biojs-io-matrix

Parse 2D matrices (e.g. PAM)

Getting Started

Install the module with: npm install biojs-io-matrix

var MParser  = require('biojs-io-matrix');

read(url)

Parses an url an calls your parse method with the returned body.

MParser.read("https://cdn.rawgit.com/greenify/biojs-io-matrix/master/test/data/pam_250", function(err, model) {
    // model is the parsed url
});

If callback is undefined, read returns a promise.

var p = MParser.read("https://cdn.rawgit.com/greenify/biojs-io-matrix/master/test/data/pam_250");
// ...
p.then(function(model) {
    // model is the parsed url
}, function(err){
    console.error("err happened during downloading", err);
});

Read a entire file

var matrix = MParser.parse("A 1\nB 1 2");
> { A: { A: 1, B: 1 },
  B: { A: 1, B: 2 } }

Line by line

var mParser = new MParser();
mParser.parseLine("A 1");
mParser.parseLine("B 2 3");
var matrix = mParser.buildMatrix();

Save a matrix

var matrix = MParser("A 1\nB 1 2");
var out = mParser.export(matrix);
> 'A\t1\nB\t1\t2'

Or you can use objects

var matrix = new MParser("A 1\nB 1 2");
matrix.buildMatrix(); \\ returns the 2D array
var out = matrix.export();
> 'A\t1\nB\t1\t2'

Contributing

Please submit all issues and pull requests to the greenify/biojs-io-matrix repository!

Support

If you have any problem or suggestion please open an issue here.

License

The MIT License

Copyright (c) 2014, greenify

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.