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fix chords bug
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@nicgirault
nicgirault committed Jul 22, 2015
1 parent 2768716 commit aff7171
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Showing 2 changed files with 106 additions and 107 deletions.
210 changes: 105 additions & 105 deletions dist/circosJS.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
var circosJS,
__indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };

circosJS = function(conf) {
var instance;
Expand All @@ -22,14 +22,14 @@ circosJS.Core = function(conf) {
};

circosJS.Core.prototype.removeTracks = function(trackIds) {
var id, store, svg, trackId, type, _i, _len, _ref;
var id, l, len, ref, store, svg, trackId, type;
svg = d3.select(this.conf.container);
_ref = this.tracks;
for (type in _ref) {
store = _ref[type];
ref = this.tracks;
for (type in ref) {
store = ref[type];
if (typeof trackIds === 'object') {
for (_i = 0, _len = trackIds.length; _i < _len; _i++) {
id = trackIds[_i];
for (l = 0, len = trackIds.length; l < len; l++) {
id = trackIds[l];
if (id in store) {
svg.select('.' + id).remove();
delete store[id];
Expand Down Expand Up @@ -82,16 +82,16 @@ circosJS.mixConf = function(conf, defaultConf) {
};

circosJS.Core.prototype.smartBorders = function() {
var border, borders, currentBorder, layout, store, track, trackId, trackType, width, _i, _len, _ref;
var border, borders, currentBorder, l, layout, len, ref, store, track, trackId, trackType, width;
width = this.conf.defaultTrackWidth;
layout = {
"in": this._layout.conf.innerRadius,
out: this._layout.conf.outerRadius
};
borders = [];
_ref = this.tracks;
for (trackType in _ref) {
store = _ref[trackType];
ref = this.tracks;
for (trackType in ref) {
store = ref[trackType];
for (trackId in store) {
track = store[trackId];
if (track.conf.innerRadius) {
Expand All @@ -112,8 +112,8 @@ circosJS.Core.prototype.smartBorders = function() {
return 0;
});
currentBorder = layout;
for (_i = 0, _len = borders.length; _i < _len; _i++) {
border = borders[_i];
for (l = 0, len = borders.length; l < len; l++) {
border = borders[l];
if (border.out < currentBorder["in"] - width) {
return {
"in": currentBorder["in"] - width,
Expand Down Expand Up @@ -304,7 +304,7 @@ circosJS.parseChordData = function(data, layoutSummary) {
target: {
id: datum[3],
start: Math.max(0, parseFloat(datum[4])),
end: Math.min(layoutSummary[datum[0]], parseFloat(datum[5]))
end: Math.min(layoutSummary[datum[3]], parseFloat(datum[5]))
},
value: parseFloat(datum[6])
};
Expand All @@ -323,7 +323,7 @@ circosJS.parseChordData = function(data, layoutSummary) {
};

circosJS.Layout = function(conf, data) {
var block_nb, gap, k, offset, size, v, _ref, _ref1;
var block_nb, gap, k, offset, ref, ref1, size, v;
if (data == null) {
circosJS.log(2, 'no layout data', '');
}
Expand All @@ -332,9 +332,9 @@ circosJS.Layout = function(conf, data) {
this.blocks = {};
this.size = 0;
offset = 0;
_ref = this.data;
for (k in _ref) {
v = _ref[k];
ref = this.data;
for (k in ref) {
v = ref[k];
this.blocks[v.id] = {
label: v.label,
len: v.len,
Expand All @@ -348,9 +348,9 @@ circosJS.Layout = function(conf, data) {
gap = this.conf.gap;
size = this.size;
block_nb = this.data.length;
_ref1 = this.data;
for (k in _ref1) {
v = _ref1[k];
ref1 = this.data;
for (k in ref1) {
v = ref1[k];
this.blocks[v.id].start = v.offset / size * (2 * Math.PI - block_nb * gap) + k * gap;
this.blocks[v.id].end = (v.offset + v.len) / size * (2 * Math.PI - block_nb * gap) + k * gap;
v.start = v.offset / size * (2 * Math.PI - block_nb * gap) + k * gap;
Expand All @@ -368,11 +368,11 @@ circosJS.Layout = function(conf, data) {
}
};
this.summary = function() {
var d, layoutSummary, _i, _len, _ref2;
var d, l, layoutSummary, len, ref2;
layoutSummary = {};
_ref2 = this._data;
for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
d = _ref2[_i];
ref2 = this._data;
for (l = 0, len = ref2.length; l < len; l++) {
d = ref2[l];
layoutSummary[d.id] = d.len;
}
return layoutSummary;
Expand Down Expand Up @@ -440,26 +440,26 @@ circosJS.Chord = function() {
circosJS.Track.call(this);
this.parseData = circosJS.parseChordData;
this.applyRules = function(rules, data) {
var datum, rule, _i, _len, _results;
var datum, l, len, results, rule;
rules = rules || [];
_results = [];
for (_i = 0, _len = data.length; _i < _len; _i++) {
datum = data[_i];
_results.push((function() {
var _j, _len1, _results1;
_results1 = [];
for (_j = 0, _len1 = rules.length; _j < _len1; _j++) {
rule = rules[_j];
results = [];
for (l = 0, len = data.length; l < len; l++) {
datum = data[l];
results.push((function() {
var len1, m, results1;
results1 = [];
for (m = 0, len1 = rules.length; m < len1; m++) {
rule = rules[m];
if (rule.condition(datum)) {
_results1.push(datum[rule.parameter] = rule.value);
results1.push(datum[rule.parameter] = rule.value);
} else {
_results1.push(void 0);
results1.push(void 0);
}
}
return _results1;
return results1;
})());
}
return _results;
return results;
};
this.getSource = (function(_this) {
return function(d, layout) {
Expand Down Expand Up @@ -710,7 +710,7 @@ circosJS.Stack = function() {
return this.applyRules(conf.rules, this.data);
};
this.buildLayers = function(data, margin) {
var block, datum, i, idx, lastDatumInLayer, layer, layers, placed, _i, _j, _len, _len1, _ref;
var block, datum, i, idx, l, lastDatumInLayer, layer, layers, len, len1, m, placed, ref;
for (idx in data) {
block = data[idx];
block.values = block.values.sort(function(a, b) {
Expand All @@ -726,11 +726,11 @@ circosJS.Stack = function() {
return 1;
});
layers = [];
_ref = block.values;
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
datum = _ref[_i];
ref = block.values;
for (l = 0, len = ref.length; l < len; l++) {
datum = ref[l];
placed = false;
for (i = _j = 0, _len1 = layers.length; _j < _len1; i = ++_j) {
for (i = m = 0, len1 = layers.length; m < len1; i = ++m) {
layer = layers[i];
lastDatumInLayer = layer.slice(0).pop();
if (lastDatumInLayer.end + margin < datum.start) {
Expand All @@ -750,43 +750,43 @@ circosJS.Stack = function() {
}
};
this.applyRules = function(rules, data) {
var datum, i, k, layer, rule, v, _results;
var datum, i, k, layer, results, rule, v;
rules = rules || [];
_results = [];
results = [];
for (k in data) {
v = data[k];
_results.push((function() {
var _ref, _results1;
_ref = v.layers;
_results1 = [];
for (i in _ref) {
layer = _ref[i];
_results1.push((function() {
var _i, _len, _results2;
_results2 = [];
for (_i = 0, _len = layer.length; _i < _len; _i++) {
datum = layer[_i];
_results2.push((function() {
var _j, _len1, _results3;
_results3 = [];
for (_j = 0, _len1 = rules.length; _j < _len1; _j++) {
rule = rules[_j];
results.push((function() {
var ref, results1;
ref = v.layers;
results1 = [];
for (i in ref) {
layer = ref[i];
results1.push((function() {
var l, len, results2;
results2 = [];
for (l = 0, len = layer.length; l < len; l++) {
datum = layer[l];
results2.push((function() {
var len1, m, results3;
results3 = [];
for (m = 0, len1 = rules.length; m < len1; m++) {
rule = rules[m];
if (rule.condition(v.parent, datum, i)) {
_results3.push(datum[rule.parameter] = rule.value);
results3.push(datum[rule.parameter] = rule.value);
} else {
_results3.push(void 0);
results3.push(void 0);
}
}
return _results3;
return results3;
})());
}
return _results2;
return results2;
})());
}
return _results1;
return results1;
})());
}
return _results;
return results;
};
this.datumRadialPosition = (function(_this) {
return function(d) {
Expand Down Expand Up @@ -867,11 +867,11 @@ circosJS.Track = function() {
return this.applyRules(conf.rules, this.data);
};
this.loadData = function(data, instance) {
var d, layoutSummary, result, _i, _len, _ref;
var d, l, layoutSummary, len, ref, result;
layoutSummary = {};
_ref = instance._layout.data;
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
d = _ref[_i];
ref = instance._layout.data;
for (l = 0, len = ref.length; l < len; l++) {
d = ref[l];
layoutSummary[d.id] = d.len;
}
result = this.parseData(data, layoutSummary);
Expand All @@ -890,35 +890,35 @@ circosJS.Track = function() {
return conf;
};
this.applyRules = function(rules, data) {
var datum, i, k, rule, v, _results;
var datum, i, k, results, rule, v;
rules = rules || [];
_results = [];
results = [];
for (k in data) {
v = data[k];
_results.push((function() {
var _ref, _results1;
_ref = v.values;
_results1 = [];
for (i in _ref) {
datum = _ref[i];
_results1.push((function() {
var _i, _len, _results2;
_results2 = [];
for (_i = 0, _len = rules.length; _i < _len; _i++) {
rule = rules[_i];
results.push((function() {
var ref, results1;
ref = v.values;
results1 = [];
for (i in ref) {
datum = ref[i];
results1.push((function() {
var l, len, results2;
results2 = [];
for (l = 0, len = rules.length; l < len; l++) {
rule = rules[l];
if (rule.condition(v.key, datum, i)) {
_results2.push(datum[rule.parameter] = rule.value);
results2.push(datum[rule.parameter] = rule.value);
} else {
_results2.push(void 0);
results2.push(void 0);
}
}
return _results2;
return results2;
})());
}
return _results1;
return results1;
})());
}
return _results;
return results;
};
this.computeMinMax = function(conf, meta) {
conf.cmin = conf.min === 'smart' ? meta.min : conf.min;
Expand All @@ -943,11 +943,11 @@ circosJS.Track = function() {
};
this.render = (function(_this) {
return function(instance, parentElement, name) {
var datumContainer, track, _ref;
var datumContainer, ref, track;
parentElement.select('.' + name).remove();
track = parentElement.append('g').attr('class', name).attr('z-index', _this.conf.zIndex);
datumContainer = _this.renderDatumContainer(instance, track, name, _this.data, _this.conf);
if ((_ref = _this.conf.axes) != null ? _ref.display : void 0) {
if ((ref = _this.conf.axes) != null ? ref.display : void 0) {
_this.renderAxes(datumContainer, _this.conf, instance._layout, _this.data);
}
return _this.renderDatum(datumContainer, _this.conf, instance._layout, _this);
Expand Down Expand Up @@ -988,12 +988,12 @@ circosJS.Track = function() {
var axes, axis, x;
if (conf.axes.minor.spacingType === 'pixel') {
axes = (function() {
var _i, _ref, _ref1, _ref2, _results;
_results = [];
for (x = _i = _ref = conf.innerRadius, _ref1 = conf.outerRadius, _ref2 = conf.axes.minor.spacing; _ref2 > 0 ? _i <= _ref1 : _i >= _ref1; x = _i += _ref2) {
_results.push(x);
var l, ref, ref1, ref2, results;
results = [];
for (x = l = ref = conf.innerRadius, ref1 = conf.outerRadius, ref2 = conf.axes.minor.spacing; ref2 > 0 ? l <= ref1 : l >= ref1; x = l += ref2) {
results.push(x);
}
return _results;
return results;
})();
}
axis = d3.svg.arc().innerRadius(function(d) {
Expand Down Expand Up @@ -1163,15 +1163,15 @@ circosJS.renderLayoutTicks = function(conf, layout, d3, instance) {
};

circosJS.Core.prototype.render = function(ids, removeTracks) {
var name, renderAll, svg, track, trackStore, trackType, tracks, translated, _ref, _ref1;
var name, ref, ref1, renderAll, svg, track, trackStore, trackType, tracks, translated;
if (typeof ids === 'undefined') {
renderAll = true;
ids = [];
}
if (removeTracks) {
_ref = this.tracks;
for (trackType in _ref) {
trackStore = _ref[trackType];
ref = this.tracks;
for (trackType in ref) {
trackStore = ref[trackType];
for (name in trackStore) {
track = trackStore[name];
svg.select('.' + name).remove();
Expand All @@ -1183,17 +1183,17 @@ circosJS.Core.prototype.render = function(ids, removeTracks) {
if (translated.empty()) {
translated = svg.append('g').attr('class', 'all').attr('transform', 'translate(' + parseInt(this.conf.width / 2) + ',' + parseInt(this.conf.height / 2) + ')');
}
_ref1 = this.tracks;
for (trackType in _ref1) {
trackStore = _ref1[trackType];
ref1 = this.tracks;
for (trackType in ref1) {
trackStore = ref1[trackType];
for (name in trackStore) {
track = trackStore[name];
if (renderAll || __indexOf.call(ids, name) >= 0) {
if (renderAll || indexOf.call(ids, name) >= 0) {
track.render(this, translated, name);
}
}
}
if (renderAll || __indexOf.call(ids, 'layout') >= 0) {
if (renderAll || indexOf.call(ids, 'layout') >= 0) {
circosJS.renderLayout(d3, translated, this);
}
tracks = svg.selectAll('.all > g').remove();
Expand Down
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