Installation

With npm:

npm install @rnacanvas/ct

Usage

All exports of this package can be accessed as named imports.

// an example import
import { parseCT } from '@rnacanvas/ct';

function parseCT()

Parses a string in CT format (e.g., the string could be the contents of a CT file).

var ctString = await ctFile.text();

var ct = parseCT(ctString);

/**
 * Information about the structure included in the header line
 * (e.g., the name of the structure, the delta-G).
 */
ct.description;

/**
 * The sequnce of the structure in the CT file.
 */
ct.sequence;

/**
 * An array of position pair tuples indicating the pairs in the structure.
 *
 * A position pair is a pairing of two positions in a sequence
 * using one-based indexing.
 */
ct.positionPairs;

/**
 * The numbering offset for the bases in the structure.
 *
 * Is 0 by default.
 */
ct.numberingOffset;

function isCT()

Returns true if a string is in CT format (e.g., could be the text contents of a CT file).

Returns false otherwise.

// a 5-nt structure (with no base-pairs)
var s = (
  '5	dG = -2.00 [Initially -2.00] 26Apr18-14-48-11\n'
  + '1	A	0	2	0	1\n'
  + '2	U	1	3	0	2\n'
  + '3	G	2	4	0	3\n'
  + '4	C	3	5	0	4\n'
  + '5	A	4	6	0	5'
);

isCT(s); // true

Extra leading and trailing empty and whitespace lines are allowed, as well as comment lines beginning with #.

var s = (
  '\n'
  + '  \n'
  + '# A comment.\n'
  + '\t\n'
  + '5	dG = -2.00 [Initially -2.00] 26Apr18-14-48-11\n'
  + '1	A	0	2	0	1\n'
  + '2	U	1	3	0	2\n'
  + '3	G	2	4	0	3\n'
  + '4	C	3	5	0	4\n'
  + '5	A	4	6	0	5\n'
  + '\n'
  + '# Another comment.\t'
  + '\t\n'
);

isCT(s); // true

However, extra lines with text content (that are not commented out) are not allowed in CT format.

var s = (
  'Not commented out.\n'
  + '\n'
  + '5	dG = -2.00 [Initially -2.00] 26Apr18-14-48-11\n'
  + '1	A	0	2	0	1\n'
  + '2	U	1	3	0	2\n'
  + '3	G	2	4	0	3\n'
  + '4	C	3	5	0	4\n'
  + '5	A	4	6	0	5\n'
  + '\n'
  + 'Not commented out either.'
);

isCT(s); // false

A header line by itself will also result in false being returned.

var s = (
  '0	dG = 0.00 [Initially 0.00] 26Apr18-14-48-11'
);

isCT(s); // false