# Code coverage report for src/FeatureFactory.js

## Statements: 29.33% (22 / 75) Branches: 0% (0 / 28) Functions: 5.26% (1 / 19) Lines: 29.33% (22 / 75) Ignored: none

All files » src/ » FeatureFactory.js

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     /*jslint node: true */
    /*jshint laxbreak: true */
    'use strict';

    var d3 = require('d3');
    var _ = require('underscore');

    var symbolSize = 10,
        gapRegion = 0,
        gapShape = 0,
        dictionary = {
            //molecular processing
            chain:'rectangle',
            transit: 'rectangle',
            init_met: "arrow",
            propep: 'rectangle',
            peptide:'rectangle',
            signal:'rectangle',
            //structural
            helix:'rectangle',
            strand:'rectangle',
            turn:'rectangle',
            //domains & sites
            region:'rectangle',
            coiled: 'rectangle',
            motif:'rectangle',
            repeat:'rectangle',
            ca_bind:'rectangle',
            dna_bind: 'rectangle',
            domain:'rectangle',
            zn_fing: 'rectangle',
            np_bind: 'rectangle',
            metal: "diamond",
            site: "chevron",
            binding: "catFace",
            act_site: "circle",
            //ptms
            mod_res: "triangle",
            lipid: "wave",
            carbohyd: "hexagon",
            disulfid:'bridge',
            crosslnk:'bridge',
            //seqInfo
            compbias:'rectangle',
            conflict:'rectangle',
            non_cons: "doubleBar",
            non_ter: "doubleBar",
            unsure: 'rectangle',
            non_std: "pentagon",
            //mutagenesis
            mutagen:'rectangle',
            //topology
            topo_dom:'rectangle',
            transmem:'rectangle',
            intramem:'rectangle',
            //variants
            var_seq:'variant',
            variant:'variant',
            missense:'variant',//CHECK
            ms_del:'variant',//CHECK
            insdel:'variant',//CHECK
            stop_lost:'variant',//CHECK
            stop_gained:'variant',//CHECK
            init_codon:'variant',//CHECK
            //proteomics
            unique:'rectangle',
            non_unique:'rectangle'
        };

    var Feature = function() {
        var feature = this;
        return feature;
    };

    var FeatureFactory = function() {
        return {
            getFeature: function(type, aaWidth, height, length) {
                var feature,
                    featureType = dictionary[type.toLowerCase()],
                    width = aaWidth * length;
                //0,0 is in the middle, so we first move to the starting of the aa at gapShape,0.
                gapShape = length === 1 ? 0 : width/length/2;
                //again a gap is needed for regions
                gapRegion = aaWidth/2;
                // if the constructor doesn't exist, rectangle is used by default
                if (typeof Feature[featureType] !== 'function') {
                    console.log(type + ' doesn\'t exist');
                    featureType = 'rectangle';
                }

                Feature[featureType].prototype = new Feature();
                feature = Feature[featureType](width, height, length);

                return feature;
            },
            isContinuous: function(type) {
                type = type.toLowerCase();
                if ((type === 'disulfid') || (type === 'crosslnk')) {
                    return false;
                }
                return true;
            }
        };
    }();

    Feature.rectangle = function(width, height) {
        return 'M' + -(gapRegion) + ',0'
                + 'L' + (width-gapRegion) + ',0'
                + 'L' + (width-gapRegion) + ',' + height
                + 'L' + -(gapRegion) + ',' + height
                + 'Z';
    };

    Feature.bridge = function(width, height, length) {
        if (length !== 1) {
            return 'M' + -(gapRegion) + ',' + height
                    + 'L' + -(gapRegion) + ',0'
                    + 'L' + (width-gapRegion) + ',0'
                    + 'L' + (width-gapRegion) + ',' + height
                    + 'L' + (width-gapRegion) + ',2'
                    + 'L' + -(gapRegion) + ',2Z';
        } else {
            return 'M' + -(gapRegion) + ',' + height
                    + 'L' + -(gapRegion) + ',' + (height/2)
                    + 'L0,' + (height/2)
                    + 'L0,0'
                    + 'L0,' + (height/2)
                    + 'L' + (width-gapRegion) + ',' + (height/2)
                    + 'L' + (width-gapRegion) + ',' + height
                    + 'Z';
        }
    };

    var getMiddleLine = function(centerx, width) {
        return 'M' + (centerx+gapShape) + ',' + centerx
                + 'L' + (width/2+gapShape) + ',' + centerx
                + 'M' + (-centerx+gapShape) + ',' + centerx
                + 'L' + (-width/2+gapShape) + ',' + centerx;
    };

    Feature.diamond = function(width, height, length) {
        var centerx = symbolSize/2;
        var shape = 'M' + gapShape + ',0'
                + 'L' + (centerx+gapShape) + ',' + centerx
                + 'L' + gapShape + ',' + symbolSize
                + 'L' + (-centerx+gapShape) + ',' + centerx;
        return length !== 1
            ? shape + 'L' + gapShape + ',0Z' + getMiddleLine(centerx, width)
            : shape + 'Z';
    };

    Feature.chevron = function(width, height, length) {
        var centerx = symbolSize/2;
        var shape = 'M' + gapShape + ',' + centerx
                + 'L' + (centerx+gapShape) + ',0'
                + 'L' + (centerx+gapShape) +',' + centerx
                + 'L' + gapShape + ',' + symbolSize
                + 'L' + (-centerx+gapShape) + ',' + centerx
                + 'L' + (-centerx+gapShape) + ',0';
        return length !== 1
            ? shape + 'L' + gapShape + ',' + centerx + getMiddleLine(centerx, width) + 'Z'
            : shape + 'Z';
    };

    Feature.catFace = function(width, height, length) {
        var centerx = symbolSize/2;
        var step = symbolSize/10;
        var shape = 'M' + (-centerx+gapShape) + ',0'
            + 'L' + (-centerx+gapShape) + ',' + (6*step)
            + 'L' + (-2*step+gapShape) + ',' + symbolSize
            + 'L' + (2*step+gapShape) + ',' + symbolSize
            + 'L' + (centerx+gapShape) + ',' + (6*step)
            + 'L' + (centerx+gapShape) + ',0'
            + 'L' + (2*step+gapShape) + ',' + (4*step)
            + 'L' + (-2*step+gapShape) + ',' + (4*step);
        return length !== 1
            ? shape + 'M' + (-centerx+gapShape) + ',0' + getMiddleLine(centerx, width) + 'Z'
            : shape + 'Z';
    };

    Feature.triangle = function(width, height, length) {
        var centerx = symbolSize/2;
        var shape = 'M' + gapShape + ',0'
                    + 'L' + (centerx+gapShape) + ',' + symbolSize
                    + 'L' + (-centerx+gapShape) + ',' + symbolSize;
        return length !== 1
            ? shape + 'L' + gapShape + ',0' + getMiddleLine(centerx, width) + 'Z'
            : shape + 'Z';
    };

    Feature.wave = function(width, height, length) {
        var rx = symbolSize/4;
        var ry = symbolSize/2;
        var shape = 'M' + (-symbolSize/2+gapShape) + ',' + ry
                + "A" + rx + "," + ry + " 0 1,1 " + gapShape + "," + ry
                + "A" + rx + "," + ry + " 0 1,0 " + (symbolSize/2+gapShape) + ',' + ry;
        return length !== 1
            ? shape + getMiddleLine(ry, width) + 'Z'
            : shape + 'Z';
    };

    var getPolygon = function(N, width, length){
        var r = symbolSize/2;
        var polygon = 'M ';
        for(var i=0; i < N;i++) {
            polygon += (r * Math.cos(2*Math.PI*i/N) + gapShape) + ',' + (r * Math.sin(2*Math.PI*i/N)+r)  + ' ';
        }
        return length !== 1
            ? polygon + ' ' + (r * Math.cos(0) + gapShape) + ',' + (r * Math.sin(0)+r)  + ' ' + getMiddleLine(r, width) + 'Z'
            : polygon + 'Z';
    };

    Feature.hexagon = function(width, height, length) {
        return getPolygon(6, width, length);
    };

    Feature.pentagon = function(width, height, length) {
        return getPolygon(5, width, length);
    };

    Feature.circle = function(width, height, length) {
      var r = Math.sqrt(symbolSize / Math.PI);
      var shape = "M" + gapShape + ",0"
          + "A" + r + "," + r + " 0 1,1 " + gapShape + "," + symbolSize
          + "A" + r + "," + r + " 0 1,1 " + gapShape + ",0";
      return length !== 1
            ? shape + getMiddleLine(symbolSize/2, width) + 'Z'
            : shape + 'Z';
    };

    Feature.arrow = function(width, height, length) {
        var step = symbolSize/10;
        var shape = 'M' + gapShape + ',0'
            + 'L' + (-step+gapShape) + ',0'
            + 'L' + (-5*step+gapShape) + ',' + (4*step)
            + 'L' + (-step+gapShape) + ',' + height
            + 'L' + gapShape + ',' + height
            + 'L' + (4*step+gapShape) + ',' + (4*step);
        return length !== 1
            ? shape + 'L' + gapShape + ',0' + getMiddleLine(symbolSize/2, width) + 'Z'
            : shape + 'Z';
    };

    Feature.doubleBar = function(width, height, length) {
        var centerx = symbolSize/2;
        var shape = 'M' + gapShape + ',0'
            + 'L' + (-centerx+gapShape) + ',' + symbolSize
            + 'L' + gapShape + ',' + symbolSize
            + 'L' + (centerx+gapShape) + ',0';
        return length !== 1
            ? shape + 'L' + gapShape + ',0' + getMiddleLine(symbolSize/2, width) + 'Z'
            : shape + 'Z';
    };

    Feature.variant = function() {

    };

    module.exports = FeatureFactory;