@gmod/jbrowse
Version:
JBrowse - client-side genome browser
98 lines (87 loc) • 3.94 kB
JavaScript
require([
'dojo/_base/array',
'dojo/_base/lang',
'dojo/request/xhr',
'JBrowse/Browser',
'JBrowse/Model/XHRBlob',
'JBrowse/Store/SeqFeature/GFF3'
], function(
array,
lang,
xhr,
Browser,
XHRBlob,
GFF3Store
) {
describe( 'GFF3 store', function() {
it( 'can parse volvox.gff3', function() {
var p = new GFF3Store({
browser: new Browser({ unitTestMode: true }),
blob: new XHRBlob( '../../sample_data/raw/volvox/volvox.gff3' ),
refSeq: { name: 'ctgA', start: 0, end: 50001 }
});
(function() {
var features = [];
var done;
p.getFeatures(
{ ref: 'ctgA', start: 1, end: 50000 },
function(f) { features.push(f); },
function() { done = true; },
function(e) { console.error(e); }
);
waitsFor( function() { return done; } );
runs( function() {
//console.log( features );
expect( features.length ).toEqual( 197 );
var edenIndex;
array.some( features, function(f,i) {
if( f.get('name') == 'EDEN' ) {
edenIndex = i;
return true;
}
return false;
});
expect( edenIndex ).toBeGreaterThan( 3 );
expect( edenIndex ).toBeLessThan( 7 );
expect( features[edenIndex].get('subfeatures').length ).toEqual( 3 );
expect( features[edenIndex].get('subfeatures')[0].get('subfeatures').length ).toEqual( 6 );
});
}).call();
(function() {
var features = [];
var done;
p.getFeatures(
{ ref: 'ctgA', start: -1, end: 2499 },
function(f) { features.push(f); },
function() { done = true; },
function(e) { console.error(e); }
);
waitsFor( function() { return done; } );
runs( function() {
//console.log( features );
expect( features.length ).toEqual( 13 );
// expect( features[191].get('subfeatures').length ).toEqual( 3 );
// expect( features[191].get('subfeatures')[0].get('subfeatures').length ).toEqual( 6 );
});
}).call();
(function() {
var features = [];
var done;
p.getFeatures(
{ ref: 'ctgB', start: -1, end: 5000 },
function(f) { features.push(f); },
function() { done = true; },
function(e) { console.error(e); }
);
waitsFor( function() { return done; } );
runs( function() {
//console.log( features );
expect( features.length ).toEqual( 4 );
// expect( features[191].get('subfeatures').length ).toEqual( 3 );
// expect( features[191].get('subfeatures')[0].get('subfeatures').length ).toEqual( 6 );
expect( features[3].get('note') ).toEqual( 'ああ、この機能は、世界中を旅しています！' );
});
}).call();
});
});
});