#include <gnGenomeSpec.h>
Inheritance diagram for gnGenomeSpec:
Public Member Functions | |
virtual uint32 | AddFeature (gnBaseFeature *feat) |
Add a feature to this spec. | |
virtual void | Clear () |
Clears all data from this spec. | |
virtual gnGenomeSpec * | Clone () const |
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 void | GetBrokenFeatures (const gnLocation <, vector< gnBaseFeature * > &feature_vector) const |
Creates a list of features which may have been broken by an edit. | |
virtual void | GetContainedFeatures (const gnLocation <, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) const |
Creates a list of all features which are contained by coordinates specified. | |
virtual gnBaseFeature * | GetFeature (const uint32 i) const |
Get the feature at index i in the list of features. | |
virtual uint32 | GetFeatureListLength () const |
Returns the number of features this spec contains. | |
virtual void | GetIntersectingFeatures (const gnLocation <, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) const |
Creates a list of all features which intersect the coordinates specified. | |
gnGenomeSpec (const gnGenomeSpec &s) | |
Copy constructor. | |
gnGenomeSpec () | |
virtual void | MergeFragments (const uint32 startC, const uint32 endC) |
virtual void | RemoveFeature (const uint32 i) |
Remove a feature from this spec. | |
virtual void | SetReverseComplement (const boolean value) |
Sets the reverse complement bit for this spec. | |
virtual | ~gnGenomeSpec () |
Destructor, frees memory. |
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.
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Definition at line 16 of file gnGenomeSpec.cpp. References gnBaseSpec::Clear(). Referenced by Clone(), and CloneRange(). |
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Copy constructor.
References gnBaseSpec::m_circular, gnMultiSpec< SubSpec >::m_headerList, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, gnMultiSpec< SubSpec >::m_sourceName, gnMultiSpec< SubSpec >::m_SpecList, and uint32. |
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Destructor, frees memory. Definition at line 38 of file gnGenomeSpec.cpp. References Clear(). |
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Add a feature to this spec.
Reimplemented from gnMultiSpec< gnFragmentSpec >. Definition at line 128 of file gnGenomeSpec.cpp. References gnFragmentSpec::AddFeature(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnBaseFeature::IsContainedBy(), Throw_gnEx, and uint32. Referenced by gnSequence::addFeature(). |
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Clears all data from this spec.
Reimplemented from gnMultiSpec< gnFragmentSpec >. Definition at line 43 of file gnGenomeSpec.cpp. References gnMultiSpec< SubSpec >::Clear(), and uint32. Referenced by ~gnGenomeSpec(). |
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Implements gnMultiSpec< gnFragmentSpec >. Definition at line 84 of file gnGenomeSpec.h. References gnGenomeSpec(). Referenced by gnSequence::assign(), CloneRange(), gnRAWSource::GetSpec(), gnSEQSource::GetSpec(), gnGBKSource::GetSpec(), gnDNXSource::GetSpec(), gnABISource::GetSpec(), gnDNXSource::gnDNXSource(), gnSequence::gnSequence(), gnSequence::insert(), gnSequence::operator=(), and gnSequence::splitContig(). |
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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.
Implements gnBaseSpec. Definition at line 67 of file gnGenomeSpec.cpp. References gnMultiSpec< SubSpec >::AddSpec(), Clone(), gnFragmentSpec::CloneRange(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< gnFragmentSpec >::GetLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecIndexByBase(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnMultiSpec< gnFragmentSpec >::GetSpecStartBase(), gnGenomeSpec(), gnSeqI, GNSEQI_END, and uint32. Referenced by gnSequence::erase(), and gnSequence::subseq(). |
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Creates a list of features which may have been broken by an edit.
Implements gnMultiSpec< gnFragmentSpec >. Definition at line 214 of file gnGenomeSpec.cpp. References gnLocation::CropEnd(), gnFragmentSpec::GetBrokenFeatures(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnSeqI, gnLocation::MoveNegative(), and uint32. Referenced by gnSequence::getBrokenFeatures(). |
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Creates a list of all features which are contained by coordinates specified.
Implements gnMultiSpec< gnFragmentSpec >. Definition at line 171 of file gnGenomeSpec.cpp. References gnLocation::CropEnd(), gnFragmentSpec::GetContainedFeatures(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnSeqI, gnLocation::MoveNegative(), and uint32. Referenced by gnSequence::getContainedFeatures(). |
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Get the feature at index i in the list of features.
Implements gnMultiSpec< gnFragmentSpec >. Definition at line 155 of file gnGenomeSpec.cpp. References gnFragmentSpec::GetFeature(), gnFragmentSpec::GetFeatureListLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnMultiSpec< gnFragmentSpec >::GetSpecStartBase(), gnBaseFeature::MovePositive(), Throw_gnEx, and uint32. Referenced by gnSequence::getFeature(). |
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Returns the number of features this spec contains.
Implements gnMultiSpec< gnFragmentSpec >. Definition at line 147 of file gnGenomeSpec.cpp. References gnFragmentSpec::GetFeatureListLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), and uint32. Referenced by gnSequence::getFeatureListLength(). |
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Creates a list of all features which intersect the coordinates specified.
Implements gnMultiSpec< gnFragmentSpec >. Definition at line 193 of file gnGenomeSpec.cpp. References gnLocation::CropEnd(), gnFragmentSpec::GetFeatureListLength(), gnFragmentSpec::GetIntersectingFeatures(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnSeqI, gnLocation::MoveNegative(), and uint32. Referenced by gnSequence::getIntersectingFeatures(). |
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Definition at line 112 of file gnGenomeSpec.cpp. References gnMultiSpec< SubSpec >::AddSpec(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), Throw_gnEx, and uint32. Referenced by gnSequence::mergeContigs(). |
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Remove a feature from this spec.
Implements gnMultiSpec< gnFragmentSpec >. Definition at line 234 of file gnGenomeSpec.cpp. References gnFragmentSpec::GetFeatureListLength(), gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnFragmentSpec::RemoveFeature(), Throw_gnEx, and uint32. Referenced by gnSequence::removeFeature(). |
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Sets the reverse complement bit for this spec.
Implements gnBaseSpec. Definition at line 52 of file gnGenomeSpec.cpp. References gnMultiSpec< gnFragmentSpec >::GetSpec(), gnMultiSpec< gnFragmentSpec >::GetSpecListLength(), gnBaseSpec::IsReverseComplement(), gnFragmentSpec::SetReverseComplement(), and uint32. Referenced by gnSequence::setReverseComplement(). |