use papa parse

Gruntfile.js

@@ -66,7 +66,7 @@ module.exports = function (grunt) {
 					'js/hopscotch.min.js', 'js/typed.min.js',
 					'js/jquery.event.drag-2.2.js',
 					'js/clipboard.min.js', 'js/slick.min.js',
-					'js/js.cookie.js', 'js/d3.layout.cloud.js']
+					'js/js.cookie.js', 'js/d3.layout.cloud.js', 'js/papaparse.min.js']
 			},
 			morpheus: {
 				nonull: true,

src/io/content_range_network_input_stream.js

-morpheus.ContentRangeNetworkInputStream = function(url, options) {
-	var _this = this;
-	this.options = options || {};
-	this.url = url;
-	this.bytePosition = 0;
-	this.chunkSize = options.chunkSize || 1024 * 1024 * 10; // 50 MB
-	this.bytesRead = 0;
-	this.fileSize = -1;
-	this.read();
-};
-
-morpheus.ContentRangeNetworkInputStream.prototype = {
-	read : function() {
-
-		var _this = this;
-		var oReq = new XMLHttpRequest();
-		oReq.open('GET', this.url, true);
-		oReq.responseType = 'arraybuffer';
-
-		oReq.onload = function(oEvent) {
-			var arrayBuffer = oReq.response;
-			var byteArray = new Uint8Array(arrayBuffer);
-			var contentRange = oReq.getResponseHeader('Content-Range');
-			var index = contentRange.lastIndexOf('/');
-			_this.fileSize = parseInt(contentRange.substring(index + 1));
-			_this.bytePosition += byteArray.length;
-			_this.bytesRead += byteArray.length;
-			_this.options.bytes(byteArray);
-			if (_this.bytesRead < _this.fileSize) {
-				_this.read();
-			} else {
-				_this.options.complete();
-			}
-		};
-		var end = this.bytePosition + this.chunkSize - 1;
-		if (this.fileSize !== -1) {
-			end = Math.min(end, this.fileSize - 1);
-		}
-		// byte range is inclusive
-		oReq
-				.setRequestHeader('Range', 'bytes=' + this.bytePosition + '-'
-						+ end);
-		oReq.setRequestHeader('If-None-Match', 'webkit-no-cache'); //
-		// https://bugs.webkit.org/show_bug.cgi?id=82672
-
-		oReq.onerror = function() {
-			console.log('error');
-		};
-		oReq.send(null);
-
-	}
-};

src/io/fetch_network_input_stream.js

-morpheus.FetchNetworkInputStream = function(url, options) {
-	var bytesRead = 0;
-	var fileSize = 0;
-
-	function pump(reader) {
-		return reader.read().then(function(result) {
-			if (result.done) {
-				options.complete();
-				return;
-			}
-			var chunk = result.value;
-			bytesRead += chunk.byteLength;
-			options.bytes(chunk);
-			return pump(reader);
-
-		});
-	}
-	fetch(url).then(function(res) {
-		// _this.fileSize = res.headers.get('Content-Length');
-		return pump(res.body.getReader());
-	});
-};

src/io/file_input_stream.js

-morpheus.FileInputStream = function(file, options) {
-	var _this = this;
-	this.options = options || {};
-	this.reader = new FileReader();
-	this.reader.onloadend = function(evt) {
-		if (evt.target.readyState === FileReader.DONE) {
-
-			var arrayBuffer = evt.target.result;
-			var byteArray = new Uint8Array(arrayBuffer);
-			_this.bytePosition += byteArray.length;
-			_this.bytesRead += byteArray.length;
-			_this.options.bytes(byteArray);
-			if (_this.bytesRead < _this.fileSize) {
-				_this.read();
-			} else {
-				options.complete();
-			}
-		}
-	};
-	this.file = file;
-	this.bytePosition = 0;
-	this.chunkSize = options.chunkSize || 1024 * 1024 * 10; // 10 MB
-	this.bytesRead = 0;
-	this.fileSize = file.size;
-	this.read();
-};
-
-morpheus.FileInputStream.prototype = {
-	read : function() {
-		var _this = this;
-		var end = this.bytePosition + this.chunkSize;
-		end = Math.min(end, this.fileSize);
-		// byte
-		// range is
-		// exclusive
-		var blob = this.file.slice(this.bytePosition, end);
-		this.reader.readAsArrayBuffer(blob);
-	}
-};
\ No newline at end of file

src/io/gct_reader.js

@@ -7,42 +7,170 @@ morpheus.GctReader.prototype = {
 		return 'gct';
 	},
 	read: function (fileOrUrl, callback) {
-		var _this = this;
-		var name = morpheus.Util.getBaseFileName(morpheus.Util
-		.getFileName(fileOrUrl));
-		morpheus.BufferedReader.getArrayBuffer(fileOrUrl, function (err,
-																	arrayBuffer) {
-			if (err) {
-				callback(err);
-			} else {
-				try {
-					callback(null, _this._read(name,
-						new morpheus.BufferedReader(new Uint8Array(
-							arrayBuffer))));
-				} catch (x) {
-					if (x.stack) {
-						console.log(x.stack);
+		var lineNumber = 0;
+		var version;
+		var numRowAnnotations = 1; // in addition to row id
+		var numColumnAnnotations = 0; // in addition to column id
+		var nrows = -1;
+		var ncols = -1;
+		var version = 2;
+		var rowMetadataNames = [];
+		var columnMetadataNames = [];
+		var rowMetadata = [[]];
+		var columnMetadata = [[]];
+		var dataColumnStart;
+		var matrix = [];
+		var dataMatrixLineNumberStart;
+		var columnIdFieldName = 'id';
+		var rowIdFieldName = 'id';
+		var columnNamesArray;
+		Papa.parse(fileOrUrl, {
+			delimiter: "\t",	// auto-detect
+			newline: "",	// auto-detect
+			header: false,
+			dynamicTyping: false,
+			preview: 0,
+			encoding: "",
+			worker: false,
+			comments: false,
+			step: function (result) {
+				if (lineNumber === 0) {
+					var text = result.data[0][0].trim();
+					if ('#1.2' === text) {
+						version = 2;
+					} else if ('#1.3' === text) {
+						version = 3;
+					} else {
+						console.log('Unknown version: assuming version 2');
+					}
+				} else if (lineNumber === 1) {
+					var dimensions = result.data[0];
+					if (version === 3) {
+						if (dimensions.length >= 4) {
+							nrows = parseInt(dimensions[0]);
+							ncols = parseInt(dimensions[1]);
+							numRowAnnotations = parseInt(dimensions[2]);
+							numColumnAnnotations = parseInt(dimensions[3]);
+						} else { // no dimensions specified
+							numRowAnnotations = parseInt(dimensions[0]);
+							numColumnAnnotations = parseInt(dimensions[1]);
+						}
+					} else {
+						nrows = parseInt(dimensions[0]);
+						ncols = parseInt(dimensions[1]);
+						if (nrows <= 0 || ncols <= 0) {
+							callback(
+								'Number of rows and columns must be greater than 0.');
+						}
+					}
+					dataColumnStart = numRowAnnotations + 1;
+				} else if (lineNumber === 2) {
+					columnNamesArray = result.data[0];
+					if (ncols === -1) {
+						ncols = columnNamesArray.length - numRowAnnotations - 1;
+					}
+					if (version == 2) {
+						var expectedColumns = ncols + 2;
+						if (columnNamesArray.length !== expectedColumns) {
+							callback('Expected ' + (expectedColumns - 2)
+								+ ' column names, but read '
+								+ (columnNamesArray.length - 2) + ' column names.');
+						}
+					}
+					var name = columnNamesArray[0];
+					var slashIndex = name.lastIndexOf('/');
+
+					if (slashIndex != -1 && slashIndex < (name.length - 1)) {
+						rowIdFieldName = name.substring(0, slashIndex);
+						columnIdFieldName = name.substring(slashIndex + 1);
+					}
+					rowMetadataNames.push(rowIdFieldName);
+					columnMetadataNames.push(columnIdFieldName);
+					for (var j = 0; j < ncols; j++) {
+						var index = j + numRowAnnotations + 1;
+						var columnName = index < columnNamesArray.length ? columnNamesArray[index]
+							: null;
+						columnMetadata[0].push(String(columnName));
+					}
+
+					for (var j = 0; j < numRowAnnotations; j++) {
+						var rowMetadataName = '' === columnNamesArray[1] ? 'description'
+							: columnNamesArray[j + 1];
+						rowMetadataNames.push(
+							rowMetadataName);
+						rowMetadata.push([]);
+					}
+					dataMatrixLineNumberStart = 3 + numColumnAnnotations;
+				} else { // lines >=3
+					var tokens = result.data[0];
+					if (lineNumber < dataMatrixLineNumberStart) {
+						var metadataName = tokens[0];
+						var v = [];
+						columnMetadata.push(v);
+						columnMetadataNames.push(metadataName);
+						for (var j = 0; j < ncols; j++) {
+							v.push(String(tokens[j + dataColumnStart]));
+						}
+					} else { // data lines
+						if (tokens[0] !== '') {
+							var array = new Float32Array(ncols);
+							matrix.push(array);
+							// we iterate to numRowAnnotations + 1 to include id row
+							// metadata field
+							for (var rowAnnotationIndex = 0; rowAnnotationIndex <= numRowAnnotations; rowAnnotationIndex++) {
+								var rowMetadataValue = tokens[rowAnnotationIndex];
+								rowMetadata[rowAnnotationIndex].push(
+									String(rowMetadataValue));
+
+							}
+
+							for (var columnIndex = 0; columnIndex < ncols; columnIndex++) {
+								var token = tokens[columnIndex + dataColumnStart];
+								array[columnIndex] = parseFloat(token);
+							}
+						}
 					}
-					callback(x);
 				}
-			}
-		});
+				lineNumber++;
 
+			},
+			complete: function () {
+				var dataset = new morpheus.Dataset({
+					name: morpheus.Util.getBaseFileName(morpheus.Util
+					.getFileName(fileOrUrl)),
+					rows: matrix.length,
+					columns: ncols,
+					array: matrix,
+					dataType: 'Float32'
+				});
+				for (var i = 0; i < rowMetadataNames.length; i++) {
+					dataset.getRowMetadata().add(rowMetadataNames[i]).array = rowMetadata[i];
+				}
+				for (var i = 0; i < columnMetadataNames.length; i++) {
+					dataset.getColumnMetadata().add(columnMetadataNames[i]).array = columnMetadata[i];
+				}
+				morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(), 1);
+				morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),
+					1);
+				callback(null, dataset);
+			},
+			error: function (err) {
+				callback(err);
+			},
+			download: !(fileOrUrl instanceof File),
+			skipEmptyLines: false,
+			chunk: undefined,
+			fastMode: true,
+			beforeFirstChunk: undefined,
+			withCredentials: undefined
+		});
 	},
 	_read: function (datasetName, reader) {
+		var tab = /\t/;
 		var versionLine = $.trim(reader.readLine());
 		if (versionLine === '') {
 			throw new Error('Missing version line');
 		}
-		var tab = /\t/;
-		var dimensionsLine = reader.readLine();
-		if (dimensionsLine == null) {
-			throw new Error('No dimensions specified');
-		}
-		var columnNamesLine = reader.readLine();
-		if (columnNamesLine == null) {
-			throw new Error('No column annotations');
-		}
 		var version = 2;
 		if ('#1.2' === versionLine) {
 			version = 2;
@@ -51,6 +179,10 @@ morpheus.GctReader.prototype = {
 		} else {
 			console.log('Unknown version: assuming version 2');
 		}
+		var dimensionsLine = reader.readLine();
+		if (dimensionsLine == null) {
+			throw new Error('No dimensions specified');
+		}
 		// <numRows> <tab> <numCols>
 		var dimensions = dimensionsLine.split(/[ \t]/);
 		var numRowAnnotations = 1; // in addition to row id
@@ -75,6 +207,10 @@ morpheus.GctReader.prototype = {
 					'Number of rows and columns must be greater than 0.');
 			}
 		}
+		var columnNamesLine = reader.readLine();
+		if (columnNamesLine == null) {
+			throw new Error('No column annotations');
+		}
 
 		var columnNamesArray = columnNamesLine.split(tab);
 		if (ncols === -1) {
@@ -281,5 +417,28 @@ morpheus.GctReader.prototype = {
 			return dataset;
 		}
 
+	},
+	_read: function (fileOrUrl, callback) {
+		var _this = this;
+		var name = morpheus.Util.getBaseFileName(morpheus.Util
+		.getFileName(fileOrUrl));
+		morpheus.BufferedReader.getArrayBuffer(fileOrUrl, function (err,
+																	arrayBuffer) {
+			if (err) {
+				callback(err);
+			} else {
+				try {
+					callback(null, _this._read(name,
+						new morpheus.BufferedReader(new Uint8Array(
+							arrayBuffer))));
+				} catch (x) {
+					if (x.stack) {
+						console.log(x.stack);
+					}
+					callback(x);
+				}
+			}
+		});
+
 	}
 };

src/io/line_reader.js

-morpheus.LineReader = function(fileOrUrl, options) {
-	var _this = this;
-	this.str = '';
-	var isString = _.isString(fileOrUrl);
-	if (typeof TextDecoder !== 'undefined') {
-		var textDecoder = new TextDecoder();
-		this.decoder = function(buf, start, end) {
-			return textDecoder.decode(buf.subarray(start, end));
-		};
-	} else {
-		this.decoder = function(buf, start, end) {
-			// TODO convert in chunks
-			var s = '';
-			for (var i = start; i < end; i++) {
-				s += String.fromCharCode(buf[i]);
-			}
-			return s;
-		};
-	}
-	var inputStreamOptions = {
-		bytes : function(buf) {
-			_this.str += _this.decoder(buf, 0, buf.length);
-			var split = morpheus.LineReader._split(_this.str);
-			if (split.lines.length > 0) {
-				var lines = split.lines;
-				for (var i = 0, nlines = lines.length; i < nlines; i++) {
-					var line = lines[i];
-					if (line !== '') {
-						options.line(line);
-					}
-				}
-				_this.str = split.remainder;
-			}
-		},
-		complete : function() {
-			options.complete();
-		}
-	};
-	isString ? new morpheus.FetchNetworkInputStream(fileOrUrl,
-			inputStreamOptions) : new morpheus.FileInputStream(fileOrUrl,
-			inputStreamOptions);
-
-};
-
-morpheus.LineReader._split = function(str) {
-	var lines = [];
-	var start = 0;
-	var length = str.length;
-	for (var i = 0; i < length; i++) {
-		var c = str[i];
-		if (c === '\n' || c === '\r') {
-			var end = i;
-			if ((i < length - 1) && (str[i + 1] === '\n')) { // check for
-				// \r\n
-
-				i++;
-			}
-
-			lines.push(str.substring(start, end));
-			start = i + 1;
-		}
-	}
-
-	return {
-		lines : lines,
-		remainder : start <= length ? str.substring(start, length) : ''
-	};
-};

src/util/events.js

 // code taken from KineticJS
-morpheus.Events = function() {
+morpheus.Events = function () {
 };
 morpheus.Events.prototype = {
 	/**
 	 * Pass in a string of events delimmited by a space to bind multiple events
 	 * at once such as 'mousedown mouseup mousemove'. Include a namespace to
 	 * bind an event by name such as 'click.foobar'.
-	 * 
+	 *
 	 * @param {String}
 	 *            evtStr e.g. 'click', 'mousedown touchstart', 'mousedown.foo
 	 *            touchstart.foo'
 	 * @param {Function}
 	 *            handler The handler function is passed an event object
 	 */
-	on : function(evtStr, handler) {
+	on: function (evtStr, handler) {
 		if (!handler) {
 			throw Error('Handler not specified');
 		}
@@ -35,19 +35,28 @@ morpheus.Events.prototype = {
 				this.eventListeners[baseEvent] = [];
 			}
 			this.eventListeners[baseEvent].push({
-				name : name,
-				handler : handler
+				name: name,
+				handler: handler
 			});
 		}
 		return this;
 	},
+	getListeners: function () {
+		if (!this.eventListeners) {
+			this.eventListeners = {};
+		}
+		return this.eventListeners;
+	},
+	setListeners: function (eventListeners) {
+		this.eventListeners = eventListeners;
+	},
 	/**
 	 * Fire an event.
-	 * 
+	 *
 	 * @param eventType
 	 * @param evt
 	 */
-	trigger : function(eventType, evt) {
+	trigger: function (eventType, evt) {
 		if (!this.eventListeners) {
 			this.eventListeners = {};
 		}
@@ -62,7 +71,7 @@ morpheus.Events.prototype = {
 		if (events) {
 			var len = events.length;
 			for (var i = 0; i < len; i++) {
-				events[i].handler.apply(this, [ evt ]);
+				events[i].handler.apply(this, [evt]);
 			}
 		}
 		return this;
@@ -73,11 +82,11 @@ morpheus.Events.prototype = {
 	 * mouseup mousemove'. include a namespace to remove an event binding by
 	 * name such as 'click.foobar'. If you only give a name like '.foobar', all
 	 * events in that namespace will be removed.
-	 * 
+	 *
 	 * @param {String}
 	 *            evtStr e.g. 'click', 'mousedown.foo touchstart', '.foobar'
 	 */
-	off : function(evtStr, handler) {
+	off: function (evtStr, handler) {
 		if (!this.eventListeners) {
 			this.eventListeners = {};
 		}
@@ -105,14 +114,14 @@ morpheus.Events.prototype = {
 		}
 		return this;
 	},
-	_off : function(type, name, handler) {
+	_off: function (type, name, handler) {
 		var evtListeners = this.eventListeners[type], i, evtName;
 		for (i = 0; i < evtListeners.length; i++) {
 			evtName = evtListeners[i].name;
 			// check if an event name is not specified, or if one is specified,
 			// it matches the current event name
 			if ((!name || evtName === name)
-					&& (handler == null || handler == evtListeners[i].handler)) {
+				&& (handler == null || handler == evtListeners[i].handler)) {
 				evtListeners.splice(i, 1);
 				if (evtListeners.length === 0) {
 					delete this.eventListeners[type];
@@ -121,5 +130,5 @@ morpheus.Events.prototype = {
 				i--;
 			}
 		}
-	},
-};
\ No newline at end of file
+	}
+};