Downloads of HSP alignments - slight reformatting

[yannickwurm]

• [ ] they should indicate a, b, c letters like so "-hit_1_hsp_c" (after the coordinate)
• [ ] they should have whitespace (one newline) between HSPs

[iQuxLE]

Getting the "hsp_a" part is pretty straight forward. Right now I am a bit struggling to call hit.number for the specific hit. My Javascript is not that good, but in other files it is simply used and I get the error of hit being undefined.

Could anybody may offer some assistance for that, maybe @Lazy-poet, @yeban?

for now its:

generate_fasta(hsps) {

        var fasta = '';

        _.each(hsps, _.bind(function (hsp) {
            fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'-hit_'+'???'+'_hsp_'+toLetters(hsp.number)+'\n';
            fasta += hsp.qseq+'\n';
            fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'-hit_'+'???'+'_hsp_'+toLetters(hsp.number)+
            '_alignment_'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
            fasta += hsp.midline+'\n';
            fasta += '>'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'-hit_'+'???'+'_hsp_'+toLetters(hsp.number)+'\n';
            fasta += hsp.sseq+'\n\n';
        }, this));
        
            return fasta;
        
    }`

And I also tried something like that:

generate_fasta() {
        var fasta = '';
        this.props.queries.forEach(
            (query) => query.hits.forEach(
                (hit) => {
                    num_hits++;
                    
                    _.each(hsps, _.bind(function (hsp) {
                        fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'-hit_'+hit.number+'_hsp_'+toLetters(hsp.number)+'\n';
                        fasta += hsp.qseq+'\n';
                        fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'hit_'+hit.number+'_hsp_'+toLetters(hsp.number)+
                        '_alignment_'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
                        fasta += hsp.midline+'\n';
                        fasta += '>'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'hit_'+hit.number+'_hsp_'+toLetters(hsp.number)+'\n';
                        fasta += hsp.sseq+'\n\n';

                    }));
                }
            ))
        ; 
        return fasta
    }

The problem is that it cannot read properties of data (and I guess everything after that as well). So I tried to add properties to the constructer and extend Components from React, but I kind of hit a wall.

Thanks for any advise.

[yeban]

The data the results page receives from the server is hierarchical: query -> hit -> hsp.

hit details are not available in hsp object.

But what you want to do is quite simple. See how the generate_fasta method is called in hit.js and sidebar.js. They attach a hit_id property to the hsp objects. You can include the hit number there, either as part of hit_id or hsp_id or a separate field.

[yeban]

Correction: see how alignment exporter is called in hit.js, sidebar.js, etc.