@gmod/jbrowse/src/JBrowse/View/FastaFileDialog.js

JBrowse - client-side genome browser

define( [
            'dojo/_base/declare',
            'dijit/form/Button',
            'dijit/form/RadioButton',
            'dojo/dom-construct',
            'JBrowse/View/FileDialog',
            './FileDialog/TrackList/BgzipIndexedFASTADriver',
            './FileDialog/TrackList/IndexedFASTADriver',
            './FileDialog/TrackList/TwoBitDriver',
            './FileDialog/TrackList/ChromSizesDriver'
        ],
        function(
            declare,
            Button,
            RadioButton,
            dom,
            FileDialog,
            BgzipIndexedFASTADriver,
            IndexedFASTADriver,
            TwoBitDriver,
            ChromSizesDriver
        ) {

return declare( FileDialog, {

    constructor: function( args ) {
        this.inherited(arguments);
        this._fileTypeDrivers = [ new BgzipIndexedFASTADriver(), new IndexedFASTADriver(), new TwoBitDriver(), new ChromSizesDriver() ];
        return this;
    },



    show: function( args ) {
        args.introMsg = "Select a FASTA file (.fa), indexed FASTA (.fa and .fai), bgzip indexed FASTA (.fa, .fai, and .gzi), twobit (.2bit) file, or a chrom.sizes file (tab separated refseq name and length)";
        this.inherited(arguments);
        this.dialog.set('title', 'Open sequence file');
    },


    _makeActionBar: function( openCallback, cancelCallback ) {
        var actionBar = dom.create(
            'div', {
                className: 'dijitDialogPaneActionBar'
            });
        var disChoices = this.refSeqOrderChoice = [
            new RadioButton({ id: 'sortAlpha',
                              value: 'sortAlpha',
                               checked: true
                             }),
            new RadioButton({ id: 'sortLength',
                              value: 'sortLength'
                            }),
            new RadioButton({ id: 'noSort',
                              value: 'noSort'
                            })
        ];

        var aux = dom.create('div',{className:'aux'},actionBar);
        disChoices[0].placeAt(aux);
        dom.create('label', { "for": 'sortAlpha', innerHTML: 'Sort refseqs by name' }, aux ),
        disChoices[1].placeAt(aux);
        dom.create('label', { "for": 'sortLength', innerHTML: 'Sort refseqs by length' }, aux );
        disChoices[2].placeAt(aux);
        dom.create('label', { "for": 'noSort', innerHTML: 'Use order from file' }, aux );

        new Button({ iconClass: 'dijitIconDelete', label: 'Cancel',
                     onClick: dojo.hitch( this, function() {
                                              cancelCallback && cancelCallback();
                                              this.dialog.hide();
                                          })
                   })
            .placeAt( actionBar );

        new Button({
            iconClass: 'dijitIconFolderOpen',
            label: 'Open',
            onClick: () => {
                if (openCallback) {
                    openCallback({
                        trackConfs: this.trackList.getTrackConfigurations(),
                        refSeqOrder: this.refSeqOrderChoice[0].checked ? "alphabetic descending" :
                                    this.refSeqOrderChoice[1].checked ? "length descending" :
                                    undefined
                    }).then( () => this.dialog.hide(), err => { console.error(err) } )
                }
            }
        })
        .placeAt( actionBar );

        return { domNode: actionBar };
    }


});
});