//   secondary_structure_prediction_creator.js

//   This is the code that initiates

//   the creation of the Mason Viewer

//   for the Secondary Structure Prediction viewer on the page 


//   Depends on jquery, Modernizr SVG support detection



//////////////////////////////////

// JavaScript directive:   all variables have to be declared with "var", maybe other things

"use strict";



 //  constructor
var Create_MasonViewer_SecondaryStructure_Pre_Built = function( params ) {


	this.coverageMapCreated = false; //

	this.masonViewers = undefined;


	this.config = params.config;

	this.$masonViewerRootDiv = this.config.$masonViewerRootDiv;

	if ( this.config.$masonViewerRootDiv === undefined || this.config.$masonViewerRootDiv === null ) {
		
		throw "invalid config, config.$masonViewerRootDiv === undefined or null";
	}
	
	if ( this.config.$masonViewerRootDiv.length === 0 ) {
		
		throw "invalid config, config.$masonViewerRootDiv.length === 0, no HTML elements found";
	}
	
	if ( this.config.$masonViewerRootDiv.length > 1 ) {
		
		throw "invalid config, config.$masonViewerRootDiv.length > 1, more than one HTML element found";
	}

	
};




Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.VIEWER_ROW_LABEL = "Secondary Struct.";  

	
Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.SECONDARY_STRUCTURE_TYPE_CONSTANTS = {
		
			 BETA_SHEET : "E",
			 ALPHA_HELIX : "H",

	};
	

	


/////////////

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.isCoverageMapCreated = function(  ) {

	return this.coverageMapCreated;
};


/////////////

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.setCoverageMapCreated = function( param ) {

	this.coverageMapCreated = param;
};



Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.createCoverageMapIfNotCreated = function(  ) {

	if ( ! this.isCoverageMapCreated() ) {

		this.createCoverageMap();
	}


};



//////////////////////////////

//

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.createCoverageMap = function(  ) {

	var objectThis = this;

	var svgSupport = Modernizr.svg;

	if ( ! svgSupport ) {  //  is false if SVG not supported


		var $svgNotSupported = this.config.$svgNotSupportedDiv;

		$svgNotSupported.show();
		
//		this.$root_block.hide();


		return null;
	}



	if ( this.config.sequence !== undefined ) {
		
		var callbackFcnParam = { data: this.config.sequence };
		
		objectThis.createCoverageMapMain( callbackFcnParam );
		
	} else {
	
		var loadMatchingProteinSequenceParams = {


				sequence_file_uri: this.config.sequence_file_uri,

				callbackFcn: function( callbackFcnParam ) {

					objectThis.createCoverageMapMain( callbackFcnParam );
				}
		};

		objectThis.loadMatchingProteinSequence( loadMatchingProteinSequenceParams );
	
	}

};



Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.createCoverageMapMain = function( param ) {


	var objectThis = this;




	//  Create context for the AJAX call back
	var context = { proteinSequenceData: param.data  };



	var serviceURL = this.config.secondary_structure_prediction_file_uri;
	

	$.ajax(
		{ url : serviceURL,

			success :  function( data ) {

				objectThis.createCoverageMapMainProcessResponse( { data: data, context: context } );



			},
			statusCode: {
				404: function() {

//					$noDataFoundDiv.show();
					
					objectThis.config.$mason_viewer_failed_to_create.show();
					
					throw "data file not found: " + serviceURL;
				}
			},
			error: function(jqXHR, textStatus, errorThrown) {

//				alert("AJAX error file Disordered Regions file: " + serviceURL );			

				objectThis.config.$mason_viewer_failed_to_create.show();
					
				throw "error retrieving data file: " + serviceURL + ", jqXHR: " + jqXHR;

			},
//			data: ajaxData,  //  The data sent as params on the URL
			dataType : "text"
		});

};


////////////////////////////////

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.createCoverageMapMainProcessResponse = function( param ) {



	var objectThis = this;

	var calledContext = param.context;


	var calledContext = param.context;
	
	var proteinSequenceData = calledContext.proteinSequenceData;

	var secondaryStructureDataFileFromServer = param.data;


	try {
		var $rootDivPeptide_coverage = this.$masonViewerRootDiv;

//		var $rootDivPeptide_coverage = this.$root_block.find(".peptide-coverage-viewer");


		var createMasonViewerInputDataParams = { secondaryStructureDataFileFromServer: secondaryStructureDataFileFromServer, 
				proteinSequenceData: proteinSequenceData };
		
		var masonViewerInputData = this.createMasonViewerInputData( createMasonViewerInputDataParams );

		
		var requestParams = { inputData: masonViewerInputData };
		
		var configParams = {};

		
		var callbackFunctionsObj = masonViewer_SecondaryStructure_Pre_Built_CallbacksCreator( { config: null } );



		var masonViewer = MasonViewer.createMasonViewer( $rootDivPeptide_coverage, requestParams, configParams, callbackFunctionsObj );

		if ( this.config.masonViewerRegistry ) {
			
			//   itemKey has to be unique across all the viewers registered with a specific registry
			this.config.masonViewerRegistry.addMasonViewer( { itemKey: "secondaryStructure", masonViewer: masonViewer } );
		}

		this.masonViewers = { masonViewer: masonViewer };
		
		this.setCoverageMapCreated( true );

		return this.masonViewers;

	} catch ( error ) {


		this.config.$mason_viewer_failed_to_create.show();
		
		throw error;

	} finally {


	}

};


////////////////////////////////////

//        Take the SecondaryStructure data from the SecondaryStructure web app and reformat as needed for the Mason coverage viewer

//            Always have one row, even if empty

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.createMasonViewerInputData = function( param  ) {


	var secondaryStructureDataFileFromServer = param.secondaryStructureDataFileFromServer;
	
	var proteinSequenceLength = param.proteinSequenceData.length;
	

	
	var blockItems = new Array();
	
	var masonViewerInputData 
		= { maxSequenceLength: proteinSequenceLength , 
			rowItems: [ { label: this.VIEWER_ROW_LABEL, blockItems: blockItems } ]
			
		  };
	
	

	//		Javascript to convert all line endings to \n

	secondaryStructureDataFileFromServer = secondaryStructureDataFileFromServer.replace(/(\r\n|\r|\n)/g, '\n');

	//    Split into an array of lines
	
	var dataLines = secondaryStructureDataFileFromServer.split(/\n/g);


	var prevType = "";
	
	var startPositionInitializationValue = -1;
	
	var startPosition = startPositionInitializationValue;
	var endPosition = startPositionInitializationValue;

	for ( var lineIndex = 0; lineIndex < dataLines.length; lineIndex++ ) {
		
		var dataLine = dataLines[ lineIndex ];
		
		if ( dataLine.length === 0 || dataLine.charAt( 0 ) === "#"  ) {
			
			continue;
		}
		
		//  dataline:  "   1 M C   1.000  0.000  0.000",  after split, index zero === "", index 1 === "1", index 2 === "M", ...
		
		var dataLineSplit = dataLine.split(/\s+/g);

		
		var type = dataLineSplit[ 3 ];
		
		if ( type === this.SECONDARY_STRUCTURE_TYPE_CONSTANTS.BETA_SHEET || type === this.SECONDARY_STRUCTURE_TYPE_CONSTANTS.ALPHA_HELIX ) {

		
			var positionString = dataLineSplit[ 1 ];
			
			var position = parseInt( positionString, 10 );
			
			if ( isNaN( position ) ) {
				
				throw "Position parse failed for position string: |" + positionString + "|, dataLine: " + dataLine;
			}
			
			if ( type !== prevType || position > ( endPosition + 1 )  ) {
				
				if ( startPosition !== startPositionInitializationValue ) {
					
					//  not first group so save this group
					
					this.addGroupToArray( { blockItems: blockItems, startPosition: startPosition, endPosition: endPosition, type: prevType  } );
				}
									
				startPosition = position;
			}
			endPosition = position;

			prevType = type;

		}
		
		
	}
	
					
	if ( startPosition !== startPositionInitializationValue ) {

		//  add last group
		
		this.addGroupToArray( { blockItems: blockItems, startPosition: startPosition, endPosition: endPosition, type: prevType  } );
	}
	
	

//   Input format to viewer core
//
//	var inputData
//		= {"maxSequenceLength": 255,
//			"rowItems": [
//							{"label":"BBpilabel1",
//							"blockItems": [
//											{
//											"blockData":{"level":42,"id":85,"otherData":"TheOtherData"},
//											"startPos":25,
//											"endPos":37
//											}
//										]
//							}
//						  ]
//			}

	
	return masonViewerInputData;
};



///////////////////////////////////

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.addGroupToArray = function( param ) {
	
	var blockData = { type: param.type };

	var blockItem = { startPos: param.startPosition , endPos: param.endPosition , blockData: blockData };

	param.blockItems.push( blockItem );
	
};




///////////////////////////////////

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.loadMatchingProteinSequence = function ( param ) {

	var objectThis = this;
	
	var sequence_file_uri = param.sequence_file_uri;

	var context = { callbackFcn : param.callbackFcn };




	var serviceURL = sequence_file_uri;

	$.ajax(
			{ url : serviceURL,

				success :  function( data ) {

					objectThis.loadMatchingProteinSequenceProcessResponse( { data: data, context: context } );

//					var timeTrackingDiffViewersCreated = (new Date).getTime() - startTimeTracking;

//					alert( "timeTrackingDiffDataRetrieved: " + timeTrackingDiffDataRetrieved + ", timeTrackingDiffViewersCreated: " + timeTrackingDiffViewersCreated );


				},
				statusCode: {
					404: function() {

//						alert("File not found: " + serviceURL );
						
						objectThis.config.$mason_viewer_failed_to_create.show();
						
						throw "data file not found: " + serviceURL;
					}
				},
				error: function(jqXHR, textStatus, errorThrown) {

//					alert("Error loading file: " + serviceURL );
					
					objectThis.config.$mason_viewer_failed_to_create.show();
					
					throw "Error loading file: " + serviceURL;


				},
				dataType : "text"
			});



};



///////////////////////////////////

Create_MasonViewer_SecondaryStructure_Pre_Built.prototype.loadMatchingProteinSequenceProcessResponse = function( param ) {

	var data = param.data;

	var context = param.context;

	var callbackFcn = context.callbackFcn;


	var callbackFcnParam = { data: data };

	callbackFcn( callbackFcnParam );

};