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gnGenomeSpec Class Reference This class contains references to the sequence data, annotation, and other related header data for an organism's genome. More... #include <gnGenomeSpec.h> Inheritance diagram for gnGenomeSpec:: List of all members. Public Methods   gnGenomeSpec ()   gnGenomeSpec (const gnGenomeSpec &s)   Copy constructor. More... virtual  ~gnGenomeSpec ()   Destructor, frees memory. More... virtual gnGenomeSpec*  Clone () const virtual void  Clear ()   Clears all data from this spec. More... virtual void  SetReverseComplement (const boolean value)   Sets the reverse complement bit for this spec. More... virtual uint32  GetSpecListLength () const   Returns the number of subspecs this spec contains. More... virtual gnFragmentSpec*  GetSpec (const uint32 i) const   Get the spec at index i in the list of subspecs. More... virtual gnFragmentSpec*  GetSpecByBase (const gnSeqI baseI) const   Get the spec from the list of subspecs which contains the specified base pair. More... virtual void  AddSpec (gnBaseSpec *spec, const uint32 i=UINT32_MAX)   Add a subspec to this spec. More... virtual void  RemoveSpec (uint32 i)   Remove a subspec from this spec. More... virtual void  MergeFragments (const uint32 startC, const uint32 endC) virtual uint32  AddFeature (gnBaseFeature *feat)   Add a feature to this spec. More... virtual uint32  GetFeatureListLength () const   Returns the number of features this spec contains. More... virtual gnBaseFeature*  GetFeature (const uint32 i) const   Get the feature at index i in the list of features. More... virtual void  GetContainedFeatures (const gnLocation &lt, vector< gnBaseFeature *> &feature_vector, vector< uint32 > &index_vector) const   Creates a list of all features which are contained by coordinates specified. More... virtual void  GetIntersectingFeatures (const gnLocation &lt, vector< gnBaseFeature *> &feature_vector, vector< uint32 > &index_vector) const   Creates a list of all features which intersect the coordinates specified. More... virtual void  GetBrokenFeatures (const gnLocation &lt, vector< gnBaseFeature *> &feature_vector) const   Creates a list of features which may have been broken by an edit. More... virtual void  RemoveFeature (const uint32 i)   Remove a feature from this spec. More... virtual gnGenomeSpec*  CloneRange (const gnSeqI startI, const gnSeqI len) const   Copies a specified range of bases and returns a pointer to the resulting gnGenomeSpec. More... Protected Attributes vector<gnFragmentSpec*>  m_SpecList Detailed Description This class contains references to the sequence data, annotation, and other related header data for an organism's genome. The genome is organized into a list of sequence fragments (specs), a list of features, and a list of headers. Definition at line 34 of file gnGenomeSpec.h. Constructor & Destructor Documentation gnGenomeSpec::gnGenomeSpec ( )   Definition at line 17 of file gnGenomeSpec.cpp. Referenced by Clone(), and CloneRange(). gnGenomeSpec::gnGenomeSpec ( const gnGenomeSpec & s )   Copy constructor. Parameters: s   the gnGenomeSpec to copy. Definition at line 22 of file gnGenomeSpec.cpp. gnGenomeSpec::~gnGenomeSpec ( ) [virtual]   Destructor, frees memory. Definition at line 39 of file gnGenomeSpec.cpp. Member Function Documentation uint32 gnGenomeSpec::AddFeature ( gnBaseFeature * feat ) [virtual]   Add a feature to this spec. Parameters: feat   The feature to add. i   The feature to insert before Returns: True if successful Reimplemented from gnMultiSpec. Definition at line 129 of file gnGenomeSpec.cpp. Referenced by gnSequence::addFeature(). void gnGenomeSpec::AddSpec ( gnBaseSpec * spec, const uint32 i = UINT32_MAX ) [inline, virtual]   Add a subspec to this spec. Throws an exception if the insertion index i is out of range Parameters: spec   The subspec to add. i   The subspec to insert before Returns: True if successful Reimplemented from gnMultiSpec. Definition at line 106 of file gnGenomeSpec.h. Referenced by CloneRange(), gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnDNXSource::ParseStream(), gnSequence::gnSequence(), and gnSequence::insert(). void gnGenomeSpec::Clear ( ) [virtual]   Clears all data from this spec. Reimplemented from gnMultiSpec. Definition at line 44 of file gnGenomeSpec.cpp. Referenced by gnGenomeSpec(), and ~gnGenomeSpec(). gnGenomeSpec * gnGenomeSpec::Clone ( ) const [inline, virtual]   Reimplemented from gnMultiSpec. Definition at line 84 of file gnGenomeSpec.h. Referenced by gnSEQSource::GetSpec(), gnRAWSource::GetSpec(), gnGBKSource::GetSpec(), gnDNXSource::GetSpec(), gnABISource::GetSpec(), gnGenomeSpec(), gnSequence::gnSequence(), gnSequence::insert(), and gnSequence::splitContig(). gnGenomeSpec * gnGenomeSpec::CloneRange ( const gnSeqI startI, const gnSeqI len ) const [virtual]   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. Parameters: startI   The first base pair to copy len   The length of the piece to copy Returns: A copy of the gnGenomeSpec containing only the specified bases Definition at line 68 of file gnGenomeSpec.cpp. Referenced by gnSequence::erase(), and gnSequence::subseq(). void gnGenomeSpec::GetBrokenFeatures ( const gnLocation & lt, vector< gnBaseFeature *> & feature_vector ) const [virtual]   Creates a list of features which may have been broken by an edit. Parameters: lt   The coordinates containing the features to return. feature_vector   The vector to store features in. Reimplemented from gnMultiSpec. Definition at line 215 of file gnGenomeSpec.cpp. Referenced by gnSequence::getBrokenFeatures(). void gnGenomeSpec::GetContainedFeatures ( const gnLocation & lt, vector< gnBaseFeature *> & feature_vector, vector< uint32 > & index_vector ) const [virtual]   Creates a list of all features which are contained by coordinates specified. Parameters: lt   The coordinates containing the features to return. feature_vector   The vector to store features in. index_vector   A vector of indices which correspond to the features. Reimplemented from gnMultiSpec. Definition at line 172 of file gnGenomeSpec.cpp. Referenced by gnSequence::getContainedFeatures(). gnBaseFeature * gnGenomeSpec::GetFeature ( const uint32 i ) const [virtual]   Get the feature at index i in the list of features. Parameters: i   The index of the feature Returns: The feature. Reimplemented from gnMultiSpec. Definition at line 156 of file gnGenomeSpec.cpp. Referenced by gnSequence::getFeature(). uint32 gnGenomeSpec::GetFeatureListLength ( ) const [virtual]   Returns the number of features this spec contains. Returns: The number of features this spec contains. Reimplemented from gnMultiSpec. Definition at line 148 of file gnGenomeSpec.cpp. Referenced by gnSequence::getFeatureListLength(). void gnGenomeSpec::GetIntersectingFeatures ( const gnLocation & lt, vector< gnBaseFeature *> & feature_vector, vector< uint32 > & index_vector ) const [virtual]   Creates a list of all features which intersect the coordinates specified. Parameters: lt   The coordinates intersecting the features to return. feature_vector   The vector to store features in. index_vector   A vector of indices which correspond to the features. Reimplemented from gnMultiSpec. Definition at line 194 of file gnGenomeSpec.cpp. Referenced by gnSequence::getIntersectingFeatures(). gnFragmentSpec * gnGenomeSpec::GetSpec ( const uint32 i ) const [inline, virtual]   Get the spec at index i in the list of subspecs. Parameters: i   The index of the spec Returns: The spec. Reimplemented from gnMultiSpec. Definition at line 94 of file gnGenomeSpec.h. Referenced by AddFeature(), CloneRange(), GetBrokenFeatures(), GetContainedFeatures(), gnDNXSource::GetContigID(), gnDNXSource::GetContigName(), gnDNXSource::GetContigSeqLength(), GetFeature(), GetFeatureListLength(), GetIntersectingFeatures(), gnDNXSource::HasContig(), RemoveFeature(), SetReverseComplement(), gnGBKSource::Write(), gnFASSource::Write(), gnDNXSource::Write(), gnSequence::addHeader(), gnSequence::contig(), gnSequence::contigByName(), gnSequence::contigLength(), gnSequence::contigName(), gnSequence::getHeader(), gnSequence::getHeaderListLength(), gnSequence::globalToSource(), gnSequence::insert(), gnSequence::isReverseComplement(), gnSequence::removeHeader(), gnSequence::setContigName(), and gnSequence::setReverseComplement(). gnFragmentSpec * gnGenomeSpec::GetSpecByBase ( const gnSeqI baseI ) const [inline, virtual]   Get the spec from the list of subspecs which contains the specified base pair. Parameters: baseI   The base pair index. Returns: The spec. Reimplemented from gnMultiSpec. Definition at line 101 of file gnGenomeSpec.h. Referenced by gnSequence::contigByBase(). uint32 gnGenomeSpec::GetSpecListLength ( ) const [inline, virtual]   Returns the number of subspecs this spec contains. Returns: The number of subspecs this spec contains. Reimplemented from gnMultiSpec. Definition at line 89 of file gnGenomeSpec.h. Referenced by AddFeature(), CloneRange(), GetBrokenFeatures(), GetContainedFeatures(), gnDNXSource::GetContigListLength(), GetFeature(), GetFeatureListLength(), GetIntersectingFeatures(), MergeFragments(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), RemoveFeature(), SetReverseComplement(), gnSequence::contigListLength(), gnSequence::contigListSize(), and gnSequence::insert(). void gnGenomeSpec::MergeFragments ( const uint32 startC, const uint32 endC ) [virtual]   Definition at line 113 of file gnGenomeSpec.cpp. Referenced by gnSequence::mergeContigs(). void gnGenomeSpec::RemoveFeature ( const uint32 i ) [virtual]   Remove a feature from this spec. Parameters: i   The index of the feature to remove. Returns: True if successful Reimplemented from gnMultiSpec. Definition at line 235 of file gnGenomeSpec.cpp. Referenced by gnSequence::removeFeature(). void gnGenomeSpec::RemoveSpec ( uint32 i ) [inline, virtual]   Remove a subspec from this spec. Parameters: i   The index of the subspec to remove. Reimplemented from gnMultiSpec. Definition at line 114 of file gnGenomeSpec.h. Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). void gnGenomeSpec::SetReverseComplement ( const boolean value ) [virtual]   Sets the reverse complement bit for this spec. Parameters: value   True for reverse complement, false otherwise. Reimplemented from gnBaseSpec. Definition at line 53 of file gnGenomeSpec.cpp. Referenced by gnSequence::setReverseComplement(). Member Data Documentation vector< gnFragmentSpec *> gnGenomeSpec::m_SpecList<gnFragmentSpec*> [protected]   Definition at line 79 of file gnGenomeSpec.h. The documentation for this class was generated from the following files: gnGenomeSpec.h gnGenomeSpec.cpp