Sha256: 3d5d3d56962479aeb05caf6efebfd8bf3b860e95c06abe0c0e35b55d7168744f
Contents?: true
Size: 1.88 KB
Versions: 7
Compression:
Stored size: 1.88 KB
Contents
import * as Exporter from './exporter';
import _ from 'underscore';
export default class AlignmentExporter {
constructor() {
this.prepare_alignments_for_export = this.prepare_alignments_for_export.bind(this);
this.export_alignments = this.export_alignments.bind(this);
}
wrap_string(str, width) {
var idx = 0;
var wrapped = '';
while(true) {
wrapped += str.substring(idx, idx + width);
idx += width;
if(idx < str.length) {
wrapped += '\n';
} else {
break;
}
}
return wrapped;
}
generate_fasta(hsps) {
var fasta = '';
_.each(hsps, _.bind(function (hsp) {
fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'\n';
fasta += hsp.qseq+'\n';
fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'_alignment_'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
fasta += hsp.midline+'\n';
fasta += '>'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
fasta += hsp.sseq+'\n';
}, this));
return fasta;
}
get_alignments_download_metadata(hsps, filename_prefix){
var fasta = this.generate_fasta(hsps);
var blob = new Blob([fasta], { type: 'text/fasta' });
var filename = Exporter.sanitize_filename(filename_prefix) + '.txt';
return {filename, blob};
}
prepare_alignments_for_export(hsps, filename_prefix) {
const { filename, blob } = this.get_alignments_download_metadata(hsps, filename_prefix);
const blob_url = Exporter.generate_blob_url(blob, filename);
return blob_url;
}
export_alignments(hsps, filename_prefix) {
const { filename, blob } = this.get_alignments_download_metadata(hsps, filename_prefix);
Exporter.download_blob(blob, filename);
}
}
Version data entries
7 entries across 7 versions & 1 rubygems