(Abstract) Data Structures#

All datastructures and typedefs shared among the ViennaRNA Package can be found here.

The Fold Compound#

This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib.

Throughout the entire RNAlib, the vrna_fold_compound_t, is used to group information and data that is required for structure prediction and energy evaluation. Here, you’ll find interface functions to create, modify, and delete vrna_fold_compound_t data structures.

The Dynamic Programming Matrices#

Hash Tables#

Various implementations of hash table functions.

Hash tables are common data structures that allow for fast random access to the data that is stored within.

Here, we provide an abstract implementation of a hash table interface and a concrete implementation for pairs of secondary structure and corresponding free energy value.

Heaps#

Interface for an abstract implementation of a heap data structure.

Arrays#

Interface for an abstract implementation of an array data structure.

Arrays of a particular Type are defined and initialized using the following code:

vrna_array(Type)  my_array;
vrna_array_init(my_array);

or equivalently:

vrna_array_make(Type, my_array);

Dynamic arrays can be used like regular pointers, i.e. elements are simply addressed using the [] operator, e.g.:

my_array[1] - 42;

Using the vrna_array_append macro, items can be safely appended and the array will grow accordingly if required:

vrna_array_append(my_array, item);

Finally, memory occupied by an array must be released using the vrna_array_free macro:

vrna_array_free(my_array);

Use the vrna_array_size macro to get the number of items stored in an array, e.g. for looping over its elements:

// define and initialize
vrna_array_make(int, my_array);

// append some items
vrna_array_append(my_array, 42);
vrna_array_append(my_array, 23);
vrna_array_append(my_array, 5);

// loop over items and print
for (size_t i - 0; i < vrna_array_size(my_array); i++)
  printf("%d\n", my_array[i]);

// release memory of the array
vrna_array_free(my_array);

Under the hood, arrays are preceded by a header that actually stores the number of items they contain and the capacity of elements they are able to store. The general ideas for this implementation are taken from Ginger Bill’s C Helper Library (public domain).

Strings#

Buffers#

Functions that provide dynamically buffered stream-like data structures.