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Class Biojs.Tree


Version 1.0.0.

Extends Biojs.

Defined in: Biojs.Tree.js.

Class Summary
Constructor Attributes Constructor Name and Description
 
Biojs.Tree(options)
Tree component
Field Summary
Field Attributes Field Name and Description
<inner>  
Array containing the supported event names
<inner>  
opt
Default values for the options
Method Summary
Method Attributes Method Name and Description
 
constructor(options)
Methods borrowed from class Biojs:
addListener, extend, getId, listen, raiseEvent, removeListener, setEventHandlers, setOptions
Class Detail
Biojs.Tree(options)
Tree component
Author: Fabian Schreiber.
			var alignment_file = "../biojs/data/tree/just_sequences.json";
			var domain_file = "../biojs/data/tree/just_domains.TF105041.json";
			var model_json_tree = "../biojs/data/tree/TF105041_model.json";

			var image_path = "../biojs/data/tree/images/species_files/";
			//var highlight_gene = "ENSBTAP00000001311";
			var highlight_gene = "";
			//var newick_tree = "../data/trees/newick_tree.nh";
			var newick_tree = "";
			var load_from_variable = 0;
		    var json_tree_string;

myTree = new Biojs.Tree({
			        target : "YourOwnDivId",
					formatOptions : {
						tree:'json'
			  		},
					// tree parameters
				    json_tree : model_json_tree, 
					alignment_file : alignment_file,
					show_real_branchlength : "false",
					annotation_option : "seq_domains",
					domains_file : domain_file,
				    two_window : true,
				    image_path : image_path,
				    highlight_gene : highlight_gene,
				    json_tree_string : json_tree_string,
				    load_from_variable : load_from_variable,
			});
Parameters:
{Object} options
An object with the options for Tree component.
Options detailed:
{string} target
Identifier of the DIV tag where the component should be displayed.
{file} tree
JSON that contains the tree information.
 
   [
   	// 
   	{ name: <name>, 
		  display_label: <display_label>,
		  duplication: <duplication>,
		  branch_length: <endVal1>,
		  common_name: <common_name>,
		  seq_length: <seq_length>,
		  type: <type>,
		  uniprot_name: <uniprot_name>,

		  children: []},
   	//
   	// Any others nodes
   	...,  
   	// 
   ]
 
tree : [
		{"name":"Amniota_1","branch_length":"0.2212","binary_alignment":"N/A","children": [..]
		,"common_name":"Chicken","seq_length":3397,"swissprot_gene_name":"N/A","display_label":"BRCA2"}
	   ]
{file} domains_file
Set of annotations for the leaves of the tree. Must be an array of objects following the syntax:
           [ 
             // An annotation:
             { name: <name>, 
               species_name: <message>, 
               alignment_length: <message>, 
               seq_length: <message>, 
               cigar_string: <color_code>, 
               domains: [{ name: name; domain_start: <startVal1>, domain_end: <endVal1> id: <HTMLColor> name : name}, ...,{ start: <startValN>, end: <endValN>, color: <HTMLColor>}] 
             }, 
             
             // ...
             // more annotations here 
             // ...
           ]
   		 
 
tree : [
		{
       "cigar_string" : "4D22MD23M3D10MD13M2D44M2D23M3D7MD13M11D16MD57M5D27MD26M2D3M9D8MD9M2D3MD12MD11M2D10M3D3MD2MDMD9MD19M4D2MD17MD10MD24M5D7MD3MD24MD19MD10M3D6M10D26M6D5M2D17M12D11M2D10M2D52M2D7M2D12MD7M5D22M2D4M2D10M3D46MD20MD6M4D4M2D3M3DM2D11M4D4MDM2D4MDMD3MD5M4D5MD9M5D5M2DM7D18M3D5MD2MD6MD21MD5MDM2D6MDMD2MD23MD9M5D19M7D3M2D19MD2MD7M7D14M5D13MD9MD7M3D45MD7M2D4M3D7M8D3M13D2M12D3M5D4MD35MD44M3D2M2D18M15D17MD18M8D4M8DMD21MD36MD17MD2MD25M2D19MD6MD2MD3MD12M6D12MD21M4D11MD17MD18M2D79MD55M2D18M2D30M4D5MD5MD8MD11MD23MD42M8D26M4DMD25MD6M5D7M2D6M2D3MD15M6DMD14MD32M10D3MD6M5D43M3D13MD21MD6MD6M3D3MD8MD10M7D11M4D23M10D44MD12M5D4MDM3D19M13D34MD4MD15MD2MD6MD53M4D2MD10MD38MD13MD25MD104M3D62M2D15M5D5M6D37M2D6MDMD234MD3MD162MD11M2D30M2D45MD20MD2MD100M13D25M4D20M4D78M8D62MD38MD2MD8MD3MD4MD5MD41MD3MD4M16D11M2DM3D38M2D",
    "species_name" : "Ailuropoda_melanoleuca",
    "alignment_length" : 4010,
    "domains" : [ ..]
    "seq_length" : 3460,
    "name" : "ENSAMEP00000009909"}
	   ]
where:
  • name is the unique name corresponding to an id in the tree
  • species_name the species the annotation belong to.
  • alignment_length the length of the alignment sequence
  • seq_length the length of the sequence
  • domains array of objects defining the intervals which belongs to the annotation.
  • domains[i].domain_start domain's start position
  • domains[i].domain_end domain's stop position.
  • domains[i].name name of the domain, e.g. BRCA-2_OB1
  • .
  • domains[i].id the domain's id in the source database. Here, e.g. PF09103.5
  • domains[i].evalue the domains evalue
{string} image_path
Path to directory which contains species images.
{string} [annotation_option="seqDomains"]
The display format for the annotations.
{boolean} [two_windows]
specifies whether the tree and the annotations should be printed into the same div/svg or separate
{string} [highlight_gene]
Gene identifier to be highlighted.
Requires:
jQuery Core 1.9.2
jQuery Tipsy
D3
Additional tree functions
BioJS Tree css
jQuery Tipsy
Field Detail
<inner> eventTypes
Array containing the supported event names

<inner> opt
Default values for the options
Method Detail
constructor(options)
Parameters:
options

Documentation generated by JsDoc Toolkit 2.3.2 on Thu Apr 17 2014 17:42:43 GMT+0100 (BST)