#include <gnSourceSpec.h>
Inheritance diagram for gnSourceSpec:
Public Member Functions | |
virtual void | Clear () |
Clears all data from this spec. | |
gnSourceSpec * | Clone () 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. | |
virtual gnBaseSource * | GetSource () const |
virtual gnSeqI | GetSourceLength () const |
Get the length of the source for this spec. | |
gnSourceSpec (const gnSourceSpec &s) | |
Copy constructor. | |
gnSourceSpec (gnBaseSource *m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp=false) | |
Constructor, creates a gnSourceSpec using sequence data in the given source. | |
gnSourceSpec () | |
Empty constructor. | |
~gnSourceSpec () | |
Protected Member Functions | |
virtual boolean | Read (const gnSeqI start, gnSeqC *buf, gnSeqI &bufLen) const |
all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement. | |
Protected Attributes | |
gnBaseSource * | m_pSource |
Definition at line 26 of file gnSourceSpec.h.
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Empty constructor. Definition at line 15 of file gnSourceSpec.cpp. References Clear(). Referenced by Clone(), and CloneRange(). |
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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.
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Copy constructor.
References gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_name, m_pSource, gnBaseSpec::m_reverseComplement, gnContigSpec::m_SourceContigIndex, gnBaseSpec::m_sourceName, and gnContigSpec::m_start. |
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Definition at line 62 of file gnSourceSpec.cpp. |
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Clears all data from this spec.
Reimplemented from gnContigSpec. Definition at line 66 of file gnSourceSpec.cpp. References gnContigSpec::Clear(), and m_pSource. Referenced by gnSourceSpec(). |
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Implements gnContigSpec. Definition at line 73 of file gnSourceSpec.h. References gnSourceSpec(). |
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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.
Implements gnContigSpec. Definition at line 73 of file gnSourceSpec.cpp. References gnSeqI, gnSourceSpec(), gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_name, m_pSource, gnBaseSpec::m_reverseComplement, gnContigSpec::m_SourceContigIndex, gnBaseSpec::m_sourceName, and gnContigSpec::m_start. |
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Definition at line 82 of file gnSourceSpec.h. References m_pSource. |
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Get the length of the source for this spec.
Implements gnContigSpec. Definition at line 78 of file gnSourceSpec.h. References gnBaseSource::GetContigSeqLength(), gnSeqI, and m_pSource. |
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all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement.
Implements gnContigSpec. Definition at line 88 of file gnSourceSpec.h. References gnSeqC, gnSeqI, m_pSource, and gnBaseSource::SeqRead(). |
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Definition at line 68 of file gnSourceSpec.h. Referenced by Clear(), CloneRange(), GetSource(), GetSourceLength(), gnSourceSpec(), and Read(). |