AnnoJ.DataTypes.GeneModels

Data structure for gene models with one nesting level for sub-components
Model types are differentiated by a class name that maps directly to CSS

Note: Gene model data may be presented in a flat form (think tab-delimited) or a nested form (think XML). Although both data structures are shown here, the gene models plugin currently only uses the flat form.

Flat Structure

		var AD = AnnoJ.DataTypes;
		
		AD.Models = [
			AD.ModelComponent
		];
		AD.ModelComponent = [
			0 : AD.TinyText,    // parent id, null for no parent
			1 : AD.TinyText,    // component id
			2 : AD.Strand,      // strand
			3 : AD.TinyText,    // class
			4 : AD.PositiveInt, // start
			5 : AD.PositiveInt  // length
		];

Flat Example

		var response = {
			success : true,
			message : 'Found 2 models',
			data : [
				[null,"AT1G01010.1","+","mRNA",3631,2269],
				["AT1G01010.1","f3","+","five_prime_UTR",3631,129],
				["AT1G01010.1","f6","+","CDS",3760,154],
				["AT1G01010.1","f7","+","CDS",3996,281],
				["AT1G01010.1","f9","+","CDS",4486,120],
				["AT1G01010.1","f11","+","CDS",4706,390],
				["AT1G01010.1","f13","+","CDS",5174,153],
				["AT1G01010.1","f15","+","CDS",5439,192],
				["AT1G01010.1","f17","+","three_prime_UTR",5631,269],
				[null,"AT1G01030.1","-","mRNA",11649,2066],
				["AT1G01030.1","f240756","-","three_prime_UTR",11649,215],
				["AT1G01030.1","f240755","-","CDS",11864,1077],
				["AT1G01030.1","f240754","-","five_prime_UTR",12941,233],
				["AT1G01030.1","f240752","-","five_prime_UTR",13335,380]
			]
		};

Nested Structure

		var AD = AnnoJ.DataTypes;
		
		AD.Models = [
			AD.Model
		];
		AD.Model = [
			0 : AD.TinyText,    // model id
			1 : AD.Strand,      // strand
			2 : AD.TinyText,    // class
			3 : AD.PositiveInt, // start
			4 : AD.PositiveInt, // length
			5 : AD.ModelComponents
		];
		AD.ModelComponents = [
			0 : AD.TinyText,    // component id
			1 : AD.TinyText,    // class
			2 : AD.PositiveInt, // start
			3 : AD.PositiveInt  // length
		];

Nested Example

		var response = {
			success : true,
			message : 'Found 3 models',
			data : [
				//model: id, strand, class, start, length
				['AT1G01010.1', '+', 'mRNA', 3631, 2269,
					[
						//component: id, class, start, length
						['f3' , 'UTR5', 3631, 129],
						['f6' , 'CDS' , 3760, 154],
						['f7' , 'CDS' , 3996, 281],
						['f9' , 'CDS' , 4486, 120],
						['f11', 'CDS' , 4706, 390],
						['f13', 'CDS' , 5174, 153],
						['f15', 'CDS' , 5439, 192],
						['f17', 'UTR3', 5631, 269]
					]
				],
				['AT1G01020.1', '-', 'mRNA', 6790, 1948, []],
				['AT1G01020.2', '-', 'mRNA', 6790, 1948,
					[
						['f240748', 'UTR3', 6790, 280]
					]
				]
			]
		};