#include <gnFragmentSpec.h>
Inheritance diagram for gnFragmentSpec:
Public Member Functions | |
virtual uint32 | AddFeature (gnBaseFeature *feat) |
Add a feature to this spec. | |
virtual void | Clear () |
Clears all data from this spec. | |
virtual gnFragmentSpec * | Clone () const |
virtual gnFragmentSpec * | CloneRange (const gnSeqI startI, const gnSeqI len) const |
Copies a specified range of bases and returns a pointer to the resulting gnFragmentSpec. | |
virtual void | CropEnd (gnSeqI cropLen) |
Crop the last cropLen bases from the sequence. | |
virtual void | CropStart (gnSeqI cropLen) |
Crop the first cropLen bases from the sequence. | |
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. | |
gnFragmentSpec (const gnFragmentSpec &s) | |
Copy constructor. | |
gnFragmentSpec () | |
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 | ~gnFragmentSpec () |
Destructor, frees memory. | |
Protected Attributes | |
vector< gnBaseFeature * > | m_featureList |
It also contains a list of features which relate to the sequence fragment. Finally it contains a list of sequence related header data. This class is usually created and filled by a file reader class like gnGBKSource.
Definition at line 34 of file gnFragmentSpec.h.
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Definition at line 16 of file gnFragmentSpec.cpp. References gnBaseSpec::Clear(). Referenced by Clone(), and CloneRange(). |
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Destructor, frees memory. Definition at line 44 of file gnFragmentSpec.cpp. References Clear(). |
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Copy constructor.
References gnBaseSpec::m_circular, m_featureList, gnMultiSpec< SubSpec >::m_headerList, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, gnMultiSpec< SubSpec >::m_sourceName, gnMultiSpec< SubSpec >::m_SpecList, and uint32. |
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Add a feature to this spec.
Reimplemented from gnMultiSpec< gnContigSpec >. Definition at line 125 of file gnFragmentSpec.h. References m_featureList, gnBaseFeature::SetSpec(), and uint32. Referenced by gnGenomeSpec::AddFeature(), gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). |
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Clears all data from this spec.
Reimplemented from gnMultiSpec< gnContigSpec >. Definition at line 50 of file gnFragmentSpec.cpp. References gnMultiSpec< SubSpec >::Clear(), m_featureList, and uint32. Referenced by ~gnFragmentSpec(). |
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Implements gnMultiSpec< gnContigSpec >. Definition at line 87 of file gnFragmentSpec.h. References gnFragmentSpec(). Referenced by CloneRange(), GetBrokenFeatures(), GetContainedFeatures(), GetIntersectingFeatures(), gnSequence::gnSequence(), and gnSequence::insert(). |
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Copies a specified range of bases and returns a pointer to the resulting gnFragmentSpec. You must delete the copy when you are finished with it.
Implements gnBaseSpec. Definition at line 102 of file gnFragmentSpec.cpp. References gnMultiSpec< SubSpec >::AddSpec(), Clone(), gnContigSpec::CloneRange(), GetIntersectingFeatures(), gnContigSpec::GetLength(), gnMultiSpec< gnContigSpec >::GetLength(), gnMultiSpec< gnContigSpec >::GetSpec(), gnMultiSpec< gnContigSpec >::GetSpecIndexByBase(), gnMultiSpec< gnContigSpec >::GetSpecListLength(), gnMultiSpec< gnContigSpec >::GetSpecStartBase(), gnFragmentSpec(), gnSeqI, GNSEQI_END, m_featureList, gnLocation::SetEnd(), gnLocation::SetStart(), and uint32. Referenced by gnGenomeSpec::CloneRange(). |
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Crop the last cropLen bases from the sequence. CropEnd will delete features and headers associated with the cropped bases.
Reimplemented from gnMultiSpec< gnContigSpec >. Definition at line 94 of file gnFragmentSpec.cpp. References gnMultiSpec< SubSpec >::CropEnd(), gnSeqI, m_featureList, and uint32. |
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Crop the first cropLen bases from the sequence. CropStart will delete features and headers associated with the cropped bases.
Reimplemented from gnMultiSpec< gnContigSpec >. Definition at line 86 of file gnFragmentSpec.cpp. References gnMultiSpec< SubSpec >::CropStart(), gnSeqI, m_featureList, and uint32. |
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Creates a list of features which may have been broken by an edit.
Implements gnMultiSpec< gnContigSpec >. Definition at line 79 of file gnFragmentSpec.cpp. References Clone(), m_featureList, and uint32. Referenced by gnGenomeSpec::GetBrokenFeatures(). |
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Creates a list of all features which are contained by coordinates specified.
Implements gnMultiSpec< gnContigSpec >. Definition at line 63 of file gnFragmentSpec.cpp. References Clone(), m_featureList, and uint32. Referenced by gnGenomeSpec::GetContainedFeatures(). |
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Get the feature at index i in the list of features.
Implements gnMultiSpec< gnContigSpec >. Definition at line 137 of file gnFragmentSpec.h. References m_featureList, and uint32. Referenced by gnGenomeSpec::GetFeature(), and gnGBKSource::Write(). |
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Returns the number of features this spec contains.
Implements gnMultiSpec< gnContigSpec >. Definition at line 132 of file gnFragmentSpec.h. References m_featureList, and uint32. Referenced by gnGenomeSpec::AddFeature(), gnGenomeSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnGenomeSpec::GetFeature(), gnGenomeSpec::GetFeatureListLength(), gnGenomeSpec::GetIntersectingFeatures(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnGenomeSpec::RemoveFeature(), and gnGBKSource::Write(). |
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Creates a list of all features which intersect the coordinates specified.
Implements gnMultiSpec< gnContigSpec >. Definition at line 71 of file gnFragmentSpec.cpp. References Clone(), m_featureList, and uint32. Referenced by CloneRange(), and gnGenomeSpec::GetIntersectingFeatures(). |
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Remove a feature from this spec.
Implements gnMultiSpec< gnContigSpec >. Definition at line 142 of file gnFragmentSpec.h. References m_featureList, Throw_gnEx, and uint32. Referenced by gnGenomeSpec::RemoveFeature(). |
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Sets the reverse complement bit for this spec.
Implements gnBaseSpec. Definition at line 154 of file gnFragmentSpec.cpp. References gnMultiSpec< gnContigSpec >::GetSpec(), gnMultiSpec< gnContigSpec >::GetSpecListLength(), gnBaseSpec::IsReverseComplement(), gnContigSpec::SetReverseComplement(), and uint32. Referenced by gnSequence::setReverseComplement(), and gnGenomeSpec::SetReverseComplement(). |
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Definition at line 82 of file gnFragmentSpec.h. Referenced by AddFeature(), Clear(), CloneRange(), CropEnd(), CropStart(), GetBrokenFeatures(), GetContainedFeatures(), GetFeature(), GetFeatureListLength(), GetIntersectingFeatures(), gnFragmentSpec(), and RemoveFeature(). |