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\nThis after the RNA container.\n\n \n \n \n```\n\n### Cofolded sequences\n\nDisplay two cofolded sequences using the format of [RNAcofold](http://rna.tbi.univie.ac.at/cgi-bin/RNAcofold.cgi):\n\n![Cofolded sequences](https://raw.githubusercontent.com/pkerpedjiev/fornac/master/doc/img/cofold_example.png \"An example of cofolded sequences displayed using the FornaContainer\")\n\n```javascript\n var container = new fornac.FornaContainer(\"#cofold_ss\",\n {'applyForce': false, 'allowPanningAndZooming': true, 'initialSize':[500,300]});\n \n var options = {'structure': '..((((...))))...((...((...((..&............))...))...))..',\n 'sequence': 'ACGAUCAGAGAUCAGAGCAUACGACAGCAG&ACGAAAAAAAGAGCAUACGACAGCAG'\n }; \n container.addRNA(options.structure, options);\n container.setSize(); \n```\n\n## Options\n\nThe `FornaContainer` supports a number of options to allow users to customize how the RNA will be presented.\n\n### applyForce\n\nIndicate whether the force-directed layout will be applied to the displayed\nmolecule. Enabling this option allows users to change the layout of the\nmolecule by selecting and dragging the individual nucleotide nodes\n\n### allowPanningAndZooming [default=true]\n\nAllow users to zoom in and pan the display. If this is enabled then pressing\nthe 'c' key on the keyboard will center the view.\n\n### circularizeExternal [default=true]\n\nThis only makes sense in connection with the `applyForce` argument. If it's\ntrue, the external loops will be arranged in a nice circle. If false, they will\nbe allowed to flop around as the force layout dictates:\n\n\n\n### labelInterval [default=10]\n\nChange how often nucleotide numbers are labelled with their number.\n\n\n## Implementation\n\nEach RNA molecule is represented as a JSON file which encodes all of the\ninformation necessary to display it. The example shows a trivial and slightly\nmodified example. `nodeType` can be either `nucleotide` or `label` or `middle`,\nthe latter of which is used only as a placeholder for maintaining an aesthetically\npleasing layout.\n\nThe links can be any of `basepair` (representing a basepair between two\nnucleotides), `backbone` (backbone bond between adjacent nodes), `pseudoknot`\n(pseudoknot, extracted from the specified structure using maximum matching\nalgorithm), `extra` (extra links specified by the user), `label_link` (links\nbetween nucleotides and their nucleotide number labels), `fake` (invisible\nlinks for maintaining the layout), and `fake_fake` (invisible links for\nmaintaining the layout).\n\nThis structure is initially created in `rnagraph.js` starting from a sequence\nand dotbracket string.\n\n```\n{\n \"nodes\": \n [ {\n \"name\": \"A\",\n \"num\": 1,\n \"radius\": 5,\n \"rna\": null,\n \"nodeType\": \"nucleotide\",\n \"structName\": \"empty\",\n \"elemType\": \"e\",\n \"uid\": \"44edb966-aca9-4058-a6bc-784a34959329\",\n \"linked\": false,\n \"prevNode\": null,\n \"nextNode\": null,\n \"x\": 100,\n \"px\": 100,\n \"y\": 100,\n \"py\": 100\n },\n ...\n ],\n \"links\": \n [ {\n \"source\": null,\n \"target\": null,\n \"linkType\": \"basepair\",\n \"value\": 1,\n \"uid\": \"6664a569-5af1-4d86-8ada-d1c00da72a899f87a224-52a0-4ede-a29c-04fddc09e4c4\"\n },\n ...\n ]\n}\n```\n\n\n## Development\n\nFirst:\n\n```\nnpm install\nbower install\n```\n\nTo debug:\n\n```\ngulp serve\n```\n\nTo build:\n\n```\ngulp build\n```\n\nThe output will be placed in the `dist` directory. To use `fornac` in a web page, simply include `dist/scripts/fornac.js` in your web page.\n\n## Acknowledgements\n\nThanks to [Benedikt Rauscher](https://github.com/bene200) for the Javascript\nversion of the NAView layout and to the creators of\n[VARNA](http://varna.lri.fr/) for the java implementation that it's based on.\n","readmeFilename":"README.md"}
![](\"https://github.com/pkerpedjiev/fornac/blob/master/doc/img/uncircularized_exterior.png\")
\n\n### labelInterval [default=10]\n\nChange how often nucleotide numbers are labelled with their number.\n\n\n## Implementation\n\nEach RNA molecule is represented as a JSON file which encodes all of the\ninformation necessary to display it. The example shows a trivial and slightly\nmodified example. `nodeType` can be either `nucleotide` or `label` or `middle`,\nthe latter of which is used only as a placeholder for maintaining an aesthetically\npleasing layout.\n\nThe links can be any of `basepair` (representing a basepair between two\nnucleotides), `backbone` (backbone bond between adjacent nodes), `pseudoknot`\n(pseudoknot, extracted from the specified structure using maximum matching\nalgorithm), `extra` (extra links specified by the user), `label_link` (links\nbetween nucleotides and their nucleotide number labels), `fake` (invisible\nlinks for maintaining the layout), and `fake_fake` (invisible links for\nmaintaining the layout).\n\nThis structure is initially created in `rnagraph.js` starting from a sequence\nand dotbracket string.\n\n```\n{\n \"nodes\": \n [ {\n \"name\": \"A\",\n \"num\": 1,\n \"radius\": 5,\n \"rna\": null,\n \"nodeType\": \"nucleotide\",\n \"structName\": \"empty\",\n \"elemType\": \"e\",\n \"uid\": \"44edb966-aca9-4058-a6bc-784a34959329\",\n \"linked\": false,\n \"prevNode\": null,\n \"nextNode\": null,\n \"x\": 100,\n \"px\": 100,\n \"y\": 100,\n \"py\": 100\n },\n ...\n ],\n \"links\": \n [ {\n \"source\": null,\n \"target\": null,\n \"linkType\": \"basepair\",\n \"value\": 1,\n \"uid\": \"6664a569-5af1-4d86-8ada-d1c00da72a899f87a224-52a0-4ede-a29c-04fddc09e4c4\"\n },\n ...\n ]\n}\n```\n\n\n## Development\n\nFirst:\n\n```\nnpm install\nbower install\n```\n\nTo debug:\n\n```\ngulp serve\n```\n\nTo build:\n\n```\ngulp build\n```\n\nThe output will be placed in the `dist` directory. To use `fornac` in a web page, simply include `dist/scripts/fornac.js` in your web page.\n\n## Acknowledgements\n\nThanks to [Benedikt Rauscher](https://github.com/bene200) for the Javascript\nversion of the NAView layout and to the creators of\n[VARNA](http://varna.lri.fr/) for the java implementation that it's based on.\n","readmeFilename":"README.md"}