yannickwurm/sequenceserver

import _ from 'underscore';
import d3 from 'd3';
export function get_colors_for_evalue(evalue, hits) {
    var colors = d3.scale
        .log()
        .domain([
            d3.min([1e-5, d3.min(hits.map(function (d) {
                if (parseFloat(d.evalue) === 0.0) return undefined;
                return d.evalue;
            }))]),
            d3.max(hits.map(function (d) {
                return d.evalue;
            }))
        ])
        .range([0,0.8]);
    var rgb = colors(evalue);
    return d3.hsl(20, 0.82 , rgb);
}

export function toLetters(num) {
    var mod = num % 26,
        pow = num / 26 | 0,
        out = mod ? String.fromCharCode(96 + mod) : (--pow, 'z');
    return pow ? toLetters(pow) + out : out;
}

/**
 * Defines how ticks will be formatted.
 *
 * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.
 *
 * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.
 */
export function tick_formatter(scale, seq_type) {
    var ticks = scale.ticks();
    var prefix = d3.formatPrefix(ticks[ticks.length - 1]);
    var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};

    var digits = 0;
    var format;
    var _ticks;

    do {
        format = d3.format('.' + digits + 'f');
        _ticks = scale.ticks().map(function (d) {
            return format(prefix.scale(d));
        });
        digits++;

    } while (_ticks.length !== _.uniq(_ticks).length);

    return function (d) {
        if (!prefix.symbol || d === scale.domain()[0]) {
            return (d + ' ' + suffixes[seq_type]);
        }
        else {
            return (format(prefix.scale(d)) +
                  ' ' + prefix.symbol + suffixes[seq_type]);
        }
    };
}

export function get_seq_type(algorithm) {
    var SEQ_TYPES = {
        blastn: {
            query_seq_type:   'nucleic_acid',
            subject_seq_type: 'nucleic_acid'
        },
        blastp: {
            query_seq_type:   'amino_acid',
            subject_seq_type: 'amino_acid'
        },
        blastx: {
            query_seq_type:   'nucleic_acid',
            subject_seq_type: 'amino_acid'
        },
        tblastx: {
            query_seq_type:   'nucleic_acid',
            subject_seq_type: 'nucleic_acid'
        },
        tblastn: {
            query_seq_type:   'amino_acid',
            subject_seq_type: 'nucleic_acid'
        }
    };
    return SEQ_TYPES[algorithm];
}

export function prettify_evalue(evalue) {
    var matches = evalue.toString().split('e');
    var base  = matches[0];
    var power = matches[1];

    if (power)
    {
        var s = parseFloat(base).toFixed(2);
        var element = '<span>'+s+' &times; 10<sup>'+power+'</sup></span>';
        return element;
    }
    else {
        if (!(base % 1==0))
            return parseFloat(base).toFixed(2);
        else
            return base;
    }
}