnSourceSpec::gnSourceSpec ( const gnSourceSpec & s )

Copy constructor. Parameters: s   the gnSourceSpec to copy. Definition at line 21 of file gnSourceSpec.cpp.

gnSourceSpec::~gnSourceSpec ( )

Definition at line 63 of file gnSourceSpec.cpp.

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Member Function Documentation

void gnSourceSpec::Clear ( ) [virtual]

Clears all data from this spec. Reimplemented from gnContigSpec. Definition at line 67 of file gnSourceSpec.cpp. Referenced by gnSourceSpec().

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

Reimplemented from gnContigSpec. Definition at line 74 of file gnSourceSpec.h.

gnSourceSpec * gnSourceSpec::CloneRange ( const gnSeqI startI, const gnSeqI len ) const [virtual]

Copies a specified range of bases and returns a pointer to the resulting gnSourceSpec. 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 gnSourceSpec containing only the specified bases Definition at line 74 of file gnSourceSpec.cpp.

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

Definition at line 83 of file gnSourceSpec.h.

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

Get the length of the source for this spec. Returns: The source length. Reimplemented from gnContigSpec. Definition at line 79 of file gnSourceSpec.h.

boolean gnSourceSpec::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. Reimplemented from gnContigSpec. Definition at line 89 of file gnSourceSpec.h.

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Member Data Documentation

gnBaseSource * gnSourceSpec::m_pSource [protected]

Definition at line 69 of file gnSourceSpec.h.

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

• gnSourceSpec.h
• gnSourceSpec.cpp

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