Provides files and formats for handling structure data.
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class | seqan3::format_vienna |
| The Vienna format (dot bracket notation) for RNA sequences with secondary structure. More...
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class | seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ > |
| A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
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struct | seqan3::structure_file_input_default_traits_aa |
| A traits type that specifies input as amino acids. More...
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struct | seqan3::structure_file_input_default_traits_rna |
| The default traits for seqan3::structure_file_input. More...
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interface | structure_file_input_format |
| The generic concept for structure file in formats. More...
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struct | seqan3::detail::structure_file_input_format_exposer< format_type > |
| Internal class used to expose the actual format interface to read structure records from the file. More...
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struct | seqan3::structure_file_input_options< seq_legal_alphabet, structured_seq_combined > |
| The options type defines various option members that influence the behaviour of all or some formats. More...
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interface | structure_file_input_traits |
| The requirements a traits_type for seqan3::structure_file_input must meet. More...
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class | seqan3::structure_file_output< selected_field_ids_, valid_formats_ > |
| A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
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interface | structure_file_output_format |
| The generic concept for structure file out formats. More...
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struct | seqan3::detail::structure_file_output_format_exposer< format_type > |
| Internal class used to expose the actual format interface to write structure records into the file. More...
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struct | seqan3::structure_file_output_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
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class | seqan3::structure_record< field_types, field_ids > |
| The record type of seqan3::structure_file_input. More...
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template<typename structure_alph_type , typename bpp_type , std::ranges::range structure_type> |
void | seqan3::detail::bpp_from_rna_structure (bpp_type &bpp, structure_type const &structure, double weight=1.) |
| Transforms a structure annotation string into a base pair probability matrix. More...
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Provides files and formats for handling structure data.
◆ bpp_from_rna_structure()
template<typename structure_alph_type , typename bpp_type , std::ranges::range structure_type>
void seqan3::detail::bpp_from_rna_structure |
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bpp_type & |
bpp, |
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structure_type const & |
structure, |
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double |
weight = 1. |
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inline |
Transforms a structure annotation string into a base pair probability matrix.
- Exceptions
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- Template Parameters
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structure_alph_type | The type of the structure alphabet; must satisfy seqan3::rna_structure_alphabet. |
bpp_type | The type of the target matrix. |
structure_type | The range type of the structure annotation. |
- Parameters
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[out] | bpp | The target matrix that receives the base pair probabilities. |
[in] | structure | The source structure annotation. |
[in] | weight | The weight to be assigned to all interactions present. As the source allows only one interaction partner, the weight defaults to 1.0. |