//   secondary_structure_prediction_HTML_config_loader.js

//   This is the code that finds the 

//   Secondary Structure Prediction Mason Viewer Divs and gets the 

//   data for creating for the Secondary Structure Prediction Prediction viewer


//   Depends on jquery, Modernizr SVG support detection



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

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

"use strict";


//jQuery method of running code when page is loaded

$(document).ready( function(){
	
	//  Run on a separate event so an error 
	//  doesn't stop anything else from running on document ready.

	setTimeout(function(){
	
	
		var $mason_viewer_secondary_structure_prediction = $(".mason-viewer-secondary-structure-prediction");

		if ( $mason_viewer_secondary_structure_prediction.length === 0 ) {

			throw "No HTML elements with class of 'mason-viewer-secondary-structure-prediction' to process";
		}


		$mason_viewer_secondary_structure_prediction.each( function( index, Element ) {

			var rootElement = this;

			//  Run creating each viewer on a separate event so an error in one
			//  doesn't stop anything else from running on document ready.

			setTimeout(function(){

				var $masonViewerRootDiv = $(rootElement);

				//  "#svg-not-supported" specifies id of div on page that will be shown if SVG is not supported.
				//  $svg_not_supported.show();  is called.

				var $svg_not_supported = $(".mason-viewer-svg-not-supported");

				var $mason_viewer_failed_to_create = $(".mason-viewer-secondary-structure-prediction-failed-to-create");

				var $mason_enclosing_div = $masonViewerRootDiv.closest(".mason-enclosing-div");

				if ( $mason_enclosing_div.length !== 0 ) {

					$svg_not_supported = $mason_enclosing_div.find(".mason-viewer-svg-not-supported");

					$mason_viewer_failed_to_create = $mason_enclosing_div.find(".mason-viewer-disordered_regions-failed-to-create");
				}


				var secondary_structure_prediction_file_uri = $masonViewerRootDiv.attr("secondary_structure_prediction_file_uri");

				var sequence_file_uri = $masonViewerRootDiv.attr("sequence_file_uri");

				var sequence = $masonViewerRootDiv.attr("sequence");

				if ( secondary_structure_prediction_file_uri === undefined || secondary_structure_prediction_file_uri === null || 
						secondary_structure_prediction_file_uri === "" ) {


					$mason_viewer_failed_to_create.show();

					throw "secondary_structure_prediction_file_uri must have a value";
				}


				if ( ( sequence_file_uri === undefined || sequence_file_uri === null || 
						sequence_file_uri === "" ) &&
						( sequence === undefined || sequence === null || 
								sequence === "" ) ) {


					$mason_viewer_failed_to_create.show();

					throw "sequence or sequence_file_uri must have a value";
				}

				if ( sequence === undefined || sequence === null || 
						sequence === "" ) {

					sequence = undefined; // standardize value for further processing
				}


				var create_MasonViewer_SecondaryStructure_Pre_Built_ConstructorParams =
				{ config: 
				{ 

					secondary_structure_prediction_file_uri: secondary_structure_prediction_file_uri,
					sequence_file_uri: sequence_file_uri,
					sequence: sequence,


					$masonViewerRootDiv: $masonViewerRootDiv,
					$svgNotSupportedDiv: $svg_not_supported,
					$mason_viewer_failed_to_create: $mason_viewer_failed_to_create } };

				var create_MasonViewer_SecondaryStructure_Pre_Built = new Create_MasonViewer_SecondaryStructure_Pre_Built( create_MasonViewer_SecondaryStructure_Pre_Built_ConstructorParams );

				create_MasonViewer_SecondaryStructure_Pre_Built.createCoverageMapIfNotCreated();


			}, 10);


		});

	}, 10);

	
});