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1 | /*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
missense:'variant',//CHECK
ms_del:'variant',//CHECK
insdel:'variant',//CHECK
stop_lost:'variant',//CHECK
stop_gained:'variant',//CHECK
init_codon:'variant'//CHECK
};
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; |