kekule/src/io/cmlspect/kekule.io.cmlspect.js

Open source JavaScript toolkit for chemoinformatics

/**
 * @fileoverview
 * File for supporting CMLSpect (The CML dialect for spectrum data).
 * @author Partridge Jiang
 */

/*
 * requires /lan/classes.js
 * requires /lan/xmlJsons.js
 * requires /core/kekule.common.js
 * requires /utils/kekule.domHelper.js
 * requires /spectroscopy/kekule.spectrum.core.js
 * requires /io/kekule.io.js
 * requires /io/jcamp/kekule.io.jcamp.base.js
 * requires /io/cml/kekule.io.cml.js
 * requires /localization
 */

(function(){

"use strict";

/*
 * Add default options to read/write CML format data.
 * @object
 */
Kekule.globalOptions.add('IO.cml', {
	// options for reader
	enableExtractSampleInsideSpectrum: true,  // if true, when reading molecule out from the child <sample> element of <spectrum>, a parent element will be created to hold both molecule and spectrum
	autoHideSampleInsideSpectrum: true,  // if true, the sample molecule inside <spectrum> will be hidden from displaying
	// options for writer
	autoInsertHiddenRefMoleculeToSample: true,  // if true, a hidden referred molecule will be automatically insert to the <sample> child element of <spectrum>
	//spectrumDataValueOutputDigitCountAfterDecimalPoint: 8,
	spectrumDataValueOutputPrecisionCount: 8,
	autoConvertNmrDataFreqToUnit: 'Hz'   // in JSpectView convention, the frequency of NMR continuous spectrum should be in unit Hz
});

var AU = Kekule.ArrayUtils;
var OU = Kekule.ObjUtils;
var DU = Kekule.DomUtils;

var CmlUtils = Kekule.IO.CmlUtils;
var CmlDomUtils = Kekule.IO.CmlDomUtils;

var ST = Kekule.Spectroscopy.SpectrumType;
var SPS = Kekule.Spectroscopy.PeakShape;
var SPM = Kekule.Spectroscopy.PeakMultiplicity

// add additional unit conversion map data
Kekule.IO.CmlUtils._cmlUnitConvMap.push(['moverz', 'm/z', 'm/z', false]);

/** @private */
Kekule.IO.CML.SPECTRUM_OBJREF_FIELDNAME = '__$objRef$__';
Kekule.IO.CML.SPECTRUM_DATA_OBJREF_FLAG_FIELDNAME = '__$hasObjRef$__'

/** @ignore */
Kekule.IO.CML.Spect = {};

/**
 * Some consts for CMLSpect.
 * @object
 */
Kekule.IO.CML.Spect.Consts = {
	SI_UNITS_NAMESPACE_DEF_PREFIX: 'siUnits',
	SI_UNITS_NAMESPACE_URI: 'http://www.xml-cml.org/units/siUnits',
	UNITS_NAMESPACE_DEF_PREFIX: 'units',
	UNITS_NAMESPACE_URI: 'http://www.xml-cml.org/units/units',
	JSPECVIEW_NAMESPACE_DEF_PREFIX: 'jspecview',
	JSPECVIEW_NAMESPACE_URI: 'http://jspecview.sf.net/convention.html',
	JCAMP_NAMESPACE_DEF_PREFIX: 'jcamp',
	JCAMP_NAMESPACE_URI: 'http://www.iupac.org/jcamp/dict',
	JCAMP_UNITS_NAMESPACE_DEF_PREFIX: 'jcampUnits',
	JCAMP_UNITS_NAMESPACE_URI: 'http://www.iupac.org/jcamp/dict/units',
	CML_DICT_NAMESPACE_DEF_PREFIX: 'cml',
	CML_DICT_NAMESPACE_URI: 'http://www.xml-cml.org/dict/cmlDict',
	XML_SCHEMA_INSTANCE_NAMESPACE_DEF_PREFIX: 'xsi',
	XML_SCHEMA_INSTANCE_NAMESPACE_URI: 'http://www.w3.org/2001/XMLSchema-instance',
	CMLSPECT_SCHEMA_LOCATIONS_ATTRIBNAME: 'schemaLocation',
	CMLSPECT_SCHEMA_LOCATIONS: [
		'http://www.xml-cml.org/dict/jcampDict dict/jcampDict.xml',
		'http://www.xml-cml.org/schema schema.xsd',
		'http://www.xml-cml.org/dict/cml dict/cmlDict.xml',
		'http://www.xml-cml.org/dict/cmlDict dict/simpleCmlDict.xml',
		'http://www.xml-cml.org/units/units dict/unitsDict.xml',
		'http://www.xml-cml.org/units/siUnits dict/siUnitsDict.xml'
	],

	ANNOTATION_METATYPE: 'annotation',
	INFO_METATYPE: 'info'
};
var CMLSpectConsts = Kekule.IO.CML.Spect.Consts;

/**
 * Util functions for CMLSpect data.
 * @class
 */
Kekule.IO.CmlSpectUtils = {
	/* @private */
	//NAMESPACE_JCAMP: 'jcamp', // in CMLSpect file, many attributes (especially the name of meta/condition/parameter element) has this namespace (e.g. 'jcamp:NMR_OBSERVERFREQUENCY')
	/** @private */
	_spectrumTypeMap: [
		['NMR', ST.NMR],
		['infrared', ST.IR],
		['ir', ST.IR],
		['massSpectrum', ST.MS],
		['mass', ST.MS],
		['UV/VIS', ST.UV_VIS],
		['uv', ST.UV_VIS],
		['vis', ST.UV_VIS]
	],
	/** @private */
	_peakShapeMap: [
		['sharp', SPS.SHARP],
		['broad', SPS.BROAD]
	],
	/** @private */
	_peakMultiplicityMap: [
		['singlet', SPM.SINGLET],
		['doublet', SPM.DOUBLET],
		['triplet', SPM.TRIPLET],
		['quartet', SPM.QUARTET],
		['quintet', SPM.QUINTET],
		['sextuplet', SPM.SEXTUPLET],
		['multiplet', SPM.MULTIPLET],
		['s', SPM.SINGLET],
		['d', SPM.DOUBLET],
		['dd', SPM.DOUBLE_DOUBLET],
		['ddd', SPM.TRIPLE_DOUBLET],
		['t', SPM.TRIPLET],
		['m', SPM.MULTIPLET]
	],
	/** @private */
	_spectrumInfoKeyMap: [
		['jcamp:NMR_OBSERVEFREQUENCY', 'NMR.ObserveFrequency'],
		['cml:field', 'NMR.ObserveFrequency'],  //???
		['jcamp:NMR_OBSERVENUCLEUS', 'NMR.ObserveNucleus'],
		['nmr:OBSERVENUCLEUS', 'NMR.ObserveNucleus'],
		['jcamp:resolution', 'Resolution']
	],
	/**
	 * Get the corresponding {@link Kekule.Spectroscopy.SpectrumType} value for a CML spectrum type string.
	 * @param {String} cmlSpectrumType
	 * @returns {String}
	 */
	cmlSpectrumTypeToKekule: function(cmlSpectrumType)
	{
		var valueTypeMap = Kekule.IO.CmlSpectUtils._spectrumTypeMap;
		var sType = ST.GENERAL;  // default
		var tValue = cmlSpectrumType.toLowerCase();
		for (var i = 0, l = valueTypeMap.length; i < l; ++i)
		{
			var item = valueTypeMap[i];
			if (tValue.indexOf(item[0].toLowerCase()) >= 0)
			{
				sType = item[1];
				break;
			}
		}
		return sType;
	},
	/**
	 * Get the corresponding CML type value from {@link Kekule.Spectroscopy.SpectrumType}.
	 * @param {String} kekuleSpectrumType
	 * @returns {String}
	 */
	kekuleSpectrumTypeToCml: function(kekuleSpectrumType)
	{
		var result = null;
		var valueTypeMap = Kekule.IO.CmlSpectUtils._spectrumTypeMap;
		for (var i = 0, l = valueTypeMap.length; i < l; ++i) {
			var item = valueTypeMap[i];
			if (kekuleSpectrumType === item[1])
			{
				result = item[0];
				break;
			}
		}
		return result;
	},
	/**
	 * Returns a key name for Kekule spectrum corresponding to the CML parameter key.
	 * @param {String} cmlKey
	 * @param {String} spectrumType
	 * @param {String} jcampNsPrefix
	 * @returns {String}
	 */
	cmlSpectrumInfoDataKeyToKekule: function(cmlKey, spectrumType, jcampNsPrefix)
	{
		if (!jcampNsPrefix)
			jcampNsPrefix = CMLSpectConsts.JCAMP_NAMESPACE_DEF_PREFIX; //CmlSpectUtils.NAMESPACE_JCAMP;
		var map = CmlSpectUtils._spectrumInfoKeyMap;
		for (var i = 0, l = map.length; i < l; ++i)
		{
			if (cmlKey === map[i][0])
				return map[i][1];
		}
		// not found, extract the core part of namespace styled key name
		var nameDetails = CmlUtils.getCmlNsValueDetails(cmlKey);
		if (nameDetails.namespace && nameDetails.namespace === jcampNsPrefix)  // we may need to check the jcamp dictionary
		{
			var localName = nameDetails.localName;
			if (spectrumType)
			{
				var spectrumPrefix = spectrumType && (spectrumType + '_');
				var p = localName.indexOf(spectrumPrefix);
				if (p >= 0)  // remove the prefix like 'NMR_', and add the '.'
					localName = Kekule.IO.Jcamp.Consts.SPECIFIC_LABEL_PREFIX + localName.substr(p + spectrumPrefix.length);
			}
			var jcampName = localName.toUpperCase();
			return Kekule.IO.Jcamp.Utils.jcampLabelNameToKekule(jcampName, spectrumType);
		}

		return CmlUtils.cmlNsTokenToKekule(cmlKey);  // default
	},
	/**
	 * Returns a key name for Kekule spectrum corresponding to the CML parameter key.
	 * @param {String} cmlKey
	 * @param {String} spectrumType
	 * @param {String} jcampNsPrefix
	 * @returns {String}
	 */
	kekuleSpectrumInfoDataKeyToCml: function(kekuleKey, spectrumType, jcampNsPrefix)
	{
		if (!jcampNsPrefix)
			jcampNsPrefix = CMLSpectConsts.JCAMP_NAMESPACE_DEF_PREFIX;  //CmlSpectUtils.NAMESPACE_JCAMP
		var map = CmlSpectUtils._spectrumInfoKeyMap;
		for (var i = 0, l = map.length; i < l; ++i)
		{
			if (kekuleKey === map[i][1])
				return map[i][0];
		}
		// not found in map, check if kekuleKey is based on JCAMP? if so, add the corresponding JCAMP namespace
		var nameDetails = Kekule.Spectroscopy.MetaPropNamespace.getPropertyNameDetail(kekuleKey);
		if (nameDetails.namespace === jcampNsPrefix)  // explicit jcamp label name
			return nameDetails.namespace + ':' + nameDetails.coreName;
		else
		{
			var jcampLabelName = Kekule.IO.Jcamp.Utils.kekuleLabelNameToJcamp(kekuleKey, spectrumType, true);
			//console.log('is jcamp?', kekuleKey, jcampLabelName);
			if (jcampLabelName)
			{
				return CmlSpectUtils._convPossibleJcampLabelNameToCml(jcampLabelName, spectrumType, jcampNsPrefix);
			}
			else  // not found in JCAMP label name map, custom name?
				return nameDetails.namespace + ':' + nameDetails.coreName;
		}
		/*
		else if (nameDetails.namespace === spectrumType && spectrumType)  // with a spectrum prefix, check in JCAMP map
		{

		}
		*/
		//return Kekule.IO.CmlUtils.kekuleNsTokenToCml(kekuleKey);  // default
	},
	/** @private */
	_convPossibleJcampLabelNameToCml: function(jcampLabelName, spectrumType, jcampNsPrefix)
	{
		var nameDetails = Kekule.IO.Jcamp.Utils.analysisLdrLabelName(jcampLabelName, false);
		var isSpecific = nameDetails.labelType === Kekule.IO.Jcamp.LabelType.SPECIFIC;
		var isPrivate = nameDetails.labelType === Kekule.IO.Jcamp.LabelType.PRIVATE;
		var coreName = nameDetails.coreName;
		var localName = (isSpecific && spectrumType)? spectrumType + '_' + coreName: coreName;
		return isPrivate? localName: /*CmlSpectUtils.NAMESPACE_JCAMP*/jcampNsPrefix + ':' + localName;
	},
	/**
	 * Convert a CML peak shape string to value of {@link Kekule.Spectroscopy.PeakShape}.
	 * @param {String} cmlMultiplicity
	 * @returns {String}
	 */
	cmlPeakShapeToKekule: function(cmlPeakShape)
	{
		var map = CmlSpectUtils._peakShapeMap;
		var s = cmlPeakShape.toLowerCase();
		for (var i = 0, l = map.length; i < l; ++i)
		{
			if (s === map[i][0])
				return map[i][1];
		}
		return cmlPeakShape;
	},
	/**
	 * Convert a Kekule peak shape string to CML value.
	 * @param {String} kPeakShape
	 * @returns {String}
	 */
	kekulePeakShapeToCml: function(kPeakShape)
	{
		var map = CmlSpectUtils._peakShapeMap;
		for (var i = 0, l = map.length; i < l; ++i)
		{
			if (kPeakShape === map[i][1])
				return map[i][0];
		}
		return kPeakShape;
	},
	/**
	 * Convert a CML peak multiplicity string to value of {@link Kekule.Spectroscopy.PeakMultiplicity}.
	 * @param {String} cmlMultiplicity
	 * @returns {Variant}
	 */
	cmlPeakMultiplicityToKekule: function(cmlMultiplicity)
	{
		var map = CmlSpectUtils._peakMultiplicityMap;
		var s = cmlMultiplicity.toLowerCase();
		for (var i = 0, l = map.length; i < l; ++i)
		{
			if (s === map[i][0])
				return map[i][1];
		}
		return cmlMultiplicity;
	},
	/**
	 * Convert a Kekule peak multiplicity const int or description string value to CML.
	 * @param {Variant} cmlMultiplicity
	 * @returns {String}
	 */
	kekulePeakMultiplicityToCml: function(kMultiplicity)
	{
		var map = CmlSpectUtils._peakMultiplicityMap;
		for (var i = 0, l = map.length; i < l; ++i)
		{
			if (kMultiplicity === map[i][1])
				return map[i][0];
		}
		return kMultiplicity;
	},

	/**
	 * Output a float to CML string.
	 * @param {Number} value
	 * @param {Int} maxDigitCount
	 * @returns {string}
	 */
	floatToCmlString: function(value, maxDigitCount)
	{
		if (maxDigitCount)
			return Kekule.NumUtils.toPrecision(value, maxDigitCount, true, true);
			//return value.toPrecision(maxDigitCount);
		else
			return value.toString();
	},

	/**
	 * Check if a variable definition already existing in spectrum. If true, returns it.
	 * @param {Kekule.Spectroscopy.Spectrum} spectrum
	 * @param {String} varSymbol
	 * @param {String} varUnit
	 * @param {String} name
	 * @param {Int} dependency
	 * @returns {Kekule.Spectroscopy.SpectrumVarDefinition}
	 */
	getSpectrumVarDef: function(spectrum, varSymbol, varUnit, name, dependency)
	{
		if (!dependency)
			dependency = Kekule.VarDependency.INDEPENDENT;
		var varDefs = spectrum.getVariables();
		for (var i = 0, l = varDefs.length; i < l; ++i)
		{
			var varDef = varDefs[i];
			if ((!varSymbol || varSymbol === varDef.getSymbol()) && (!varUnit || varUnit === varDef.getUnit()) && (!name || name === varDef.getName()) && (dependency === varDef.getDependency()))
				return varDef;
		}
		return null;
	}
};
var CmlSpectUtils = Kekule.IO.CmlSpectUtils;

/**
 * CML <sample> element reader.
 * @class
 * @augments Kekule.IO.CmlBaseListReader
 */
Kekule.IO.CmlSampleReader = Class.create(Kekule.IO.CmlBaseListReader,
/** @lends Kekule.IO.CmlSampleReader# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSampleReader'
});

/**
 * Base writer to write spectrum data section object to CML.
 * @class
 * @augments Kekule.IO.CmlSpectrumDataSectionBaseWriter
 */
Kekule.IO.CmlSpectrumDataSectionBaseWriter = Class.create(Kekule.IO.CmlElementWriter,
/** @lends Kekule.IO.CmlSpectrumDataSectionBaseWriter# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumDataWriter',
	/** @private */
	getSpectrumDataSectionVarInfos: function(targetDataSection)
	{
		var result = {
			'dependent': {},
			'independent': {}
		};
		// get the independant and denpendant vars
		var varInfos = targetDataSection.getActualLocalVarInfos();
		var varUnitSymbols = {};
		var varSymbols = {};
		for (var i = 0, l = varInfos.length; i < l; ++i)
		{
			var varDef = targetDataSection.getLocalVarDef(i);
			var currKey;
			if (varDef.getDependency() === Kekule.VarDependency.DEPENDENT)
				currKey = 'dependent';
			else
				currKey = 'independent';

			var currInfoItem = result[currKey];
			currInfoItem.symbol = varDef.getSymbol();
			currInfoItem.unitSymbol = varDef.getUnit();
			currInfoItem.name = varDef.getName();
			currInfoItem.description = varDef.getDescription();

			var continuosRange = targetDataSection.getContinuousVarRange(i);
			if (continuosRange)
			{
				currInfoItem.range = {
					'fromValue': continuosRange.fromValue,
					'toValue': continuosRange.toValue,
					'count': targetDataSection.getDataCount()
				}
			}

			if (result.dependent.symbol && result.independent.symbol)
				break;
		}
		result.varCount = (!result.dependent.symbol? 0: 1) + (!result.independent.symbol? 0: 1);
		return result;
	}
});

/**
 * Reader to read a <peaklist> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlElementReader
 */
Kekule.IO.CmlSpectrumPeakListReader = Class.create(Kekule.IO.CmlElementReader,
/** @lends Kekule.IO.CmlSpectrumPeakListReader# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumPeakListReader',
	/** @constructs */
	initialize: function()
	{
		this.tryApplySuper('initialize');
		this._peakDetailsWithAssignments = [];  // a private field to storing all involved child readers
	},
	/** @ignore */
	doFinalize: function()
	{
		this._peakDetailsWithAssignments = null;
		this.tryApplySuper('doFinalize');
	},
	/** @ignore */
	doReadElement: function(elem, parentObj, parentReader, options)
	{
		var spectrum = (parentObj instanceof Kekule.Spectroscopy.Spectrum)? parentObj: null;
		if (spectrum)  // we need to set the variables of parent spectrum
		{
			var peaks = [];
			// TODO: ignoring <peakGroup> in list, since lacking the document of <peakGroup>. We simply iterate all child <peak> elements.
			var domHelper = this.getDomHelper();
			var peakElems = domHelper.getElementsByTagNameNS(this.getCoreNamespaceURI(), 'peak', elem);
			//var peakReader = Kekule.IO.CmlElementReaderFactory.getReader('peak');
			var peakReader = this.doGetChildElementReader('peak');
			if (peakReader)
			{
				//this.copySettingsToChildHandler(peakReader);
				try
				{
					for (var i = 0, l = peakElems.length; i < l; ++i)
					{
						var peakResult = peakReader.readElement(peakElems[i], null, this);
						if (peakResult)
							peaks.push(peakResult);
					}
				}
				finally
				{
					//peakReader.finalize();   // child readers will be released at the finalized method of parent reader
				}
			}
			if (peaks.length)
			{
				var result;
				var spectrumData = spectrum.getData();
				var varInfos = this._analysisPeakVarInfo(peaks, spectrum);
				if (varInfos)
				{
					var varSymbols = this._addPeakVariablesToSpectrumData(varInfos, spectrumData, spectrum);
					if (varSymbols && varSymbols.length)
					{
						result = spectrumData.createSection(varSymbols, Kekule.Spectroscopy.DataMode.PEAK); //new Kekule.Spectroscopy.SpectrumDataSection();
						//result.setLocalVarSymbols(varSymbols);
						//result.setMode(Kekule.Spectroscopy.DataMode.PEAK);
						this._setVarLocalInfos(varInfos, result);
						this._addPeakDataToSpectrumData(peaks, varSymbols, result, spectrumData, spectrum);
					}
				}
				return result;
			}
			else
				return null;
		}
		else
			return null;
	},
	/** @ignore */
	doDoneReadingDocument: function()
	{
		// after the document is build, try set the assignments of peaks
		var details = this._peakDetailsWithAssignments;
		for (var i = 0, l = details.length; i < l; ++i)
		{
			var d = details[i];
			if (d instanceof Kekule.Spectroscopy.SpectrumPeakDetails)
			{
				var owner = d.getOwner();
				//if (owner && owner.getObjById)
				{
					var ids = d.getInfoValue(Kekule.IO.CML.SPECTRUM_OBJREF_FIELDNAME);
					var objs = [];
					for (var j = 0, k = ids.length; j < k; ++j)
					{
						var id = ids[j];
						var obj = this.getLoadedObjById(id) || (owner && owner.getObjById && owner.getObjById(id));

						if (obj)
							objs.push(obj);
					}
					if (objs.length)
						d.setAssignments(objs);
					//console.log('set assignment', d, ids, objs);
					delete d.getInfo()[Kekule.IO.CML.SPECTRUM_OBJREF_FIELDNAME];
				}
			}
		}
		this._peakDetailsWithAssignments = [];
	},
	/** @private */
	_analysisPeakVarInfo: function(peaks, spectrumObj)  // iterate peaks data and find out the variable informations
	{
		var variableInfos = {};
		var varCount = 0;
		//var
		for (var i = 0, l = peaks.length; i < l; ++i)
		{
			var peak = peaks[i];
			var value = peak.value;
			var symbols = (value && Kekule.ObjUtils.getOwnedFieldNames(value, false)) || [];
			for (var j = 0, k = symbols.length; j < k; ++j)
			{
				if (!variableInfos[symbols[j]])
				{
					variableInfos[symbols[j]] = {};
					++varCount;
				}
			}
			//TODO: fill units info of var, here we simply assume all peaks uses the same units system
			var units = peak.units;
			if (units)
			{
				var symbols = Kekule.ObjUtils.getOwnedFieldNames(units, false) || [];
				for (var j = 0, k = symbols.length; j < k; ++j)
				{
					if (variableInfos[symbols[i]] && !variableInfos[symbols[i]].units)
					{
						var unitSymbol = Kekule.IO.CmlUtils.cmlUnitStrToMetricsUnitSymbol(units[symbols[i]]);
						variableInfos[symbols[i]].units = unitSymbol;
						if (!unitSymbol)
							variableInfos[symbols[i]].title = Kekule.IO.CmlUtils.getCmlNsValueLocalPart(units[symbols[i]]);
					}
				}
			}
		}
		if (varCount <= 0)  // no variables, just returns null
			return null;
		else if (varCount === 1)   // only one explicit symbol, may be ommitted the y values in NMR?
		{
			if (spectrumObj && spectrumObj.getSpectrumType() === Kekule.Spectroscopy.SpectrumType.NMR)  // we manually add the implicit y
			{
				variableInfos.y = {
					'units': Kekule.Unit.Arbitrary.ARBITRARY.symbol,
					'displayLabel': Kekule.Unit.Arbitrary.ARBITRARY.name,
					'defaultValue': 1
				};
			}
		}

		return variableInfos;
	},
	/** @private */
	_addPeakVariablesToSpectrumData: function(varInfos, spectrumDataObj, spectrumObj)
	{
		if (!varInfos)  // no var info, returns directly
			return null;
		var symbols = Kekule.ObjUtils.getOwnedFieldNames(varInfos, false);
		// get the independent var, should be x/X, or the first varibale
		var indepIndex = symbols.indexOf('x');
		if (indepIndex < 0)
			indepIndex = symbols.indexOf('X');
		if (indepIndex < 0)
			indepIndex = 0;

		// ensure the independent var at first
		var indepInfo = symbols.splice(indepIndex, 1);
		symbols.unshift(indepInfo[0]);

		// add var definitions
		var varSymbols = [];
		for (var i = 0, l = symbols.length; i < l; ++i)
		{
			var initParams = {
				'symbol': symbols[i],
				'dependency': (i === 0)? Kekule.VarDependency.INDEPENDENT: Kekule.VarDependency.DEPENDENT
			};
			if (varInfos[symbols[i]].title)
				initParams.displayLabel = varInfos[symbols[i]].title;
			if (varInfos[symbols[i]].units)
				initParams.unit = varInfos[symbols[i]].units;

			// check if there is already a varDef of this condition
			var varDef = Kekule.IO.CmlSpectUtils.getSpectrumVarDef(spectrumObj, initParams.symbol, initParams.unit, null, initParams.dependency);
			if (varDef && !varDef.getDisplayLabel() && initParams.displayLabel)
				varDef.setDisplayLabel(initParams.displayLabel);
			if (!varDef)
			{
				varDef = new Kekule.Spectroscopy.SpectrumVarDefinition(initParams);
				spectrumDataObj.appendVariable(varDef);
			}
			/*
			if (varInfos[symbols[i]].defaultValue)  // set default value at data section, avoid affect existed varDef in spectrumData
				spectrumDataSection.setDefaultVarValue(varDef, varInfos[symbols[i]].defaultValue);
				//spectrumDataObj.setDefaultVarValue(varDef, varInfos[symbols[i]].defaultValue);
			*/
			varSymbols.push(initParams.symbol);
		}

		return varSymbols;  // A flag means variable adding successful
	},
	/** @private */
	_setVarLocalInfos: function(varInfos, spectrumDataSection)
	{
		var symbols = Kekule.ObjUtils.getOwnedFieldNames(varInfos, false);
		for (var i = 0, l = symbols.length; i < l; ++i)
		{
			var info = varInfos[symbols[i]];
			if (Kekule.ObjUtils.notUnset(info.defaultValue))
			{
				spectrumDataSection.setDefaultVarValue(symbols[i], info.defaultValue);
			}
		}
	},
	/** @private */
	_addPeakDataToSpectrumData: function(peaks, varSymbols, spectrumDataSection, spectrumDataObj, spectrumObj)
	{
		for (var i = 0, ii = peaks.length; i < ii; ++i)
		{
			var peak = peaks[i];
			var values = [];
			for (var j = 0, jj = varSymbols.length; j < jj; ++j)
			{
				var symbol = varSymbols[j];
				var value = peak.value[symbol];
				values.push(value);
			}
			this._setPeakDetails(peak, values, spectrumDataSection);
			spectrumDataSection.appendData(values);
		}
		spectrumDataSection.setDataSorted(true);
	},
	/** @private */
	_setPeakDetails: function(peak, dataValue, spectrumDataSection)
	{
		if (peak.subStructure || peak.multiplicity || peak.shape)
		{
			var detail = new Kekule.Spectroscopy.SpectrumPeakDetails({
				'multiplicity': peak.multiplicity,
				'shape': peak.shape
			});
			if (peak.subStructure)  // has <peakStructure> child element
				detail.setInfoValue('structure', peak.subStructure);
			var objRefIds = this._getPeakObjRefIds(peak);
			if (objRefIds)
			{
				detail.setInfoValue(Kekule.IO.CML.SPECTRUM_OBJREF_FIELDNAME, objRefIds);  // save the ref ids, handling it when the spectrum is added to chem space
				//spectrumDataSection[Kekule.IO.CML.SPECTRUM_DATA_OBJREF_FLAG_FIELDNAME] = true;  // flag, indicating the cross ref should be handled later
				this._peakDetailsWithAssignments.push(detail);
			}
			spectrumDataSection.setExtraInfoOf(dataValue, detail);
			return detail;
		}
		return null;
	},
	/** @private */
	_getPeakObjRefIds: function(peak)
	{
		var ids = [];
		for (var i = 0 , l = Kekule.IO.CML.ATOMS_REF_ATTRIBS.length; i < l; ++i)
		{
			var key = Kekule.IO.CML.ATOMS_REF_ATTRIBS[i];
			if (peak[key])
				ids = ids.concat(peak[key].split(/\s/));
		}
		for (var i = 0 , l = Kekule.IO.CML.BONDS_REF_ATTRIBS.length; i < l; ++i)
		{
			var key = Kekule.IO.CML.BONDS_REF_ATTRIBS[i];
			if (peak[key])
				ids = ids.concat(peak[key].split(/\s/));
		}
		var result = [];
		for (var i = 0, l = ids.length; i < l; ++i)
		{
			var id = ids[i].trim();
			if (id)
				result.push(id);
		}
		return result.length? result: null;
	}
});

/**
 * Writer to write a <peaklist> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlSpectrumDataSectionBaseWriter
 */
Kekule.IO.CmlSpectrumPeakListWriter = Class.create(Kekule.IO.CmlSpectrumDataSectionBaseWriter,
/** @lends Kekule.IO.CmlSpectrumPeakListWriter# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumPeakListWriter',
	/** @ignore */
	doCreateElem: function(obj, parentElem)
	{
		return this.createChildElem('peakList', parentElem);
	},
	/** @ignore */
	doWriteObject: function(obj, targetElem, options)
	{
		return this.writePeaks(obj, targetElem, options);
	},
	/** @private */
	writePeaks: function(dataSection, targetElem, options)
	{
		var dataVarInfo = this.getSpectrumDataSectionVarInfos(dataSection);
		if (dataVarInfo.varCount < 2)  // less than two vars, illegal
		{
			// TODO: error message here?
		}
		else  // output data peaks
		{
			var peakWriter = this.getChildPeakWriter();
			if (peakWriter)
			{
				var indepSymbol = dataVarInfo.independent.symbol;
				var indepUnit = dataVarInfo.independent.unitSymbol;
				var depSymbol = dataVarInfo.dependent.symbol;
				var depUnit = dataVarInfo.dependent.unitSymbol;

				var self = this;
				dataSection.forEach(function (value, index) {
					// form a peak hash and use it to write to CML
					var peakObj = {
						xValue: value[indepSymbol],
						xUnits: indepUnit,
						yValue: value[depSymbol],
						yUnits: depUnit
					};
					var extra = dataSection.getExtraInfoOf(value);
					var extraHash;
					if (extra instanceof Kekule.Spectroscopy.SpectrumPeakDetails)
						extraHash = self._peakDetailsToHash(extra);
					else if (DataType.isObjectValue(extra))
						extraHash = extra;
					if (extraHash)
						peakObj = Object.extend(peakObj, extraHash);
					peakWriter.writeObject(peakObj, targetElem, options);
				});
			}
		}
	},
	/** @private */
	getChildPeakWriter: function()
	{
		var result = new Kekule.IO.CmlSpectrumPeakWriter();
		if (result)
		{
			this.copySettingsToChildHandler(result);
			this._appendChildHandler(result);
		}
		return result;
	},
	/** @private */
	_peakDetailsToHash: function(peakDetails)
	{
		var result = {
			'shape': peakDetails.getShape(),
			'multiplicity': peakDetails.getMultiplicity(),
			'assignments': peakDetails.getAssignments()
		};
		var subStructure = peakDetails.getInfoValue('structure');
		if (subStructure)
			result.structure = subStructure;
		return result;
	}
});

/**
 * Reader to read a <peak> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlElementReader
 */
Kekule.IO.CmlSpectrumPeakReader = Class.create(Kekule.IO.CmlElementReader,
/** @lends Kekule.IO.CmlSpectrumPeakReader# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumPeakReader',
	/** @ignore */
	doReadElement: function(elem, parentObj, parentReader, options)
	{
		var result = {};
		this.readPeakAttribs(result, elem, this.getDomHelper());
		this.iterateChildElements(elem, result, this, function(childElem, childResult)
		{
			var tagName = DU.getLocalName(childElem);
			var tagNameLower = tagName.toLowerCase();
			if (tagNameLower === 'peakstructure')
			{
				if (!result.subStructure)
					result.subStructure = [];
				result.subStructure.push(childResult);
			}
		});
		return result;
	},
	/** @private */
	readPeakAttribs: function(peakObj, elem, domHelper)
	{
		// important attribs are id, type, title and convention
		var attribs = Kekule.IO.CmlDomUtils.fetchCmlElemAttributeValuesToJson(elem, null, true, domHelper);
		var attribKeys = Kekule.ObjUtils.getOwnedFieldNames(attribs);
		for (var i = 0, l = attribKeys.length; i < l; ++i)
		{
			var key = attribKeys[i];
			var keyLower = key.toLowerCase();
			if (keyLower === 'peakheight')  // regard the peakheight as the same of yValue
			{
				key = 'yValue';
				keyLower = 'yvalue';
			}
			var value = attribs[key];
			if (keyLower.indexOf('units') >= 0)  // xUnits/yUnits attrib
			{
				var symbol = this._getVarSymbolInName(key, 'units');
				if (!peakObj.units)
					peakObj.units = {};
				peakObj.units[symbol] = Kekule.IO.CmlUtils.cmlUnitStrToMetricsUnitSymbol(value);
			}
			else if (keyLower.indexOf('value') >= 0)  // xValue/yValue attrib
			{
				var symbol = this._getVarSymbolInName(key, 'value');
				if (!peakObj.value)
					peakObj.value = {};
				peakObj.value[symbol] = Kekule.IO.CmlUtils.tryParseFloat(value);
			}
			else if (keyLower === 'peakmultiplicity')
			{
				peakObj.multiplicity = CmlSpectUtils.cmlPeakMultiplicityToKekule(value);
			}
			else if (keyLower === 'peakshape')
			{
				peakObj.shape = CmlSpectUtils.cmlPeakShapeToKekule(value);
			}
			else
				peakObj[key] = value;
		}
	},
	/** @private */
	_getVarSymbolInName: function(name, baseName)
	{
		var p = name.toLowerCase().indexOf(baseName.toLowerCase());
		return (p > 0)? name.substring(0, p): null;
	}
});

/**
 * Writer to write a <peak> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlElementWriter
 */
Kekule.IO.CmlSpectrumPeakWriter = Class.create(Kekule.IO.CmlElementWriter,
/** @lends Kekule.IO.CmlSpectrumPeakWriter# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumPeakWriter',
	/** @ignore */
	doCreateElem: function(obj, parentElem)
	{
		return this.createChildElem('peak', parentElem);
	},
	/** @ignore */
	doWriteObject: function(obj, targetElem, options)
	{
		this.writePeakAttribs(obj, targetElem, options);
	},
	/** @private */
	writePeakAttribs: function(peakObj, targetElem, options)
	{
		var domHelper = this.getDomHelper();
		var cmlHash= this._peakHashToCmlHash(peakObj);
		var keys = Kekule.ObjUtils.getOwnedFieldNames(cmlHash);
		var decimalCount = options.spectrumDataValueOutputPrecisionCount || 0;
		for (var i = 0, l = keys.length; i < l; ++i)
		{
			var key = keys[i];
			var value = cmlHash[key];
			if (['xvalue', 'yvalue'].indexOf(key.toLowerCase()) >= 0)
				CmlDomUtils.setCmlElemAttribute(targetElem, key, CmlSpectUtils.floatToCmlString(value, decimalCount), domHelper);
			if (key.toLowerCase() === 'structure' && DataType.isObjectValue(value))  // sub structure
				this.writePeakSubStructure(value, targetElem, options);
			else
				CmlDomUtils.setCmlElemAttribute(targetElem, key, value, domHelper);
		}
	},
	/** @private */
	getChildPeakStructureWriter: function()
	{
		var result = new Kekule.IO.CmlSpectrumPeakStructureWriter();
		if (result)
		{
			this.copySettingsToChildHandler(result);
			this._appendChildHandler(result);
		}
		return result;
	},
	/** @private */
	writePeakSubStructure: function(subStructure, peakElem, options)
	{
		var writer = this.getChildPeakStructureWriter();
		if (writer)
			writer.writeObj(subStructure, peakElem, options);
	},
	/** @private */
	_peakHashToCmlHash: function(peakHash)
	{
		var result = {};
		var basicFields = ['xValue', 'yValue'];
		for (var i = 0, l = basicFields.length; i < l; ++i)
		{
			var key = basicFields[i];
			var value = peakHash[key];
			if (Kekule.ObjUtils.notUnset(value))
			{
				result[key] = value;
			}
		}
		if (peakHash.xUnits)
			result.xUnits = CmlUtils.metricsUnitSymbolToCmlUnitStr(peakHash.xUnits);
		if (peakHash.yUnits)
			result.yUnits = CmlUtils.metricsUnitSymbolToCmlUnitStr(peakHash.yUnits);
		if (peakHash.shape)
			result.peakShape = CmlSpectUtils.kekulePeakShapeToCml(peakHash.shape);
		if (peakHash.multiplicity)
			result.peakMultiplicity = CmlSpectUtils.kekulePeakMultiplicityToCml(peakHash.multiplicity);
		if (peakHash.assignments && peakHash.assignments.length)
		{
			var atomIds = [], bondIds = [];
			for (var i = 0, l = peakHash.assignments.length; i < l; ++i)
			{
				var obj = peakHash.assignments[i];
				var currIds = (obj instanceof Kekule.AbstractAtom)? atomIds:
					(obj instanceof Kekule.ChemStructureConnector)? bondIds:
						null;
				if (currIds)
				{
					var id = (obj.getId && obj.getId()) || this.autoIdentifyForObj(obj);
					if (id)
						currIds.push(id);
				}
			}
			if (atomIds.length)
				result.atomRefs = atomIds.join(' ');
			if (bondIds.length)
				result.bondRefs = bondIds.join(' ');
		}
		return result;
	}
});

/**
 * Reader to read a <peakStructure> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlElementReader
 */
Kekule.IO.CmlSpectrumPeakStructureReader = Class.create(Kekule.IO.CmlElementReader,
/** @lends Kekule.IO.CmlSpectrumPeakStructureReader# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumPeakStructureReader',
	/** @ignore */
	doReadElement: function(elem, parentObj, parentReader, options)
	{
		var result = {};
		var attribs = Kekule.IO.CmlDomUtils.fetchCmlElemAttributeValuesToJson(elem, null, true, this.getDomHelper());
		var attribKeys = Kekule.ObjUtils.getOwnedFieldNames(attribs);
		for (var i = 0, l = attribKeys.length; i < l; ++i)
		{
			var key = attribKeys[i];
			var keyLower = key.toLowerCase();
			var value = attribs[key];
			// TODO: currently do not handle object ref in sub structures
			if (Kekule.IO.CML.ATOMS_REF_ATTRIBS.indexOf(key) >= 0 || Kekule.IO.CML.BONDS_REF_ATTRIBS.indexOf(key) >= 0)
				continue;
			if (keyLower === 'units')
			{
				result.unit = Kekule.IO.CmlUtils.cmlUnitStrToMetricsUnitSymbol(value) || Kekule.IO.CmlUtils.getCmlNsValueLocalPart(value);
			}
			else
				result[key] = value;
		}
		return result;
	}
});

/**
 * Writer to write a <peakStructure> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlElementWriter
 */
Kekule.IO.CmlSpectrumPeakStructureWriter = Class.create(Kekule.IO.CmlElementWriter,
/** @lends Kekule.IO.CmlSpectrumPeakStructureWriter# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumPeakStructureWriter',
	/** @ignore */
	doCreateElem: function(obj, parentElem)
	{
		return this.createChildElem('peakStructure', parentElem);
	},
	/** @ignore */
	doWriteObject: function(obj, targetElem, options)
	{
		var domHelper = this.getDomHelper();
		var keys = Kekule.ObjUtils.getOwnedFieldNames(obj);
		for (var i = 0, l = keys.length; i < l; ++i)
		{
			var key = keys[i];
			var value = obj[key];
			if (key === 'unit')
				value = CmlUtils.metricsUnitSymbolToCmlUnitStr(value);
			CmlDomUtils.setCmlElemAttribute(targetElem, key, value, domHelper);
		}
		return targetElem;
	},
});

/**
 * Reader to read a <xaxis>/<yaxis> element inside <spectrumData>.
 * @class
 * @augments Kekule.IO.CmlElementReader
 */
Kekule.IO.CmlSpectrumDataAxisReader = Class.create(Kekule.IO.CmlElementReader,
/** @lends Kekule.IO.CmlSpectrumDataAxisReader# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumDataAxisReader',
	/** @private */
	initProperties: function()
	{
		// a private property, stores the symbol of axis
		this.defineProp('axisSymbol', {'dataType': DataType.STRING, 'serializable': false});
		// a private property, stores the array object read from child <array> element
		this.defineProp('childArrayObj', {'dataType': DataType.OBJECT, 'serializable': false});
	},
	/** @private */
	doReadElement: function(elem, parentObj, parentReader, options)
	{
		var tagName = DU.getLocalName(elem).toLowerCase();
		var p = tagName.indexOf('axis');
		var symbol = tagName.substring(0, p);
		var dataMultiplier = DU.getSameNSAttributeValue(elem, 'multiplierToData', this.getDomHelper());
		if (dataMultiplier)
			dataMultiplier = parseFloat(dataMultiplier);
		this.setAxisSymbol(symbol);
		this.tryApplySuper('doReadElement', [elem, parentObj, parentReader]);
		this.iterateChildElements(elem, parentObj, parentReader);
		var result = {
			'symbol': this.getAxisSymbol(),
			'array': this.getChildArrayObj()
		};
		if (dataMultiplier)
			result.dataMultiplier = dataMultiplier;
		//console.log('read axis', tagName, result);
		return result;
	},
	/** @ignore */
	doReadChildElement: function(elem, parentObj, parentReader)
	{
		var tagName = DU.getLocalName(elem).toLowerCase();
		if (tagName === 'array')  // TODO: now we only handles the <array> element inside <axis>
		{
			//var reader = Kekule.IO.CmlElementReaderFactory.getReader(elem);
			var reader = this.doGetChildElementReader(elem);
			if (reader)
			{
				//this.copySettingsToChildHandler(reader);
				if (reader.setExpandSteppedArray)  // do not expand an array with start/end/size
					reader.setExpandSteppedArray(false);
				if (reader.setDefaultItemDataType)  // automatically convert the values in array to number
					reader.setDefaultItemDataType('xsd:float');
				var arrayObj = reader.readElement(elem, parentObj, parentReader);
				if (arrayObj)
				{
					this.setChildArrayObj(arrayObj);
				}
			}
		}
		else
			return this.tryApplySuper('doReadChildElement', [elem, parentObj, parentReader]);
	}
});

/**
 * Reader to read a <spectrumData> element inside <spectrum>.
 * The <spectrumData> element is used to hold the continous data in CMLSpect.
 * Usually, it should containing child element <xaxis> and <yaxis>.
 * @class
 * @augments Kekule.IO.CmlElementReader
 */
Kekule.IO.CmlSpectrumDataReader = Class.create(Kekule.IO.CmlElementReader,
/** @lends Kekule.IO.CmlSpectrumDataReader# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumDataReader',
	/** @private */
	doReadElement: function(elem, parentObj, parentReader, options)
	{
		if (parentObj instanceof Kekule.Spectroscopy.Spectrum)  // we need to set the variables to parent spectrum
		{
			//var result = new Kekule.Spectroscopy.SpectrumData();
			var result = new Kekule.Spectroscopy.SpectrumDataSection();
			parentObj.appendDataSection(result);
			//console.log(parentObj.getData(), parentObj.getData().getActiveSection() === result);
			//var result = this.tryApplySuper('doReadElement', [elem]);  // do not pass parentObj to it, since we will handle with the return values later
			var childResults = this.iterateChildElements(elem, parentObj, parentReader);
			this._handleChildResults(childResults, result);
			// append spectrumData to spectrum
			/*
			if (parentObj && parentObj instanceof Kekule.Spectroscopy.Spectrum)
				parentObj.setData(result);
			*/
			return result;
		}
		//else   // parent is not spectrum, use the default handling process inherited
		//	return this.tryApplySuper('doReadElement', [elem, parentObj, parentReader]);
	},
	/** @private */
	_handleChildResults: function(childResults, spectrumDataSectionObj)
	{
		var axisDataObjs = [];
		for (var i = 0, l = childResults.length; i < l; ++i)
		{
			var childResult = childResults[i];
			var childElem = childResult.element;
			var childElemTagName = DU.getLocalName(childElem).toLowerCase();
			if (childElemTagName.indexOf('axis') >= 0)  // is <xaxis>/<yaxis> child element, need to store the array values of it
			{
				if (childResult.result.symbol.toLowerCase() === 'x')  // ensure xaxis as the first item of axisDataObjs
					axisDataObjs.unshift(childResult.result);
				else
					axisDataObjs.push(childResult.result);
			}
		}
		if (axisDataObjs.length >= 2)   // we should have at least two axis to form a spectrum
			this._fillSpectrumData(axisDataObjs, spectrumDataSectionObj);
	},
	/** @private */
	_fillSpectrumData: function(axisDataObjs, spectrumDataSectionObj)
	{
		var spectrumObj = spectrumDataSectionObj.getParentSpectrum();
		var spectrumDataObj = spectrumObj.getData();
		var dataSize = 0;
		var axisVarDefParamList = [];
		var localVarSymbols = [];

		// get the var definition informations and calc the data size
		for (var i = 0, l = axisDataObjs.length; i < l; ++i)
		{
			var isIndependent = (i === 0);  // TODO: here we simply regard the first axis (x) as the independent var
			//var varDef = this._addSpectrumDataVariables(axisDataObjs[i], spectrumDataSectionObj, spectrumDataObj, spectrumObj, isIndependent);
			var axisVarDefParams = this._getAxisVarDefParams(axisDataObjs[i], isIndependent);
			axisVarDefParamList.push(axisVarDefParams)
			//spectrumDataObj.appendVariable(varDef);
			//localVarSymbols.push(varDef.getSymbol());
			//localVarSymbols.push(axisVarDefParams.symbol);
			//console.log('varDef', axisDataObjs[i], varDef, spectrumDataObj.getVariables());
			var size = axisDataObjs[i].array.size || (axisDataObjs[i].array.values && axisDataObjs[i].array.values.length);
			if (size > dataSize)
				dataSize = size;
		}

		// create var definitions and local settings
		var localVarSymbols = this._addSpectrumDataVarDefs(axisVarDefParamList, spectrumDataObj, spectrumObj); // add varDef to spectrum first
		spectrumDataSectionObj.setLocalVarSymbols(localVarSymbols);  // then set the local var infos
		this._setDataSectionLocalVarInfos(axisVarDefParamList, spectrumDataSectionObj);

		// then the data
		for (var i = 0; i < dataSize; ++i)
		{
			var dataItem = [];
			for (var j = 0, k = axisDataObjs.length; j < k; ++j)
			{
				var dataMultiplier = axisDataObjs[j].dataMultiplier || 1;
				var arrayValues = axisDataObjs[j].array.values;
				if (!arrayValues)  // a continuous var
					dataItem.push(undefined);
				else
					{
					dataItem.push(arrayValues[i] * dataMultiplier);
				}
			}
			spectrumDataSectionObj.appendData(dataItem);
		}
		spectrumDataSectionObj.setDataSorted(true);
	},
	/** @private */
	_getAxisVarDefParams: function(axisDataObj, isIndependent)
	{
		var symbol = axisDataObj.symbol;
		var initParams = {'symbol': symbol, 'dependency': isIndependent? Kekule.VarDependency.INDEPENDENT: Kekule.VarDependency.DEPENDENT};
		var extraInfo = {};
		var arrayObj = axisDataObj.array;
		var fieldNames = OU.getOwnedFieldNames(arrayObj);
		var hasExtraInfo = false;
		for (var i = 0, l = fieldNames.length; i < l; ++i)
		{
			var fname = fieldNames[i].toLowerCase();
			var value = arrayObj[fieldNames[i]];
			if (fname === 'unit' || fname === 'units')
			{
				initParams.unit = Kekule.IO.CmlUtils.cmlUnitStrToMetricsUnitSymbol(value);
				// if label not set, use unit text as the label
				// this rule is for unit like arbitrary, which do not has a metrics symbol (initParam.unit === ''),
				// setting a display label may help to recognize the graph
				if (!initParams.unit && !initParams.displayLabel)
					initParams.displayLabel = Kekule.IO.CmlUtils.getCmlNsValueLocalPart(value);
			}
			else if (fname === 'title')
			{
				initParams.name = value;
			}
			else if (fname === 'start' || fname === 'end' || fname === 'size' || fname === 'stepsize')
			{
				// do nothing here, we will handle this continous var info later
			}
			else if (fname === 'value' || fname === 'values' || fname === 'datatype')  // value of axis, no need to be handled in var definition part
			{

			}
			else
			{
				extraInfo[fieldNames[i]] = value;
				hasExtraInfo = true;
			}
		}
		var isContinuousVar = !arrayObj.values && Kekule.ObjUtils.notUnset(arrayObj.start) && Kekule.ObjUtils.notUnset(arrayObj.end);
		var continuousInfo;
		if (isContinuousVar)
		{
			continuousInfo = {'start': arrayObj.start, 'end': arrayObj.end};
		}

		return {
			'symbol': symbol,
			'initParams': initParams,
			'continuousInfo': continuousInfo,
			'hasExtraInfo': hasExtraInfo,
			'extraInfo': extraInfo
		};
	},
	/** @private */
	_addSpectrumDataVarDefs: function(axisVarDefParamList, spectrumDataObj, spectrumObj)
	{
		var varSymbols = [];
		for (var i = 0, l = axisVarDefParamList.length; i < l; ++i)
		{
			var varDefParams = axisVarDefParamList[i];
			var initParams = varDefParams.initParams;

			var varDef = Kekule.IO.CmlSpectUtils.getSpectrumVarDef(spectrumObj, initParams.symbol, initParams.unit, initParams.name, initParams.dependency);
			if (varDef && !varDef.getDisplayLabel() && initParams.displayLabel)
				varDef.setDisplayLabel(initParams.displayLabel);
			if (!varDef)
			{
				varDef = new Kekule.Spectroscopy.SpectrumVarDefinition(initParams);
				spectrumDataObj.appendVariable(varDef);
			}
			varSymbols.push(varDef.getSymbol());
		}
		return varSymbols;
	},
	/** @private */
	_setDataSectionLocalVarInfos: function(axisVarDefParamList, spectrumDataSection)
	{
		for (var i = 0, l = axisVarDefParamList.length; i < l; ++i)
		{
			var varDefParams = axisVarDefParamList[i];
			var varSymbol = varDefParams.symbol;
			var continuousInfo = varDefParams.continuousInfo;
			if (continuousInfo)
			{
				spectrumDataSection.setContinuousVarRange(varSymbol, continuousInfo.start, continuousInfo.end);
			}
			if (varDefParams.hasExtraInfo)
			{
				var extraInfo = varDefParams.extraInfo;
				var fnames = Kekule.ObjUtils.getOwnedFieldNames(extraInfo);
				for (var i = 0, l = fnames.length; i < l; ++i)
				{
					spectrumDataSection.setLocalVarInfoValue(varSymbol, fnames[i], extraInfo[fnames[i]]);
				}
			}
		}
	}
	/* @private */
	/*
	_addSpectrumDataVariables(axisDataObj, spectrumDataSection, spectrumDataObj, spectrumObj, isIndependent)
	{
		// fill the variables of spectrumData
		var axisVarDefInfos = this._getAxisVarDefParams(axisDataObj, isIndependent);
		var initParams = axisVarDefInfos.initParams;
		var extraInfo = axisVarDefInfos.extraInfo;
		var hasExtraInfo = axisVarDefInfos.hasExtraInfo;

		var varDef = Kekule.IO.CmlSpectUtils.getSpectrumVarDef(spectrumObj, initParams.symbol, initParams.unit, null, initParams.dependency);
		if (varDef && !varDef.getDisplayLabel() && initParams.displayLabel)
			varDef.setDisplayLabel(initParams.displayLabel);
		if (!varDef)
		{
			varDef = new Kekule.Spectroscopy.SpectrumVarDefinition(initParams);
			spectrumDataObj.appendVariable(varDef);
		}

		// set extra info at section level, avoid affecting the global settings in spectrumData
		if (hasExtraInfo)
		{
			var fnames = Kekule.ObjUtils.getOwnedFieldNames(extraInfo);
			for (var i = 0, l = fnames.length; i < l; ++i)
			{
				spectrumDataSection.setLocalVarInfoValue(varDef.getSymbol(), fnames[i], extraInfo[fnames[i]]);
			}
		}
		var isContinuousVar = !arrayObj.values && arrayObj.start && arrayObj.end;
		if (isContinuousVar)
		{
			//spectrumDataObj.setContinuousVarRange(varDef, arrayObj.start, arrayObj.end);
			spectrumDataSection.setContinuousVarRange(varDef, arrayObj.start, arrayObj.end);
		}
		return varDef;
	}
	*/
});

/**
 * Writer to write a <spectrumData> element inside <spectrum>.
 * @class
 * @augments Kekule.IO.CmlSpectrumDataSectionBaseWriter
 */
Kekule.IO.CmlSpectrumDataWriter = Class.create(Kekule.IO.CmlSpectrumDataSectionBaseWriter,
/** @lends Kekule.IO.CmlSpectrumDataWriter# */
{
	/** @private */
	CLASS_NAME: 'Kekule.IO.CmlSpectrumDataWriter',
	/** @ignore */
	doCreateElem: function(obj, parentElem)
	{
		return this.createChildElem('spectrumData', parentElem);
	},
	/** @ignore */
	doWriteObject: function(obj, targetElem, options)
	{
		return this.writeSpectrumData(obj, targetElem, options);
	},
	/** @private */
	writeSpectrumData: function(spectrumDataSection, targetElem, options)
	{
		//var varInfos = spectrumDataSection.getActualLocalVarInfos();
		var dataVarInfo = this.getSpectrumDataSectionVarInfos(spectrumDataSection);
		if (dataVarInfo.varCount < 2)  // less than two vars, illegal
		{
			// TODO: error message here?
		}
		else  // output data axis
		{
			var keys = ['independent', 'dependent'];
			var arrays = [];
			for (var i = 0, l = keys.length; i < l; ++i)
			{
				var key = keys[i];
				var isIndep = (key === 'independent');
				var arrayObj = {
					'_tagName': isIndep? 'xaxis': 'yaxis',
					'varSymbol': dataVarInfo[key].symbol,
					'unit': dataVarInfo[key].unitSymbol,
					'title': dataVarInfo[key].name,
					'dataType': DataType.FLOAT,
					'size': DataType.count || spectrumDataSection.getDataCount()
				};
				var range = dataVarInfo[key].range;
				if (range)
				{
					arrayObj.start = range.fromValue;
					arrayObj.end = range.toValue;
					arrayObj.isContinuous = true;
				}
				else
					arrayObj.values = [];
				arrayObj = this._prepareUnitConversionInfoForArrayObj(arrayObj, isIndep, spectrumDataSection, options);
				arrays.push(arrayObj);
			}

			// collect array values
			var decimalCount = (options && options.spectrumDataValueOutputPrecisionCount) || 0;
			spectrumDataSection.forEach(function(value, index){
				for (var i = 0, l = arrays.length; i < l; ++i)
				{
					var needUnitConversion = arrays[i]._originUnitObj && arrays[i]._unitObj;
					if (!arrays[i].isContinuous)  // bypass continuous range vars
					{
						var symbol = arrays[i].varSymbol;
						// TODO: here we simple convert the unavailable value (NaN or undefined) to 0, is it safe?
						var dvalue = value[symbol] || 0;
						if (needUnitConversion)  // need to do unit conversion
						{
							dvalue = arrays[i]._originUnitObj.convertValueTo(dvalue, arrays[i]._unitObj);
						}
						//var allowedError = allowedErrorRate? dvalue * allowedErrorRate
						arrays[i].values.push(CmlSpectUtils.floatToCmlString(dvalue, decimalCount));
					}
				}
			});
			// write values to element
			var arrayWriter = this.doGetChildObjectWriter(DataType.ARRAY, spectrumDataSection, this);
			if (arrayWriter)
			{
				for (var i = 0, l = arrays.length; i < l; ++i)
				{
					var arrayObj = arrays[i];
					var axisElem = this.createChildElem(arrayObj._tagName, targetElem);
					arrayWriter.writeObject(arrayObj, axisElem, options);
				}
			}
		}
	},
	/** @private */
	_prepareUnitConversionInfoForArrayObj: function(arrayObj, isIndep, spectrumDataSection, options)
	{
		var spectrum = spectrumDataSection.getParentSpectrum();
		if (isIndep && spectrum && spectrum.getSpectrumType() === Kekule.Spectroscopy.SpectrumType.NMR && options.autoConvertNmrDataFreqToUnit)
		{
			var unitObj = arrayObj.unit && Kekule.Unit.ge