Germline mutation

.gitignore

@@ -38,5 +38,10 @@ Session.vim
 .netrwhist
 *~
 
-# Compiled assets
-dist
+### emacs ###
+\#*\#
+
+# DS_Store
+.DS_Store
+src/.DS_Store
+test/.DS_Store

.npmignore

@@ -0,0 +1,55 @@
+# Created by https://www.gitignore.io
+
+### Repo Files ###
+# src/
+test/
+server.js
+gulpfile.js
+.gitignore
+.travis.yml
+
+### Node ###
+# Logs
+logs
+*.log
+
+# Runtime data
+pids
+*.pid
+*.seed
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (http://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directory
+# https://www.npmjs.org/doc/misc/npm-faq.html#should-i-check-my-node_modules-folder-into-git-
+node_modules
+
+
+### vim ###
+[._]*.s[a-w][a-z]
+[._]s[a-w][a-z]
+*.un~
+Session.vim
+.netrwhist
+*~
+
+### emacs ###
+\#*\#
+
+# DS_Store
+.DS_Store
+src/.DS_Store
+test/.DS_Store

.oldsrc/css/oncoprint.css

@@ -0,0 +1,96 @@
+.oncoprint-toolbar-ctr {
+	display: inline-block;
+	vertical-align: top;
+	float: right;
+}
+.oncoprint-label-area-ctr {
+	float:left;
+	overflow: auto;
+	width: auto;
+}
+.oncoprint-cell-area-ctr {
+	overflow: auto;
+	width: auto;
+	position:relative;
+}
+
+.oncoprint-cell-area {
+	background-color: transparent;
+    	position: relative;
+}
+
+.oncoprint-column-highlight {
+	position:absolute;
+	width: 1px;
+	border-left: 1px dashed rgba(0,0,0,0.75);
+	top: 0px;
+}
+
+.oncoprint-cell {
+	position: absolute;
+}
+
+.oncoprint-animated {
+	-webkit-transition: 0.5s ease-out;
+	-moz-transition: 0.5s ease-out;
+	-o-transition: 0.5s ease-out;
+	transition: 0.5s ease-out;
+}
+
+.oncoprint-cell-hover {
+	outline: 1px solid DarkGray;
+	position: absolute;
+}
+
+.oncoprint-legend-header {
+	font-family: Arial !important;
+	font-weight: bold !important;
+	fill: gray !important;
+	text-anchor: start;
+	alignment-baseline: hanging;
+	font-size: 12px;
+	padding-right: 30px;
+}
+
+.oncoprint-legend-label {
+	font-family: Arial;
+	alignment-baseline: hanging;
+	font-size: 12px;
+}
+
+.oncoprint-legend-block {
+	display: inline-block;
+}
+.oncoprint-legend-element {
+	display: inline-block;
+}
+
+.oncoprint-track-label {
+	font-size: 12px;
+}
+
+.oncoprint-track-label-draggable {
+	cursor: move;
+}
+.oncoprint-label-dragging {
+	font-weight: bold !important;
+	color: #ff0000;
+}
+
+.noselect {
+	-webkit-touch-callout: none;
+    	-webkit-user-select: none;
+    	-khtml-user-select: none;
+    	-moz-user-select: none;
+    	-ms-user-select: none;
+    	user-select: none;
+}
+
+.oncoprint-cell-qtip {
+	background-color: rgba(0,0,0,0) !important;
+	//border: none !important;
+}
+.oncoprint-cell-qtip .qtip-content {
+	background-color: rgba(255,255,255,0.92) !important;
+	font-size: 13px !important;
+}

.oldsrc/js/OncoprintRenderer.js

@@ -0,0 +1,152 @@
+/*
+ * Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
+ * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
+ * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
+ * obligations to provide maintenance, support, updates, enhancements or
+ * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
+ * liable to any party for direct, indirect, special, incidental or
+ * consequential damages, including lost profits, arising out of the use of this
+ * software and its documentation, even if Memorial Sloan-Kettering Cancer
+ * Center has been advised of the possibility of such damage.
+ */
+
+/*
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+window.OncoprintRenderer = (function() {
+	var events = oncoprint_events;
+	var utils = oncoprint_utils;
+	var RuleSet = oncoprint_RuleSet;
+
+	function OncoprintRenderer(oncoprint, config) {
+		this.rule_sets = {};
+		this.clipping = true;
+		this.oncoprint = oncoprint;
+		this.config = config;
+		this.upper_padding = utils.ifndef(config.upper_padding, 0);
+		this.max_label_length = utils.ifndef(config.max_label_length, 20);
+		this.track_group_separation = 12;
+
+		(function computeLabelAreaWidth(self) {
+			var label_font = self.getLabelFont();
+			var max_label_width = utils.textWidth((Math.pow(10,self.max_label_length)-1).toString(), label_font);
+			var max_percent_altered_width = utils.textWidth('100%', label_font);
+			var buffer_width = 20;
+			self.label_area_width = max_label_width + buffer_width + max_percent_altered_width;
+		})(this);
+	};
+	OncoprintRenderer.prototype.getCellCSSClass = function() {
+		return 'oncoprint-cell';	
+	};
+	OncoprintRenderer.prototype.getTrackCellCSSClass = function(track_id) {
+		return this.getCellCSSClass()+track_id;
+	};
+	OncoprintRenderer.prototype.getTrackLabelCSSClass = function(track_id) {
+		return 'oncoprint-track-label oncoprint-track-label'+track_id;
+	};
+	OncoprintRenderer.prototype.getTrackLabelCSSSelector = function(track_id) {
+		// TODO: replace with utils.cssClassToSelector
+		return "."+this.getTrackLabelCSSClass(track_id).split(" ").join(".");
+	};
+	OncoprintRenderer.prototype.getTrackCellCtrCSSClass = function(track_id) {
+		return 'oncoprint-track-cell-ctr'+track_id;
+	};
+	OncoprintRenderer.prototype.getLabelFont = function() {
+		return this.config.label_font;
+	};
+	OncoprintRenderer.prototype.setRuleSet = function(track_id, type, params) {
+		var new_rule_set = RuleSet.makeRuleSet(type, params);
+		this.rule_sets[track_id] = new_rule_set;
+		if (new_rule_set.sort_cmp) {
+			this.oncoprint.setTrackSortComparator(track_id, new_rule_set.sort_cmp);
+		}
+	};
+	OncoprintRenderer.prototype.useSameRuleSet = function(target_track_id, source_track_id) {
+		var rule_set = this.rule_sets[source_track_id];
+		this.rule_sets[target_track_id] = rule_set;
+		if (rule_set.sort_cmp) {
+			this.oncoprint.setTrackSortComparator(target_track_id, rule_set.sort_cmp);
+		}
+	};
+	OncoprintRenderer.prototype.getRuleSet = function(track_id) {
+		return this.rule_sets[track_id];
+	};
+	OncoprintRenderer.prototype.getTrackTops = function() {
+		var ret = {};
+		var y = this.upper_padding;
+		var self = this;
+		_.each(this.oncoprint.getTrackGroups(), function(group) {
+			if (group.length === 0) {
+				return;
+			}
+			_.each(group, function(id) {
+				ret[id] = y;
+				y+= self.getRenderedTrackHeight(id);
+			});
+			y += self.track_group_separation;
+		});
+		return ret;
+	};
+	OncoprintRenderer.prototype.getTrackCellTops = function() {
+		return this.track_cell_tops || this.computeTrackCellTops();
+	};
+	OncoprintRenderer.prototype.computeTrackCellTops = function() {
+		var tops = this.getTrackTops();
+		var self = this;
+		_.each(tops, function(top, id) {
+			tops[id] = top + self.oncoprint.getTrackPadding(id);
+		});
+		this.track_cell_tops = tops;
+		return tops;
+	};
+	OncoprintRenderer.prototype.getTrackLabelTops = function() {
+		return this.getTrackCellTops();
+	};
+	OncoprintRenderer.prototype.getRenderedTrackHeight = function(track_id) {
+		return this.oncoprint.getTrackHeight(track_id) + 2*this.oncoprint.getTrackPadding(track_id);
+	};
+	OncoprintRenderer.prototype.getCellX = function(index) {
+		return (typeof index === 'number' ? index*(this.oncoprint.getZoomedCellWidth()+this.oncoprint.getCellPadding()) : -1);
+	};
+	OncoprintRenderer.prototype.getCellXArray = function(length) {
+		var cell_unit = this.oncoprint.getZoomedCellWidth() + this.oncoprint.getCellPadding();
+		return _.map(_.range(0,length), function(x) { return x*cell_unit; });
+	};
+	OncoprintRenderer.prototype.getCellAreaWidth = function() {
+		return this.oncoprint.getVisibleIdOrder().length*(this.oncoprint.getZoomedCellWidth() + this.oncoprint.getCellPadding());
+	};
+	OncoprintRenderer.prototype.getCellAreaHeight = function() {
+		var track_tops = this.getTrackTops();
+		var track_order = this.oncoprint.getTracks();
+		if (track_order.length === 0) {
+			return 0;
+		} else {
+			var last_track = track_order[track_order.length-1];
+			return track_tops[last_track] + this.getRenderedTrackHeight(last_track);
+		}
+	};
+	OncoprintRenderer.prototype.getLabelAreaWidth = function() {
+		return this.label_area_width;
+	};
+	OncoprintRenderer.prototype.getLabelAreaHeight = function() {
+		return this.getCellAreaHeight();
+	};
+	OncoprintRenderer.prototype.render = function() {
+		throw "not implemented in abstract class";
+	}
+	return OncoprintRenderer;
+})();