if (Application === "undefined" || !Application) {

    var Application = {};

}

InputMotif = function(containerId, options) {

    new Application.ManualInputMotif(containerId, options);

};

Application.ManualInputMotif = function() {

    this._init.apply(this, arguments);

};

Application.ManualInputMotif.prototype = {

    _manulaMotifInputAreaId : null,

    _manulaMotifInputAreaInsertButId : null,

    _manulaMotifInputAreaAddButId : null,

    _manulaMotifDialogCancelButId : null,

    _containerId : null,

    _baseSequence : null,

    _workId : null,

    _fileName : null,

    _errorMessageAreaClass : null,

    _motifProperty : null,

    _geneInfoContainerId : null,

    _callBackFunc : null,

    _motifView : null,

    _appSequence : null,

    _appUtil : null,

    _fixedSequence : null,

    _validCharcters : ['A','T','C','G','-'],

    defaults : {

        motifSequenceProperty : "motif sequence",

        motifPositionProperty : "motif position",

        replaceSequenceClass : "replaceSequence",

        resultAreaClass : "resultArea",

        databaseInfoClass : "databaseInfo",

        errorMessageAreaClass : "errorMessage",

        replaceButtonAreaClass : "replaceButtonArea",

        geneLabelClass : "geneUrl",

        fixedSequenceShowClass : "fixedSequenceMotif",

        wrappedMotifSequenceShowClass : "wrappedSequenceMotif",

        baseSequenceLength : 550,

        baseSequenceMinLength : 50,

        resultAreaUserMessage : "Scroll Left/Right to inspect motifs from this promoter. Click on a motif sequence to enter the advanced motif view.",

        resultAreaUserMessageClass : "resultAreaUserMessageClass",

        conflictionDialogTitle : "Confliction",

        nonValidCharcterErrorMessage : "Warning: Motif contains nonstandard characters for DNA design. All characters except A, T, C, G will be treated as unique special characters. Currently IUPAC codes are not supported.",

        invalidCharErrMessageClass : "invalidCharError"

    },

    _initDefaults : function() {

        var date = new Date();

        this._manulaMotifInputAreaId = "_manulaMotifMotif_Div_" + self._containerId + "_" + date.getTime();

        this._manulaMotifInputAreaInsertButId = "_manulaMotifMotif_Div_Insert_But_" + this._containerId;

        this._manulaMotifInputAreaAddButId = "_manulaMotifMotif_Div_Add_But_" + this._containerId;

    },

    _initMotifView : function() {

        var self = this;

        var obj = {

            baseSequenceMinLength : self.defaults.baseSequenceMinLength,

            baseSequence : self._baseSequence,

            replaceSequenceClass : self.defaults.replaceSequenceClass,

            callerObj : self,

            geneLabelClass : self.defaults.geneLabelClass,

            motifMethod : '-'

        };

         this._motifView = new Application.MotifView(this._containerId,obj);

    },

    _initAppUtil : function() {

        var self = this;

        var obj = {

            containerId : self._containerId,

            errTextClass : 'errorText',

            baseSequenceMinLength : self.defaults.baseSequenceMinLength,

            baseSequenceLength : self.defaults.baseSequenceLength

        }

        self._appUtil = new Application.Util(obj);

    },

    _init : function(containerId, options) {

        var date = new Date();

        this._containerId = containerId;

        this._baseSequence = options.baseSequence;

        this._workId = options.workId;

        this._fileName = options.fileName;

        this._callBackFunc = options.callback;

        this._fixedSequence = options.fixedSequence;

        this._geneInfoContainerId = "gene_info_containerId_" + date.getTime();

        this._initDefaults();

        $("#" + this._containerId).html("");    

        this._initManualMotifComps();

        this._initManualMotifCompButtons();

        this._initConflictConfirmDialogView();

        this._initMotifConflictConfirmDialog();

        var obj = {

            workId : options.workId,