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MDAT::SequenceFeatures< FeatureType > Class Template Reference

Public Member Functions

void read_gff (const std::string &gff_f)
 Reads a GFF file. More...
 
void write_gff (const std::string &out_f)
 Write data to disk. More...
 
SequenceFeatures_iter begin ()
 
SequenceFeatures_iter end ()
 
SequenceFeatures_iter begin (const std::string &seq_name)
 Iterator to the first feature of a given sequence. More...
 
SequenceFeatures_iter end (const std::string &seq_name)
 Iterator to the element behind the last element of a given sequence. More...
 
void append (const std::string &seq_id, const SingleSequenceFeature &feature)
 
void add_introns ()
 Add introns to each gene.
 
bool empty () const
 

Member Function Documentation

template<typename FeatureType>
SequenceFeatures_iter MDAT::SequenceFeatures< FeatureType >::begin ( const std::string &  seq_name)
inline

Iterator to the first feature of a given sequence.

Parameters
seq_idThe sequence name.
Returns
Iterator to the first feature of a sequence.
template<typename FeatureType>
bool MDAT::SequenceFeatures< FeatureType >::empty ( ) const
inline

Checks if any features have been found.

Returns
True if nothing found, else false.
template<typename FeatureType>
SequenceFeatures_iter MDAT::SequenceFeatures< FeatureType >::end ( const std::string &  seq_name)
inline

Iterator to the element behind the last element of a given sequence.

Parameters
seq_idThe sequence name.
Returns
Iterator to just behind the last feature of a sequence.
template<typename FeatureType >
void MDAT::SequenceFeatures< FeatureType >::read_gff ( const std::string &  gff_f)

Reads a GFF file.

Parameters
gff_fThe file to read in gff format.
template<typename FeatureType >
void MDAT::SequenceFeatures< FeatureType >::write_gff ( const std::string &  out_f)

Write data to disk.

Parameters
out_fThe output file to write to.