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gnMultiSpec Class Reference This class defines an interface for specs which have multiple subspecs containing sequence data. More... #include <gnMultiSpec.h> Inheritance diagram for gnMultiSpec:: List of all members. Public Methods   gnMultiSpec () virtual  ~gnMultiSpec ()   Destructor, frees memory. More... virtual gnMultiSpec*  Clone () const=0 virtual gnSeqI  GetLength () const   Get the length of all the sequence data covered by this spec. More... virtual void  CropStart (gnSeqI cropLen)   Crop the first cropLen bases from the sequence. More... virtual void  CropEnd (gnSeqI cropLen)   Crop the last cropLen bases from the sequence. More... virtual string  GetSourceName () const virtual void  SetSourceName (const string &sourceName) virtual void  Clear ()   Clears all data from this spec. More... virtual boolean  SeqRead (const gnSeqI start, gnSeqC *buf, uint32 &bufLen, const uint32 contigI) const   Reads sequence data from this spec. More... virtual uint32  GetSpecListLength () const=0   Returns the number of subspecs this spec contains. More... virtual gnBaseSpec*  GetSpec (const uint32 i) const=0   Get the spec at index i in the list of subspecs. More... virtual gnBaseSpec*  GetSpecByBase (const gnSeqI baseI) const=0   Get the spec from the list of subspecs which contains the specified base pair. More... virtual uint32  GetSpecIndexByBase (const gnSeqI baseI) const   Get the index of the subspec which contains the specified base pair. More... virtual uint32  GetSpecIndexByName (const string &name) const   Get the index of the spec which has the given name. More... virtual gnSeqI  GetSpecStartBase (const uint32 specI) const   Get the starting base pair, in this spec's sequence, of the given subspec. More... virtual gnSeqI  GetSpecEndBase (const uint32 specI) const   Get the ending base pair, in this spec's sequence, of the given subspec. More... virtual void  AddSpec (gnBaseSpec *spec, const uint32 i=UINT32_MAX)=0   Add a subspec to this spec. More... virtual void  RemoveSpec (uint32 i)=0   Remove a subspec from this spec. More... virtual uint32  GetHeaderListLength () const   Returns the number of headers this spec contains. More... virtual void  AddHeader (gnBaseHeader *head, const uint32 i=UINT32_MAX)   Add a header to this spec, adds to the end of the header list by default. More... virtual gnBaseHeader*  GetHeader (const uint32 i) const   Get the headers at index i in the list of headers. More... virtual gnBaseHeader*  GetHeader (const string &name, uint32 &i) const   Find the first header with the specified name, starting at index i. More... virtual void  RemoveHeader (uint32 i)   Remove a header from this spec. More... uint32  AddFeature (gnBaseFeature *feat)   Add a feature to this spec. More... virtual uint32  GetFeatureListLength () const=0   Returns the number of features this spec contains. More... virtual gnBaseFeature*  GetFeature (const uint32 i) const=0   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=0   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=0   Creates a list of all features which intersect the coordinates specified. More... virtual void  GetBrokenFeatures (const gnLocation &lt, vector< gnBaseFeature *> &feature_vector) const=0   Creates a list of features which may have been broken by an edit. More... virtual void  RemoveFeature (const uint32 i)=0   Remove a feature from this spec. More... Protected Attributes string  m_sourceName vector<gnBaseHeader*>  m_headerList Detailed Description This class defines an interface for specs which have multiple subspecs containing sequence data. Definition at line 30 of file gnMultiSpec.h. Constructor & Destructor Documentation gnMultiSpec::gnMultiSpec ( ) [inline]   Definition at line 33 of file gnMultiSpec.h. gnMultiSpec::~gnMultiSpec ( ) [inline, virtual]   Destructor, frees memory. Definition at line 37 of file gnMultiSpec.h. Member Function Documentation uint32 gnMultiSpec::AddFeature ( gnBaseFeature * feat )   Add a feature to this spec. Parameters: feat   The feature to add. i   The feature to insert before Returns: True if successful Reimplemented in gnFragmentSpec, and gnGenomeSpec. void gnMultiSpec::AddHeader ( gnBaseHeader * head, const uint32 i = UINT32_MAX ) [virtual]   Add a header to this spec, adds to the end of the header list by default. Parameters: head   The header to add. i   The header to insert before. If i is larger than the size of the header list the header will be added to the end of the list. Definition at line 126 of file gnMultiSpec.cpp. Referenced by gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnSequence::addHeader(). void gnMultiSpec::AddSpec ( gnBaseSpec * spec, const uint32 i = UINT32_MAX ) [pure 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 in gnFragmentSpec, and gnGenomeSpec. void gnMultiSpec::Clear ( ) [virtual]   Clears all data from this spec. Reimplemented from gnBaseSpec. Reimplemented in gnFragmentSpec, and gnGenomeSpec. Definition at line 24 of file gnMultiSpec.cpp. Referenced by gnGenomeSpec::Clear(), and gnFragmentSpec::Clear(). gnMultiSpec * gnMultiSpec::Clone ( ) const [pure virtual]   Reimplemented from gnBaseSpec. Reimplemented in gnFragmentSpec, and gnGenomeSpec. void gnMultiSpec::CropEnd ( gnSeqI cropLen ) [virtual]   Crop the last cropLen bases from the sequence. CropEnd will delete features and headers associated with the cropped bases. Parameters: cropLen   The number of base pairs to delete from the end. Reimplemented from gnBaseSpec. Reimplemented in gnFragmentSpec. Definition at line 105 of file gnMultiSpec.cpp. Referenced by gnFragmentSpec::CropEnd(), gnSequence::erase(), gnSequence::insert(), and gnSequence::splitContig(). void gnMultiSpec::CropStart ( gnSeqI cropLen ) [virtual]   Crop the first cropLen bases from the sequence. CropStart will delete features and headers associated with the cropped bases. Parameters: cropLen   The number of base pairs to delete from the beginning. Reimplemented from gnBaseSpec. Reimplemented in gnFragmentSpec. Definition at line 86 of file gnMultiSpec.cpp. Referenced by gnFragmentSpec::CropStart(), gnSequence::insert(), and gnSequence::splitContig(). void gnMultiSpec::GetBrokenFeatures ( const gnLocation & lt, vector< gnBaseFeature *> & feature_vector ) const [pure 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 in gnFragmentSpec, and gnGenomeSpec. void gnMultiSpec::GetContainedFeatures ( const gnLocation & lt, vector< gnBaseFeature *> & feature_vector, vector< uint32 > & index_vector ) const [pure 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 in gnFragmentSpec, and gnGenomeSpec. gnBaseFeature * gnMultiSpec::GetFeature ( const uint32 i ) const [pure virtual]   Get the feature at index i in the list of features. Parameters: i   The index of the feature Returns: The feature. Reimplemented in gnFragmentSpec, and gnGenomeSpec. uint32 gnMultiSpec::GetFeatureListLength ( ) const [pure virtual]   Returns the number of features this spec contains. Returns: The number of features this spec contains. Reimplemented in gnFragmentSpec, and gnGenomeSpec. gnBaseHeader * gnMultiSpec::GetHeader ( const string & name, uint32 & i ) const [virtual]   Find the first header with the specified name, starting at index i. Parameters: name   The name of the header to find. i   The index to start looking at. Returns: The header or NULL if none was found. Definition at line 132 of file gnMultiSpec.cpp. gnBaseHeader * gnMultiSpec::GetHeader ( const uint32 i ) const [inline, virtual]   Get the headers at index i in the list of headers. Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced Parameters: i   The index of the header Returns: The header. Definition at line 199 of file gnMultiSpec.h. Referenced by gnGBKSource::Write(), gnFASSource::Write(), gnDNXSource::Write(), gnGBKSource::WriteHeader(), and gnSequence::getHeader(). uint32 gnMultiSpec::GetHeaderListLength ( ) const [inline, virtual]   Returns the number of headers this spec contains. Returns: The number of headers this spec contains. Definition at line 194 of file gnMultiSpec.h. Referenced by gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnGBKSource::Write(), and gnSequence::getHeaderListLength(). void gnMultiSpec::GetIntersectingFeatures ( const gnLocation & lt, vector< gnBaseFeature *> & feature_vector, vector< uint32 > & index_vector ) const [pure 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 in gnFragmentSpec, and gnGenomeSpec. gnSeqI gnMultiSpec::GetLength ( ) const [virtual]   Get the length of all the sequence data covered by this spec. Returns: This spec's length in base pairs. Reimplemented from gnBaseSpec. Definition at line 33 of file gnMultiSpec.cpp. Referenced by gnGenomeSpec::AddFeature(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), CropEnd(), gnGenomeSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnSEQSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnDNXSource::GetContigSeqLength(), gnGenomeSpec::GetIntersectingFeatures(), gnGBKSource::Write(), gnSequence::contigLength(), gnSequence::erase(), gnSequence::insert(), gnSequence::length(), and gnSequence::size(). string gnMultiSpec::GetSourceName ( ) const [inline, virtual]   Definition at line 208 of file gnMultiSpec.h. Referenced by gnDNXSource::Write(). gnBaseSpec * gnMultiSpec::GetSpec ( const uint32 i ) const [pure virtual]   Get the spec at index i in the list of subspecs. Parameters: i   The index of the spec Returns: The spec. Reimplemented in gnFragmentSpec, and gnGenomeSpec. Referenced by CropEnd(), CropStart(), GetLength(), GetSpecEndBase(), GetSpecIndexByBase(), GetSpecIndexByName(), GetSpecStartBase(), and SeqRead(). gnBaseSpec * gnMultiSpec::GetSpecByBase ( const gnSeqI baseI ) const [pure 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 in gnFragmentSpec, and gnGenomeSpec. gnSeqI gnMultiSpec::GetSpecEndBase ( const uint32 specI ) const [virtual]   Get the ending base pair, in this spec's sequence, of the given subspec. Parameters: specI   The subspec index. Returns: The subspec's ending base pair. Definition at line 74 of file gnMultiSpec.cpp. uint32 gnMultiSpec::GetSpecIndexByBase ( const gnSeqI baseI ) const [virtual]   Get the index of the subspec which contains the specified base pair. Parameters: baseI   The base pair index. Returns: The subspec index. Definition at line 42 of file gnMultiSpec.cpp. Referenced by gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnGenomeSpec::GetSpecByBase(), gnFragmentSpec::GetSpecByBase(), gnSequence::contigIndexByBase(), and gnSequence::globalToSource(). uint32 gnMultiSpec::GetSpecIndexByName ( const string & name ) const [virtual]   Get the index of the spec which has the given name. Parameters: name   The name of the spec to find. Returns: The spec index. Definition at line 53 of file gnMultiSpec.cpp. Referenced by gnSequence::contigByName(), and gnSequence::contigIndexByName(). uint32 gnMultiSpec::GetSpecListLength ( ) const [pure virtual]   Returns the number of subspecs this spec contains. Returns: The number of subspecs this spec contains. Reimplemented in gnFragmentSpec, and gnGenomeSpec. Referenced by CropEnd(), CropStart(), GetLength(), GetSpecEndBase(), GetSpecIndexByBase(), GetSpecIndexByName(), GetSpecStartBase(), gnGenomeSpec::RemoveSpec(), gnFragmentSpec::RemoveSpec(), and SeqRead(). gnSeqI gnMultiSpec::GetSpecStartBase ( const uint32 specI ) const [virtual]   Get the starting base pair, in this spec's sequence, of the given subspec. Parameters: specI   The subspec index. Returns: The subspec's starting base pair. Definition at line 62 of file gnMultiSpec.cpp. Referenced by gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnGenomeSpec::GetFeature(), gnSequence::contigStart(), and gnSequence::globalToSource(). void gnMultiSpec::RemoveFeature ( const uint32 i ) [pure virtual]   Remove a feature from this spec. Parameters: i   The index of the feature to remove. Returns: True if successful Reimplemented in gnFragmentSpec, and gnGenomeSpec. void gnMultiSpec::RemoveHeader ( uint32 i ) [virtual]   Remove a header from this spec. Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced Parameters: i   The index of the header to remove. Definition at line 140 of file gnMultiSpec.cpp. Referenced by gnSequence::removeHeader(). void gnMultiSpec::RemoveSpec ( uint32 i ) [pure virtual]   Remove a subspec from this spec. Parameters: i   The index of the subspec to remove. Reimplemented in gnFragmentSpec, and gnGenomeSpec. Referenced by CropEnd(), and CropStart(). boolean gnMultiSpec::SeqRead ( const gnSeqI start, gnSeqC * buf, uint32 & bufLen, const uint32 contigI ) const [virtual]   Reads sequence data from this spec. SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence. Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with a valid contig index. SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen". SeqRead will return false if a serious error occurs. Parameters: start   The base pair to start reading at. buf   The character array to store base pairs into. bufLen   The number of base pairs to read. This will be modified to reflect the actual number of bases read. contigI   The index of the subspec to read or ALL_CONTIGS by default. Returns: True if the operation was successful. Reimplemented from gnBaseSpec. Definition at line 148 of file gnMultiSpec.cpp. Referenced by gnSequence::GetSeqC(), gnDNXSource::SeqRead(), gnSequence::ToArray(), and gnSequence::ToString(). void gnMultiSpec::SetSourceName ( const string & sourceName ) [inline, virtual]   Definition at line 213 of file gnMultiSpec.h. Referenced by gnFASSource::GetSpec(), and gnDNXSource::ParseStream(). Member Data Documentation vector< gnBaseHeader *> gnMultiSpec::m_headerList<gnBaseHeader*> [protected]   Definition at line 188 of file gnMultiSpec.h. string gnMultiSpec::m_sourceName [protected]   Reimplemented from gnBaseSpec. Definition at line 186 of file gnMultiSpec.h. The documentation for this class was generated from the following files: gnMultiSpec.h gnMultiSpec.cpp