// JavaScript Document
/**
* load the xml alignment file fom the server
*/
function ajaxCall(url,callback){
var http_request = false;
if (window.XMLHttpRequest) {
http_request = new XMLHttpRequest();
} else if (window.ActiveXObject) { // IE.
try {
http_request = new ActiveXObject("Msxml2.XMLHTTP");
} catch (e) {
try {
http_request = new ActiveXObject("Microsoft.XMLHTTP");
} catch (e) {}
}
}
http_request.open('GET', url, true);
http_request.onreadystatechange = function(){
if (http_request.readyState == 4) {
if (http_request.status == 200) {
if(http_request.responseXML && http_request.responseXML.contentType=="text/xml"){
callback(http_request.responseXML);
}else
if(http_request.responseText){
callback(http_request.responseText);
}else
alert("error");
}else
alert("error");
}
}
http_request.send(null);
}
//------------------------------------------------------------------------------------------
// AJAX FUNCTION TO CREATE A http_resquest OBJECT // WHICH WILL FACILITATE THE PARSING OF XML FILES
//------------------------------------------------------------------------------------------
function ajax()
{
if (window.XMLHttpRequest) { // Mozilla, Safari,...
http_request = new XMLHttpRequest();
if (http_request.overrideMimeType) {
http_request.overrideMimeType('text/xml');
}
} else if (window.ActiveXObject) { // IE
try {
http_request = new ActiveXObject("Msxml2.XMLHTTP");
} catch (e) {
try {
http_request = new ActiveXObject("Microsoft.XMLHTTP");
} catch (e) {}
}
}
if (!http_request) {
alert('Giving up :( Cannot create an XMLHTTP instance');
return false;
}
if(query_id_null == 1)
{
document.getElementById("system_information").innerHTML = "Please enter a \"Protein ID\" to start to use Dasty2.";
}
else
{
if(use_das_registry == true)
{
makeDasRegistryRequest();
}
else
{
das_registry_label = [];
das_registry_label.push("any");
createLabelOptions(das_registry_label, "feature_label_list_select");
makeSequenceRequest();
}
}
}
function ajax_feature(featureXML_num)
{
if (window.XMLHttpRequest) { // Mozilla, Safari,...
feature_http_request[featureXML_num] = new XMLHttpRequest();
if (feature_http_request[featureXML_num].overrideMimeType) {
feature_http_request[featureXML_num].overrideMimeType('text/xml');
}
} else if (window.ActiveXObject) { // IE
try {
feature_http_request[featureXML_num] = new ActiveXObject("Msxml2.XMLHTTP");
} catch (e) {
try {
feature_http_request[featureXML_num] = new ActiveXObject("Microsoft.XMLHTTP");
} catch (e) {}
}
}
if (!feature_http_request[featureXML_num]) {
alert('Giving up :( Cannot create an XMLHTTP instance');
return false;
}
}
// "ajax_elements(num)" not in uset yet
function ajax_elements(num)
{
// num 0 = sequence
// num 1 = stylesheet
// num 2 = das_registry
if (window.XMLHttpRequest) { // Mozilla, Safari,...
elements_http_request[num] = new XMLHttpRequest();
if (elements_http_request[num].overrideMimeType) {
elements_http_request[num].overrideMimeType('text/xml');
}
} else if (window.ActiveXObject) { // IE
try {
elements_http_request[num] = new ActiveXObject("Msxml2.XMLHTTP");
} catch (e) {
try {
elements_http_request[num] = new ActiveXObject("Microsoft.XMLHTTP");
} catch (e) {}
}
}
if (!elements_http_request[num]) {
alert('Giving up :( Cannot create an XMLHTTP instance');
return false;
}
} // JavaScript Document
//------------------------------------------------------------------------------------------
// Change Graphic width
//------------------------------------------------------------------------------------------
function change_graphic_width(graphic_width_ID)
{
document.getElementById("system_information").innerHTML = "Dasty2 is resizing the graphic ...";
var pixels = parseInt(document.getElementById(graphic_width_ID).value);
//alert(pixels);
var minimun_feature_size = 50;
var minimun_size = (col_category_width * show_col_category) + (col_method_width * show_col_method) + (col_type_width * show_col_type) + (col_id_width * show_col_id) + (col_server_width * show_col_server) + (col_warning_width * show_col_warning) + minimun_feature_size;
if(pixels > minimun_size)
{
graphic_width = parseInt(pixels);
document.getElementById("graphic_width_px").value = graphic_width;
sorting();
document.getElementById("system_information").innerHTML = "... Dasty2 finished to resize the graphic.";
}
else
{
document.getElementById("system_information").innerHTML = "The graphic width can not be lower than the minimun width (" + minimun_size + " px)
If you wish to reduce the minimun width value try to hide some graphic columns.";
}
}
/*
function info_message(type)
{
switch (type)
{
case "sort" :
document.getElementById("system_information").innerHTML = "Dasty2 is sorting the graphic ...";
break;
case "zoom" :
document.getElementById("system_information").innerHTML = "Dasty2 is zooming the graphic ...";
break;
case "resize" :
document.getElementById("system_information").innerHTML = "Dasty2 is resizing the graphic ...";
break;
case "show_hide" :
document.getElementById("system_information").innerHTML = "Dasty2 is modifying the columns of the graphic ...";
break;
case "show_hide" :
document.getElementById("system_information").innerHTML = "Dasty2 is modifying the columns of the graphic ...";
break;
}
}
*/// JavaScript Document
/**
* CONFIGURATION VARIABLES
*/
function configuration()
{
/**
* TEMPLATES VARIABLES
*/
if(dasty_mainpage_name == "ebi.php")
{
/**
* VARIABLES FOR THE EBI TEMPLATE
*/
isPDBVisible=true;
isOntologyTreeVisible=true;
collapsedOntologyTypeTerms = ['binding_site','polypeptide_region','polypeptide_sequencing_information'];
sequence_limit = 110; // Define the "number" of aa per line in the sequence view. 75
graphic_width = 1100; //1100
height_graphic_feature = 7; // Height for the features shown in the graphic.
tittle_height = height_graphic_feature + 6;
col_category_width = 170;
col_type_width = 190;
col_method_width = 110;
col_id_width = 110; //110
col_warning_width = 26;
col_server_width = 110;
// 0=no / 1=yes
show_col_category = 1;
show_col_type = 1;
show_col_method = 0;
show_col_id = 1; //label
show_col_graphic = 1;
show_col_warning = 1;
show_col_server = 1;
// 0=no / 1=yes
show_graphic_tittle = 1;
show_scale_bar = 1;
show_slide_bar =1;
show_popup =2;
// boolean 0/1. 0=no / 1=yes
color_line_background = 0;
vertical_bars = 12;
// If true it allows to group features from the same source with the have the same ID
dasty2_grouping = false;
// Do you want to exclude DAS sources from the visuzlization?
excluded_das_sources = []; // No
//excluded_das_sources = ['netphos', 'tmhmm']; // Yes, Netphos and Tmhmm
excluded_das_sources = ['CATH Structural Domains in UniProt', 'cath_uniprot_mapping', 'cbs_ptm', 'cbs_func', 'cbs_sort', 'PDBsum_protprot', 'PDBsum_ligands', 'PDBsum_DNAbinding', 'UniProt Tryptic Peptides', 'UniProt GO Annotation', 'uniprot aristotle'];
// Do you want to load at the beggining one specific DAS source?
first_das_source = []; // No
//first_das_source = ['pride', 'uniprot']; // Yes, Pride and Uniprot following this order.
non_positional_features_coulmns = ["type_id", "method_data", "feature_label", "note_data", "link_data", "score_data", "annotation_server", "type_category"];
non_positional_feature_table_width= "98%";
//non_positional_feature_table_width= "900px";
use_das_registry = true;
}
else if(dasty_mainpage_name == "uniprot.php")
{
/**
* VARIABLES FOR THE UNIPROT BETA TEMPLATE
*/
isPDBVisible=true;
isOntologyTreeVisible=true;
collapsedOntologyTypeTerms = ['binding_site','polypeptide_region','polypeptide_sequencing_information'];
sequence_limit = 110; // Define the "number" of aa per line in the sequence view. 75
graphic_width = 770;
height_graphic_feature = 7; // Height for the features shown in the graphic.
tittle_height = height_graphic_feature + 6;
col_category_width = 170;
col_type_width = 200;
col_method_width = 110;
col_id_width = 110;
col_warning_width = 26;
col_server_width = 140;
// boolean 0/1. 0=no / 1=yes
show_col_category = 0;
show_col_type = 1;
show_col_method = 0;
show_col_id = 1;
show_col_graphic = 1;
show_col_warning = 1;
show_col_server = 1;
// boolean 0/1. 0=no / 1=yes
show_graphic_tittle = 1;
show_scale_bar = 1;
show_slide_bar =1;
show_popup =2;
// boolean 0/1. 0=no / 1=yes
color_line_background = 0;
vertical_bars = 12;
// If true it allows to group features from the same source with the have the same ID
dasty2_grouping = false;
// Do you want to exclude DAS sources from the visuzlization?
//excluded_das_sources = []; // No
//excluded_das_sources = ['netphos', 'tmhmm']; // Yes, Netphos and Tmhmm
excluded_das_sources = ['uniprot', 'CATH Structural Domains in UniProt', 'cath_uniprot_mapping', 'cbs_ptm', 'cbs_func', 'cbs_sort', 'PDBsum_protprot', 'PDBsum_ligands', 'PDBsum_DNAbinding', 'UniProt Tryptic Peptides', 'UniProt GO Annotation', 'uniprot aristotle'];
// Do you want to load at the beggining one specific DAS source?
first_das_source = []; // No
//first_das_source = ['pride', 'uniprot']; // Yes, Pride and Uniprot following this order.
//first_das_source = ['signal'];
non_positional_features_coulmns = ["type_id", "score_data", "method_data", "link_data", "feature_id", "note_data", "annotation_server", "type_category"];
non_positional_feature_table_width= "98%";
//non_positional_feature_table_width= "900px";
use_das_registry = true;
}
else if(dasty_mainpage_name == "biosapiens.html")
{
/**
* VARIABLES FOR THE BIOSAPIENS TEMPLATE
*/
isPDBVisible=true;
isOntologyTreeVisible=true;
collapsedOntologyTypeTerms = ['binding_site','polypeptide_region','polypeptide_sequencing_information'];
sequence_limit = 110; // Define the "number" of aa per line in the sequence view. 75
graphic_width = 900;
height_graphic_feature = 7; // Height for the features shown in the graphic.
tittle_height = height_graphic_feature + 6;
col_category_width = 170;
col_type_width = 200;
col_method_width = 110;
col_id_width = 110;
col_warning_width = 26;
col_server_width = 140;
// boolean 0/1. 0=no / 1=yes
show_col_category = 0;
show_col_type = 1;
show_col_method = 0;
show_col_id = 0;
show_col_graphic = 0;
show_col_warning = 0;
show_col_server = 0;
// boolean 0/1. 0=no / 1=yes
show_graphic_tittle = 1;
show_scale_bar = 1;
show_slide_bar =1;
show_popup =2;
// boolean 0/1. 0=no / 1=yes
color_line_background = 0;
vertical_bars = 8;
// If true it allows to group features from the same source with the have the same ID
dasty2_grouping = false;
// Do you want to exclude DAS sources from the visuzlization?
excluded_das_sources = []; // No
//excluded_das_sources = ['netphos', 'tmhmm']; // Yes, Netphos and Tmhmm
excluded_das_sources = ['CATH Structural Domains in UniProt', 'cath_uniprot_mapping', 'cbs_ptm', 'cbs_func', 'cbs_sort', 'PDBsum_protprot', 'PDBsum_ligands', 'PDBsum_DNAbinding', 'UniProt Tryptic Peptides', 'UniProt GO Annotation', 'uniprot aristotle'];
// Do you want to load at the beggining one specific DAS source?
first_das_source = []; // No
//first_das_source = ['pride', 'uniprot']; // Yes, Pride and Uniprot following this order.
//first_das_source = ['signal'];
non_positional_features_coulmns = ["type_id", "method_data", "score_data", "link_data", "feature_id", "note_data", "annotation_server", "type_category"];
non_positional_feature_table_width= "98%";
//non_positional_feature_table_width= "900px";
use_das_registry = true;
}
else
{
/**
* VARIABLES FOR OTHER TEMPLATES. EXAMPLE: INTERACTOR VIEW
*/
isPDBVisible=false;
isOntologyTreeVisible=true;
collapsedOntologyTypeTerms = ['binding_site','polypeptide_region','polypeptide_sequencing_information'];
sequence_limit = 110; // Define the "number" of aa per line in the sequence view. 75
graphic_width = 870;
height_graphic_feature = 7; // Height for the features shown in the graphic.
tittle_height = height_graphic_feature + 6;
col_category_width = 170;
col_type_width = 200;
col_method_width = 110;
col_id_width = 110;
col_warning_width = 26;
col_server_width = 140;
// boolean 0/1. 0=no / 1=yes
show_col_category = 0;
show_col_type = 1;
show_col_method = 0;
show_col_id = 0;
show_col_graphic = 0;
show_col_warning = 0;
show_col_server = 0;
// boolean 0/1. 0=no / 1=yes
show_graphic_tittle = 1;
show_scale_bar = 1;
show_slide_bar =0;
show_popup =1;
// boolean 0/1. 0=no / 1=yes
color_line_background = 0;
vertical_bars = 12;
// If true it allows to group features from the same source with the have the same ID
dasty2_grouping = false;
// Do you want to exclude DAS sources from the visuzlization?
excluded_das_sources = []; // No
//excluded_das_sources = ['netphos', 'tmhmm']; // Yes, Netphos and Tmhmm
//excluded_das_sources = ['CATH Structural Domains in UniProt', 'cath_uniprot_mapping', 'cbs_ptm', 'cbs_func', 'cbs_sort', 'PDBsum_protprot', 'PDBsum_ligands', 'PDBsum_DNAbinding', 'UniProt Tryptic Peptides', 'UniProt GO Annotation', 'uniprot aristotle', 'netphos', 'everest', 'interpro', 'Gene3D-CATH Domain Assigments', 'tmhmm', 'cbs_total', 'gene3d_cath'];
// Do you want to load at the beggining one specific DAS source?
first_das_source = []; // No
//first_das_source = ['pride', 'uniprot']; // Yes, Pride and Uniprot following this order.
//first_das_source = ['signal'];
non_positional_features_coulmns = ["type_id", "link_data", "note_data", "annotation_server"];
//non_positional_feature_table_width= "98%";
non_positional_feature_table_width= "900px";
use_das_registry = false;
}
/**
* DAS SOURCES VARIALES
*/
stylesheet_url = [];
sequence_url = [];
feature_url = [];
/**
* PROXY
*/
/**
* PHP PROXY
*/
proxy_url = '/7tm/dasty2/server/proxy.php';
/**
* CGI PROXY
*/
//proxy_url = 'http://www.ebi.ac.uk/cgi-bin/dasty/proxy.cgi';
//proxy_url = 'http://www.ebi.ac.uk/~rafael/cgi-bin/proxy.cgi';
//proxy_url = 'http://localhost/cgi-bin/proxy.cgi';
//proxy_url = 'http://wwwdev.ebi.ac.uk/cgi-bin/dasty/proxy.cgi';
/**
* STYLESHEET
*/
//stylesheet_url[0] = ['uniprot', proxy_url + '?t=' + timeout + '&m=stylesheet&s=http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/'];
stylesheet_url[0] = ['uniprot', proxy_url + '?t=' + timeout + '&m=stylesheet&s=http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/'];
//stylesheet_url[0] = ['uniprot', 'files/stylesheet.xml']; // LOCAL STYLESHEET
/**
* REFERENCE SERVER
*/
//sequence_url[0] = ['uniprot', proxy_url + '?t=' + timeout + '&m=sequence&q=' + query_id + '&s=http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/']; // UNIPROT REFERENCE SERVER
sequence_url[0] = ['uniprot', proxy_url + '?t=' + timeout + '&m=sequence&q=' + query_id + '&s=http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/']; // UNIPROT REFERENCE SERVER
//sequence_url[0] = ['uniprot', 'files/seq_A4_Human_uniprot02.xml']; // LOCAL SEQUENCE (just for testing purposes)
/**
* ANNOTATION SERVERS
* - If use_das_registry = false please Set specific DAS annotation servers
*/
if(use_das_registry == true)
{
/**
* ANNOTATIONS FROM THE DAS REGISTRY
*/
das_registry_url = proxy_url + '?t=' + timeout + '&m=registry&c=protein%20sequence&a=UniProt&s=http://www.dasregistry.org/das1/sources';
//das_registry_url = proxy_url + '?m=registry&s=http://das.sanger.ac.uk/registry/das1/sources/';
//das_registry_url = 'files/dasregistry250508.xml'; // LOCAL REGISTRY
// Exceptions. For example ...
if(dasty_mainpage_name.indexOf("interactor") != -1)
{
das_registry_url = 'files/dasregistry020208.xml';
}
}
else
{
/**
* SPECIFIC DAS ANNOTATION SERVERS
*/
feature_url_prefix = proxy_url + '?m=features&q=' + query_id + '&t=' + timeout + '&s=';
feature_url[0] = {id : 'uniprot', url : feature_url_prefix + 'http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/'};
//feature_url[1] = {id : 'msdmotif', url : feature_url_prefix + 'http://www.ebi.ac.uk/msd-srv/msdmotif/das/s3dm/'};
//feature_url[2] = {id : 'netphos', url : feature_url_prefix + 'http://genome.cbs.dtu.dk:9000/das/netphos/'};
//feature_url[3] = {id : 'uniprot2', url : feature_url_prefix + 'http://tc-test-1.ebi.ac.uk:8113/tc-test/proteomics/das-srv/uniprot/das/uniprot/'};
//feature_url[4] = {id : 'interpro', url : feature_url_prefix + 'http://das.ensembl.org/das/interpro/'};
/**
* SPECIFIC DAS ANNOTATION SERVERS. LOCAL COPIES.
*/
// feature_url[0] = {id : 'uniprot', url : 'files/fea_A4_Human_uniprot03.xml'};
// feature_url[1] = {id : 'cbs_total', url : 'files/fea_A4_Human_cbs_total.xml'};
// feature_url[2] = {id : 'netphos', url : 'files/fea_A4_Human_netphos.xml'};
//feature_url[3] = {id : 'intact', url : 'files/intact_EBI-466029.xml'};
}
/**
* ALIGNMENTS
*/
//uniprot_pdb_alignment = proxy_url + '?t=30&m=alignment&q=' + query_id + '&s=http://das.sanger.ac.uk/das/msdpdbsp/';
// uniprot_pdb_alignment = proxy_url + '?t=30&m=alignment&q=' + query_id + '&s=http://das.sanger.ac.uk/das/biojavapdbuniprot/';
/**
* ONTOLOGY
*/
// onto_path_type = proxy_url + '?t=30&m=ontology&q=biosapiens.obo_types_250508.xml&s=http://www.ebi.ac.uk/dasty/server/pdb/';
// onto_path_category = proxy_url + '?t=30&m=ontology&q=categories.xml&s=http://www.ebi.ac.uk/dasty/server/pdb/';
//onto_path_type = proxy_url + '?t=30&m=ontology&q=biosapiens.obo_types_250508.xml&s=http://localhost/dasty/server/pdb/';
//onto_path_category = proxy_url + '?t=30&m=ontology&q=categories.xml&s=http://localhost/dasty/server/pdb/';
//onto_path_type = proxy_url + '?t=30&m=ontology&q=biosapiens_lite.xml&s=http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/mi/controlledVocab/biosapiens/';
//onto_path_category = proxy_url + '?t=30&m=ontology&q=categories.xml&s=http://www.ebi.ac.uk/dasty/client/pdb/';
/**
* Path to load pdb files
*/
// path_pdb_files="../server/pdb/";
}
/**
* DEFAULT QUERY PARAMETERS
*/
function default_query_parameters()
{
//default_query_id = "P05067";
default_query_id = "";
default_filterLabel = "BioSapiens";
default_timeout = 10;
default_dasty_mainpage_name = "biosapiens.html"
}
//------------------------------------------------------------------------------------------
// CREATE FEATURE DETAILS FIELD // display_feature_details
//------------------------------------------------------------------------------------------
function createFeatureDetails(object_row, xmlnumber)
{
var fetureDetails = feature_info[xmlnumber][object_row];
var tagId = "display_feature_details";
fields = ["feature_id", "feature_label", "type_data", "type_id", "type_category", "method_data", "start_data", "end_data", "score_data", "orientation_data", "phase_data", "note_data", "link_data"];
fields_names = ["Feature ID: ", "Feature label: ", "Type: ", "Type ID: ", "Category: ", "Method: ", "Start: ", "End: ", "Score: ", "Orientation: ", "Phase: ", "Note: ", "Link: "];
var div = document.getElementById(tagId);
div.innerHTML = '';
for(var i = 0; i < fields.length; i++)
{
var feature_details_content = fetureDetails[fields[i]];
//printOnTest(fields[i] + " / " + typeof(feature_details_content) + " / " + feature_details_content.length);
if(typeof(feature_details_content) == "object") // Content is an array of information. Ex: note_data
{
for(var a = 0; a < feature_details_content.length; a++)
{
if(fields[i] == "link_data")
{
var content_link = fetureDetails["link_href"][a];
}
else
{
var content_link = null;
}
var fieldElements = createFieldFeatureDetails(fields[i], fields_names[i], feature_details_content[a], content_link);
div.appendChild(fieldElements[0]);
div.appendChild(fieldElements[1]);
div.appendChild(fieldElements[2]);
}
}
else // Content just have one variable
{
var fieldElements = createFieldFeatureDetails(fields[i], fields_names[i], feature_details_content, null);
div.appendChild(fieldElements[0]);
div.appendChild(fieldElements[1]);
div.appendChild(fieldElements[2]);
}
}
var contentDiv = div.innerHTML;
div.innerHTML = contentDiv + "
![](\"http://www.gpcr.org/7tm/dasty2/client/img/blast_icon.gif\")
";
}
function createFieldFeatureDetails(fieldType, fieldTitle, content, fdlink)
{
var textNode = document.createTextNode(content);
var a = document.createElement("span");
a.setAttribute("id", "display_feature_details_" + fieldType);
a.setAttribute("class", "title");
a.setAttribute("className", "title");
a.appendChild(document.createTextNode(fieldTitle));
var b = document.createElement("span");
b.setAttribute("id", "display_feature_details_" + fieldType + "_content");
//b.appendChild(document.createTextNode(content));
if(fdlink != null)
{
var link_href = document.createElement("a");
link_href.setAttribute("target", "_featurelinks");
link_href.setAttribute("href", fdlink);
link_href.appendChild(textNode);
b.appendChild(link_href);
}
else
{
b.appendChild(textNode);
}
var c = document.createElement("br");
var fieldElements = [a, b, c];
return fieldElements;
}
//------------------------------------------------------------------------------------------
// CREATE GRAPHIC
//------------------------------------------------------------------------------------------
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// When Dasty2 is executed and displays asyncronously annotations, the function
// createGraphic2 is called as many times as DAS sources are retrieved by AJAX. After
// any other operation like sorting, zoom, etc. the function crreateGraphic2 is called
// just once.
// So the firt time the graphic is composed of several , as many as DAS sources
// displyed. Nonthless after a modification is performed on the graphic, the annotations
// are rearragend in just one
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
function createGraphic2(featureXML_num, tagId, segment_start, segment_stop, origin)
{
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// The origin attributes 'sorting' and 'exapanding' are defined in this function when the
// user wants to modify the view of the first graphic loaded. Then the first graphic is
// deleted from the main display, the annotation are rearraged acording to the users
// request and a new graphic is created by calling the createGraphic2 function. If origin
// is different to one of these two mentioned before Dasty2 will perform a multiple
// asyncronous load.
// Dasty2 doesn't display one annotation per line but it rearrages as many annotation
// one line as possible considering they belong to the same type. Information about this
// rearragement is stored in the "feature_list" variable. "finfo" contains all the
// properties of the annotation being loaded like attribute, note, link, etc. This
// information comes from parse feature.
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(origin == 'sorting')
{
var feature_list = one_feature_list;
var finfo = feature_info;
features_row_number = feature_list.length; // features_row_number is Global
}
else if(origin == 'expanding')
{
var feature_list = expanded_feature_list;
var finfo = feature_info;
features_row_number = feature_list.length; // features_row_number is Global
}
else if(origin == 'noresults')
{
var feature_list = [];
}
else
{
var feature_list = new_feature_list_info2[featureXML_num];
var finfo = feature_info[featureXML_num];
features_row_number = features_row_number + feature_list.length; // features_row_number is Global
}
var firstTimeSortByType_temp = dasty2.firstTimeSortByType;
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Defining variables used to create the graphic
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(feature_list.length > 0)
{
show_col_graphic = 1;
//if(isExpanded == 1 && show_col_id == 1)
if(show_col_id == 1)
{
var show_col_id_temp = 1;
}
else
{
var show_col_id_temp = 0;
}
var seq_start = segment_start -1;
var seq_stop = segment_stop;
var seq_width = (seq_stop - seq_start);
var gr_gap = 1;
var cols = show_col_category + show_col_type + show_col_method + show_col_id_temp + show_col_graphic + show_col_warning + show_col_server;
var total_gap = (cols + 1) * gr_gap;
var width_ul = graphic_width; // 523 for short and 700 for long display in the dasty2 website. Graphic_width is global!
var width_div_category = col_category_width * show_col_category; // col_category_width is global!
var width_div_type = col_type_width * show_col_type; // col_type_width is global!
var width_div_method = col_method_width * show_col_method; // col_method_width is global!
var width_div_id = col_id_width * show_col_id_temp; // col_id_width is global!
var width_div_server = col_server_width * show_col_server; // col_server_width is global!
var width_div_warning = col_warning_width * show_col_warning; // col_server_width is global!
var width_div_graphic = width_ul - (width_div_category + width_div_type + width_div_method + width_div_id + width_div_warning + width_div_server) - (total_gap);
width_div_graphic_correction = width_div_graphic - 2; // Border correction. The border is actually adding two pixels more.
//var left_div_category = (show_col_category * gr_gap) - gr_gap; //show_col_category * gr_gap;
//var left_div_type = left_div_category + width_div_category + (show_col_type * gr_gap);
var left_div_type = (show_col_type * gr_gap) - gr_gap; //show_col_category * gr_gap;
var left_div_method = left_div_type + width_div_type + (show_col_method * gr_gap);
var left_div_id = left_div_method + width_div_method + (show_col_id_temp * gr_gap);
var left_div_graphic = left_div_id + width_div_id + (show_col_graphic * gr_gap);
var left_div_warning = left_div_graphic + width_div_graphic + (show_col_server * gr_gap);
var left_div_server = left_div_warning + width_div_warning + (show_col_warning * gr_gap);
var left_div_category = left_div_server + width_div_server + (show_col_server * gr_gap);
var height_div = height_graphic_feature + 6; // height_graphic_feature is global!
var feature_unique_id = [];
if(browser_name == "Microsoft Internet Explorer")
{
var height_graphic_feature_correction = height_graphic_feature; //IE6
var height_li = height_div -2; //IE6
//printOnTest("Microsoft Internet Explorer");
}
else
{
var height_graphic_feature_correction = height_graphic_feature;
var height_li = height_div;
}
var div = document.getElementById(tagId);
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// SHOW ZOOM SLIDE BAR
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(show_slide_bar == 1)
{
if(origin == "grouping")
{
if(show_slide_bar_temp == 1)
{
var slidebar_ul = createSlideBar(width_ul,left_div_graphic, width_div_graphic);
div.appendChild(slidebar_ul);
activateSlideBar(zoom_start,zoom_end,'gr_slidebar_div_thumb_01','gr_slidebar_div_thumb_02','gr_slidebar_div_track','zoom_start_px','zoom_end_px');
show_slide_bar_temp = 0;
} // if(show_graphic_tittle_temp == 1)
}
else
{
var slidebar_ul = createSlideBar(width_ul,left_div_graphic, width_div_graphic);
div.appendChild(slidebar_ul);
activateSlideBar(zoom_start + 1,zoom_end,'gr_slidebar_div_thumb_01','gr_slidebar_div_thumb_02','gr_slidebar_div_track','zoom_start_px','zoom_end_px');
} // if(origin == "grouping")
} // (show_graphic_tittle == 1)
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// SHOW SCALE-BAR
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(show_scale_bar == 1)
{
if(origin == "grouping")
{
if(show_scale_bar_temp == 1)
{
var scalebar_ul = createScaleBar(vertical_bars, seq_width, width_ul, left_div_graphic, width_div_graphic);
div.appendChild(scalebar_ul);
show_scale_bar_temp = 0;
} // if(show_graphic_tittle_temp == 1)
}
else
{
var scalebar_ul = createScaleBar(vertical_bars, seq_width, width_ul, left_div_graphic, width_div_graphic);
div.appendChild(scalebar_ul);
//alert(bar_px_distance_list);
//alert(bar_aa_distance_list);
//fillScaleBar();
} // if(origin == "grouping")
} // (show_graphic_tittle == 1)
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// SHOW TITTLE
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(show_graphic_tittle == 1)
{
if(origin == "grouping")
{
if(show_graphic_tittle_temp == 1)
{
createGraphicTittle(tagId, width_ul, left_div_category, width_div_category, left_div_type, width_div_type, left_div_method, width_div_method,left_div_id, width_div_id, left_div_graphic, width_div_graphic, left_div_server, width_div_server, height_div, show_col_id_temp, left_div_warning, width_div_warning);
show_graphic_tittle_temp = 0;
} // if(show_graphic_tittle_temp == 1)
}
else
{
createGraphicTittle(tagId, width_ul, left_div_category, width_div_category, left_div_type, width_div_type, left_div_method, width_div_method, left_div_id, width_div_id, left_div_graphic, width_div_graphic, left_div_server, width_div_server, height_div, show_col_id_temp, left_div_warning, width_div_warning);
} // if(origin == "grouping")
} // (show_graphic_tittle == 1)
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// DEFINE UL TAG
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var my_ul = document.createElement("ul");
if(origin == 'sorting' || origin == 'expanding')
{
my_ul.setAttribute("id", "gr_list0");
}
else
{
my_ul.setAttribute("id", "gr_list" + featureXML_num);
}
my_ul.setAttribute("class", "gr_list_class");
my_ul.setAttribute("className", "gr_list_class");
//my_ul.setAttribute("style", "width:" + width_ul + "px;");
my_ul.style.cssText = "width:" + width_ul + "px;";
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Reading the information about the rearragement of annotations (one or many annotation per line)
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for(var c = 0; c < feature_list.length; c++)
{
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// TAKING COLORS FROM THE STYLESHEET
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
feature_color_loop:
for(var p = 0; p < stylesheet_properties_info.length; p++)
{
if(stylesheet_properties_info[p]["type_id"] == feature_list[c]["type"] )
{
feature_border_color = stylesheet_properties_info[p]["fgcolor_data"];
feature_background_color = stylesheet_properties_info[p]["bgcolor_data"];
var aborder_type = 'solid';
break feature_color_loop;
} else
{
feature_border_color = stylesheet_properties_info[0]["fgcolor_data"];
feature_background_color = stylesheet_properties_info[0]["bgcolor_data"];
var aborder_type = 'dotted';
}
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// DEFINING COLORS FROM THE BACKGOUNG OF THE LINES IN THE GRAPHIC. Alterning two colors
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(color_line_background == 1)
{
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// DEFINING COLORS BY LINE
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(feature_list[c]["version"] == 1)
{
if (feature_list[c]["feature_group"] == 1)
{
if ( bg_color == 2 || bg_color == 4 || bg_color == 6 || bg_color == 8) { bg_color = 3 } else { bg_color = 4 }
}
else
{
if ( bg_color == 2 || bg_color == 4 || bg_color == 6 || bg_color == 8) { bg_color = 1 } else { bg_color = 2 }
}
}
else
{
if (feature_list[c]["feature_group"] == 1)
{
if ( bg_color == 2 || bg_color == 4 || bg_color == 6 || bg_color == 8) { bg_color = 7 } else { bg_color = 8 }
}
else
{
if ( bg_color == 2 || bg_color == 4 || bg_color == 6 || bg_color == 8) { bg_color = 5 } else { bg_color = 6 }
}
}
} // if(color_line_background == 1)
else
{
if ( bg_color == 2 ) { bg_color = 1 } else { bg_color = 2 }
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// FINDING das sources loaded.
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(dasty2.loadedDasSources.length == 0)
{
var lds_temp = dasty2.loadedDasSources_temp.length;
var duplicated_source = 0;
for(var w = 0; w < lds_temp; w++)
{
if(dasty2.loadedDasSources_temp[w] == feature_list[c]["server"])
{
duplicated_source = 1;
}
}
if(duplicated_source == 0)
{
dasty2.loadedDasSources_temp.push(feature_list[c]["server"]);
}
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE LISTS - (one line) inside the
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var mycurrent_li = document.createElement("li");
if(origin == 'sorting' || origin == 'expanding')
{
var feature_xmlnumber = feature_list[c]["xmlnumber"];
var li_id_name = "gr_item" + feature_xmlnumber + "_" + feature_list[c]["type"] + "_" + feature_list[c]["line"];
mycurrent_li.setAttribute("id", li_id_name);
}
else
{
var li_id_name = "gr_item" + featureXML_num + "_" + feature_list[c]["type"] + "_" + feature_list[c]["line"];
mycurrent_li.setAttribute("id", li_id_name);
}
if(dasty2.line_id_name2[li_id_name] == 1)
{
dasty2.countVisibleLines++;
mycurrent_li.style.cssText = "height:" + height_li + "px; display:block;";
}
else
{
mycurrent_li.style.cssText = "height:" + height_li + "px; display:none;";
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE CATEGORY COLUMN INSIDE THE LIST -
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (show_col_category == 1)
{
var mycurrent_div_category = document.createElement("div");
mycurrent_div_category.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_category.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_01");
//mycurrent_div_category.setAttribute("style", "top:0px; left:" + left_div_category + "px; width:" + width_div_category + "px; height:" + height_div + "px;");
mycurrent_div_category.style.cssText = "top:0px; left:" + left_div_category + "px; width:" + width_div_category + "px; height:" + height_div + "px;";
//var mycurrent_category_text = document.createElement("a");
//mycurrent_category_text.setAttribute("class", "gr_text_01");
//mycurrent_category_text.setAttribute("className", "gr_text_01");
//mycurrent_category_text.setAttribute("href", "");
var mycurrent_category_text = document.createElement("span");
mycurrent_category_text.setAttribute("class", "gr_text_01");
mycurrent_category_text.setAttribute("className", "gr_text_01");
var mycurrent_category_text_content = document.createTextNode(feature_list[c]["category"]);
mycurrent_category_text.appendChild(mycurrent_category_text_content);
mycurrent_div_category.appendChild(mycurrent_category_text);
mycurrent_li.appendChild(mycurrent_div_category);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE METHOD COLUMN INSIDE THE LIST
-
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (show_col_method == 1)
{
var mycurrent_div_method = document.createElement("div");
mycurrent_div_method.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_method.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_01");
//mycurrent_div_category.setAttribute("style", "top:0px; left:" + left_div_category + "px; width:" + width_div_category + "px; height:" + height_div + "px;");
mycurrent_div_method.style.cssText = "top:0px; left:" + left_div_method + "px; width:" + width_div_method + "px; height:" + height_div + "px;";
//var mycurrent_method_text = document.createElement("a");
//mycurrent_method_text.setAttribute("class", "gr_text_01");
//mycurrent_method_text.setAttribute("className", "gr_text_01");
//mycurrent_method_text.setAttribute("href", "");
var mycurrent_method_text = document.createElement("span");
mycurrent_method_text.setAttribute("class", "gr_text_01");
mycurrent_method_text.setAttribute("className", "gr_text_01");
var mycurrent_method_text_content = document.createTextNode(feature_list[c]["method"]);
mycurrent_method_text.appendChild(mycurrent_method_text_content);
mycurrent_div_method.appendChild(mycurrent_method_text);
mycurrent_li.appendChild(mycurrent_div_method);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE TYPE COLUMN INSIDE LIST
-
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (show_col_type == 1)
{
var mycurrent_div_type = document.createElement("div");
mycurrent_div_type.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_type.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_type.style.cssText = "top:0px; left:" + left_div_type + "px; width:" + width_div_type + "px; height:" + height_div + "px;";
var mycurrent_type_text_content = document.createTextNode(feature_list[c]["type_data"]);
var useOlsUrl = false;
for(var w = 0; w < ontologyPrefix.length; w++)
{
if(feature_list[c]["type"].indexOf(ontologyPrefix[w]) != -1)
{
useOlsUrl = true;
}
}
if(useOlsUrl == true)
{
var mycurrent_type_text = document.createElement("a");
mycurrent_type_text.setAttribute("class", "gr_text_01");
mycurrent_type_text.setAttribute("className", "gr_text_01");
mycurrent_type_text.setAttribute("target", "_type");
mycurrent_type_text.setAttribute("href", "http://www.ebi.ac.uk/ontology-lookup/?termId=" + feature_list[c]["type"]);
}
else
{
var mycurrent_type_text = document.createElement("span");
mycurrent_type_text.setAttribute("class", "gr_text_01");
mycurrent_type_text.setAttribute("className", "gr_text_01");
}
mycurrent_type_text.appendChild(mycurrent_type_text_content);
mycurrent_div_type.appendChild(mycurrent_type_text);
mycurrent_li.appendChild(mycurrent_div_type);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE ID COLUMN INSIDE LIST
-
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (show_col_id_temp == 1)
{
var mycurrent_div_id = document.createElement("div");
mycurrent_div_id.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_id.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_01");
//mycurrent_div_id.setAttribute("style", "top:0px; left:" + left_div_id + "px; width:" + width_div_id + "px; height:" + height_div + "px;");
mycurrent_div_id.style.cssText = "top:0px; left:" + left_div_id + "px; width:" + width_div_id + "px; height:" + height_div + "px;";
var mycurrent_id_text = document.createElement("a");
mycurrent_id_text.setAttribute("class", "gr_text_01");
mycurrent_id_text.setAttribute("className", "gr_text_01");
mycurrent_id_text.style.cssText = "color:#7E7E7E;"
//mycurrent_id_text.setAttribute("href", "");
//var id_row = feature_list[c]["features"][0];
//var mycurrent_id_text_content = document.createTextNode(finfo[feature_xmlnumber][id_row]["feature_id"]);
var mycurrent_id_text_content = document.createTextNode(feature_list[c]["feature_label"].slice(0,12) + "...");
mycurrent_id_text.appendChild(mycurrent_id_text_content);
mycurrent_div_id.appendChild(mycurrent_id_text);
mycurrent_li.appendChild(mycurrent_div_id);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE FEATURE COLUMN INSIDE LIST
-
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var mycurrent_div_graphic = document.createElement("div");
mycurrent_div_graphic.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_02");
mycurrent_div_graphic.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_02");
//mycurrent_div_graphic.setAttribute("style", "top:0px; left:" + left_div_graphic + "px; width:" + width_div_graphic + "px; height:" + height_div + "px;");
mycurrent_div_graphic.style.cssText = "top:0px; left:" + left_div_graphic + "px; width:" + width_div_graphic + "px; height:" + height_div + "px;";
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// RECALCULATE FEATURE SIZE TO FIT IT IN THE GRAPHIC
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for(var n = 0; n < feature_list[c]["features"].length; n++)
{
var row = feature_list[c]["features"][n];
if(origin == 'sorting' || origin == 'expanding')
{
// var feature_xmlnumber is defined in the creation of "LISTs"
var feature_id = finfo[feature_xmlnumber][row]["feature_id"];
var feature_start = finfo[feature_xmlnumber][row]["start_data"];
var feature_end =finfo[feature_xmlnumber][row]["end_data"];
}
else
{
var feature_id = finfo[row]["feature_id"];
var feature_start = finfo[row]["start_data"];
var feature_end =finfo[row]["end_data"];
var feature_xmlnumber = finfo[row]["xmlnumber"];
}
var feature_width = feature_end - feature_start;
var original_feature_start = feature_start;
var original_feature_end = feature_end;
var original_feature_width = feature_width;
feature_start = feature_start -1;
feature_width = feature_end - feature_start; // It is 1 pixel bigger
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// ZOOM IMPLEMENTATION
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if( zoom_end != 0)
{
var zoom_width = zoom_end - zoom_start;
feature_start = feature_start - zoom_start;
feature_end = feature_start + feature_width;
var temp_feature_start = feature_start;
var temp_feature_end = feature_end;
if(temp_feature_start > zoom_end)
{
feature_start = -1;
} // -1 => out of range
else if(temp_feature_start < 0)
{
feature_start = 0;
} // (feature_start > zoom_end)
var new_zoom_width = zoom_width;
if(temp_feature_end > new_zoom_width && temp_feature_start > new_zoom_width)
{
feature_end = -1;
}
else if(temp_feature_end > new_zoom_width)
{
feature_end = zoom_width;
}
else if (temp_feature_end < 0)
{
feature_end = -1;
} // -1 => out of range
var seq_width = zoom_width;
feature_width = feature_end - feature_start;
}
else
{
var temp_feature_start = feature_start;
var temp_feature_end = feature_end;
if(temp_feature_start > (seq_stop -1))
{
feature_start = -1;
} // -1 => out of range
// else if(temp_feature_start < seq_stop && temp_feature_end > seq_stop)
if(temp_feature_end > seq_stop)
{
feature_end = seq_stop;
}
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// IF ANNOTATION IS OUT OF THE RAGE OF AMINOACIDS TO DISPLAY THEN DON'T DISPLAY, OTHERWISE DISPLAY
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(feature_start == -1 || feature_end == -1)
{
// Don't create features
}
else
{
var feature_start_value = ((width_div_graphic_correction * feature_start) / seq_width);
var feature_end_value = ((width_div_graphic_correction * feature_end) / seq_width);
var feature_width_value = ((width_div_graphic_correction * feature_width) / seq_width);
var mycurrent_graphic_feature = document.createElement("a");
mycurrent_graphic_feature.setAttribute("id", feature_id + "_" + feature_start); // feature_id is not unique
mycurrent_graphic_feature.setAttribute("class", "feature");
mycurrent_graphic_feature.setAttribute("className", "feature");
//mycurrent_graphic_feature.setAttribute("href", "");
mycurrent_graphic_feature.style.cssText = "font-size:1px; top:2px; left:" + feature_start_value + "px; width:" + feature_width_value + "px; height:" + height_graphic_feature_correction + "px; border: 1px " + aborder_type + " " + feature_border_color + "; background-color:" + feature_background_color + ";";
mycurrent_graphic_feature.onmouseover = new Function("this.style.backgroundColor = '" + feature_border_color + "';" + "feature_mouse_action(findPosX(this), findPosY(this), '" + feature_id + "', " + feature_xmlnumber + ", " + row + ", 'mouseover');");
mycurrent_graphic_feature.onmouseout = new Function("this.style.backgroundColor = '" + feature_background_color + "';");
mycurrent_graphic_feature.onclick = new Function("highlightSequence(" + original_feature_start + ", " + original_feature_end + ", " + sequence_limit + ", '" + feature_border_color + "'); " + "feature_mouse_action(findPosX(this), findPosY(this), '" + feature_id + "', " + feature_xmlnumber + ", " + row + ", 'mouseclick');");
feature_unique_id.push(feature_id + "_" + feature_start);
mycurrent_div_graphic.appendChild(mycurrent_graphic_feature); // DIV with the Graphic
} // if(feature_start == -1 || feature_end == -1)
} // for(var n = 0; n < feature_list[c]["features"].length; n++)
mycurrent_li.appendChild(mycurrent_div_graphic);
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// WARNING ICONS
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (show_col_warning == 1)
{
var mycurrent_div_warning = document.createElement("div");
mycurrent_div_warning.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_warning.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_warning.style.cssText = "top:0px; left:" + left_div_warning + "px; width:" + width_div_warning + "px; height:" + height_div + "px;";
var mycurrent_warning_img_01 = document.createElement("img");
if(feature_list[c]["version"] == 1)
{
mycurrent_warning_img_01.setAttribute("src", "/site_media/js/dasty2/client/img/checkmark.gif");
}
else
{
mycurrent_warning_img_01.setAttribute("src", "/site_media/js/dasty2/client/img/warning.gif");
}
var mycurrent_warning_img_02 = document.createElement("img");
if (feature_list[c]["feature_group"] == 1)
{
mycurrent_warning_img_02.setAttribute("src", "/site_media/js/dasty2/client/img/group.gif");
}
else
{
mycurrent_warning_img_02.setAttribute("src", "/site_media/js/dasty2/client/img/group2.gif");
}
mycurrent_div_warning.appendChild(mycurrent_warning_img_01);
mycurrent_div_warning.appendChild(mycurrent_warning_img_02);
mycurrent_li.appendChild(mycurrent_div_warning);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// SERVERs
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (show_col_server == 1)
{
var mycurrent_div_server = document.createElement("div");
mycurrent_div_server.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_server.setAttribute("className", "gr_div gr_row_0" + bg_color + " gr_cell_01");
mycurrent_div_server.style.cssText = "top:0px; left:" + left_div_server + "px; width:" + width_div_server + "px; height:" + height_div + "px;";
var mycurrent_server_text = document.createElement("a");
mycurrent_server_text.setAttribute("class", "gr_text_01");
mycurrent_server_text.setAttribute("className", "gr_text_01");
mycurrent_server_text.setAttribute("target", "_dasregistry")
mycurrent_server_text.setAttribute("href", "http://www.dasregistry.org/showdetails.jsp?auto_id=" + feature_list[c]["registry_uri"]);
var mycurrent_server_text_content = document.createTextNode(feature_list[c]["server"]);
mycurrent_server_text.appendChild(mycurrent_server_text_content);
mycurrent_div_server.appendChild(mycurrent_server_text);
mycurrent_li.appendChild(mycurrent_div_server);
}
my_ul.appendChild(mycurrent_li);
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// FINISHED Reading the information about the rearragement of annotations
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
} // for(var c = 0; c < feature_list.length; c++)
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CLOSING UL TAG
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
div.appendChild(my_ul);
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Tooltip Manager creates HTML code embeded below the BODY for each annotation to
// be able to display feature deatails Pop-Ups on on mouse-over.
// I don't like but this is what I've got at the moment.
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for(var n = 0; n < feature_unique_id.length; n++)
{
TooltipManager.addHTML(feature_unique_id[n], "display_feature_details");
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// FINISH condition if there are annotations
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
} // if(feature_list.length > 0)
if(origin == "grouping" || origin == "noresults")
{
count_displayed_groups++;
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// ONCE ALL THE ANNOTATIONS HAVE BEEN LOADED FROM ALL THE SERVERS ...
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(count_displayed_groups == feature_url.length) // feature_url is global!
{
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE POSITIONAL VERTICAL LINES ON THE GRAPHIC
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fillScaleBar();
dasty2.countVisibleLines = 0;
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// MESSAGE TO DISPLAY WHEN FINISH LOADING
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
document.getElementById("system_information").innerHTML = "... Dasty2 has finished loading the data.";
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE TABLE WITH DAS SOURCES DISPLAYED IN DASTY
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(dasty2.loadedDasSources.length == 0)
{
dasty2.loadedDasSources = dasty2.loadedDasSources_temp;
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE ONTOLOGY
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (isOntologyTreeVisible==true)
{
create_ontology_tree();
}
create_server_tree();
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// MAKE NPF SORTABLE
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
sortables_init();
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// MESSAGE - NO ENTRIES FOUND
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if(feature_results_count == 0)
{
var system_information = document.getElementById("system_information").innerHTML
document.getElementById("system_information").innerHTML = system_information + "
There were no entries found with the Protein ID: \"" + query_id + "\" and the Registry label: \"" + filterLabel + "\" ";
}
if(firstTimeSortByType_temp == true)
{
dasty2.firstTimeSortByType = false;
sorting('type');
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// AFTER EVERY ASYCRONOUS LOADING ...
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
/*
else
{
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// CREATE SORTABLE LISTS BETWEEN UL - It just works with the first s
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var gr_list_array = [];
for(var fu = 0; fu < results_XML_order.length; fu++)
{
gr_list_array.push('gr_list' + results_XML_order[fu]);
}
for(var fu = 0; fu < results_XML_order.length; fu++)
{
if(fu== 0)
{
Sortable.create('gr_list' + results_XML_order[fu], {dropOnEmpty:true,containment:gr_list_array,constraint:false});
}
else
{
Sortable.create('gr_list' + results_XML_order[fu], {dropOnEmpty:true,handle:'handle',containment:gr_list_array,constraint:false});
} // if(fu== 0)
} // for(var fu = 0; fu < results_XML_order.length; fu++)
} //if(feature_url.length == 1)
*/
} // if(count_displayed_groups == feature_url.length)
} // if(origin == "grouping" || origin == "noresults")
else
{
fillScaleBar();
dasty2.countVisibleLines = 0;
}
} // function createGraphic(tagId, segment_start, segment_stop)
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Calculate Position X and Y for the mouse
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
function findPosX(obj)
{
var curleft = 0;
if(obj.offsetParent)
while(1)
{
curleft += obj.offsetLeft;
if(!obj.offsetParent)
break;
obj = obj.offsetParent;
}
else if(obj.x)
curleft += obj.x;
return curleft;
}
function findPosY(obj)
{
var curtop = 0;
if(obj.offsetParent)
while(1)
{
curtop += obj.offsetTop;
if(!obj.offsetParent)
break;
obj = obj.offsetParent;
}
else if(obj.y)
curtop += obj.y;
return curtop;
}
//------------------------------------------------------------------------------------------
// GRAPHIC TITTLE
//------------------------------------------------------------------------------------------
function createGraphicTittle(tagId, width_ul, left_div_category, width_div_category, left_div_type, width_div_type, left_div_method, width_div_method, left_div_id, width_div_id, left_div_graphic, width_div_graphic, left_div_server, width_div_server, height_div, show_col_id_temp, left_div_warning, width_div_warning)
{
var div = document.getElementById(tagId);
var my_ul = document.createElement("ul");
my_ul.setAttribute("id", "gr_list_tittle");
my_ul.setAttribute("class", "gr_list_class");
my_ul.setAttribute("className", "gr_list_class");
//my_ul.setAttribute("style", "width:" + width_ul + "px;"); // tagId, width_ul
my_ul.style.cssText = "width:" + width_ul + "px;";
//------------------------------------------
// LIsts
//------------------------------------------
var mycurrent_li = document.createElement("li");
mycurrent_li.setAttribute("id", "gr_item_tittle");
//mycurrent_li.setAttribute("style", "height:" + tittle_height + "px;"); // height_li // tittle_height is global!
mycurrent_li.style.cssText = "height:" + tittle_height + "px;";
//------------------------------------------
// CATEGORIes
//------------------------------------------
if (show_col_category == 1)
{
var mycurrent_div_category = document.createElement("div");
mycurrent_div_category.setAttribute("class", "gr_div gr_row_tittle");
mycurrent_div_category.setAttribute("className", "gr_div gr_row_tittle");
//mycurrent_div_category.setAttribute("style", "top:0px; left:" + left_div_category + "px; width:" + width_div_category + "px; height:" + height_div + "px;");
mycurrent_div_category.style.cssText = "top:0px; left:" + left_div_category + "px; width:" + width_div_category + "px; height:" + height_div + "px;";
var mycurrent_category_text = document.createElement("a");
mycurrent_category_text.setAttribute("class", "gr_text_02");
mycurrent_category_text.setAttribute("className", "gr_text_02");
//mycurrent_category_text.setAttribute("href", "");
//mycurrent_category_text.setAttribute("onclick", "sorting('category')");
mycurrent_category_text.onclick = new Function("sorting('category');");
var mycurrent_category_text_content = document.createTextNode("EVIDENCE (Category) ");
var mycurrent_category_img_content = document.createElement("img");
if(sortOrderCategory == 1)
{
mycurrent_category_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowup.gif");
}
else if(sortOrderCategory == -1)
{
mycurrent_category_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowdown.gif");
}
else
{
mycurrent_category_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrownone.gif");
}
mycurrent_category_text.appendChild(mycurrent_category_text_content);
mycurrent_category_text.appendChild(mycurrent_category_img_content);
mycurrent_div_category.appendChild(mycurrent_category_text);
mycurrent_li.appendChild(mycurrent_div_category); // left_div_category, width_div_category, height_div
}
//------------------------------------------
// METHOD
//------------------------------------------
if (show_col_method == 1)
{
var mycurrent_div_method = document.createElement("div");
mycurrent_div_method.setAttribute("class", "gr_div gr_row_tittle");
mycurrent_div_method.setAttribute("className", "gr_div gr_row_tittle");
//mycurrent_div_method.setAttribute("style", "top:0px; left:" + left_div_method + "px; width:" + width_div_method + "px; height:" + height_div + "px;");
mycurrent_div_method.style.cssText = "top:0px; left:" + left_div_method + "px; width:" + width_div_method + "px; height:" + height_div + "px;";
var mycurrent_method_text = document.createElement("a");
mycurrent_method_text.setAttribute("class", "gr_text_02");
mycurrent_method_text.setAttribute("className", "gr_text_02");
//mycurrent_category_text.setAttribute("href", "");
//mycurrent_category_text.setAttribute("onclick", "sorting('category')");
mycurrent_method_text.onclick = new Function("sorting('method');");
var mycurrent_method_text_content = document.createTextNode("METHOD ");
var mycurrent_method_img_content = document.createElement("img");
if(sortOrderMethod == 1)
{
mycurrent_method_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowup.gif");
}
else if(sortOrderMethod == -1)
{
mycurrent_method_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowdown.gif");
}
else
{
mycurrent_method_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrownone.gif");
}
mycurrent_method_text.appendChild(mycurrent_method_text_content);
mycurrent_method_text.appendChild(mycurrent_method_img_content);
mycurrent_div_method.appendChild(mycurrent_method_text);
mycurrent_li.appendChild(mycurrent_div_method); // left_div_category, width_div_category, height_div
}
//------------------------------------------
// TYPEs
//------------------------------------------
if (show_col_type == 1)
{
var mycurrent_div_type = document.createElement("div");
mycurrent_div_type.setAttribute("class", "gr_div gr_row_tittle");
mycurrent_div_type.setAttribute("className", "gr_div gr_row_tittle");
//mycurrent_div_type.setAttribute("style", "top:0px; left:" + left_div_type + "px; width:" + width_div_type + "px; height:" + height_div + "px;");
mycurrent_div_type.style.cssText = "top:0px; left:" + left_div_type + "px; width:" + width_div_type + "px; height:" + height_div + "px;";
var mycurrent_type_text = document.createElement("a");
mycurrent_type_text.setAttribute("class", "gr_text_02");
mycurrent_type_text.setAttribute("className", "gr_text_02");
//mycurrent_type_text.setAttribute("href", "");
//mycurrent_type_text.setAttribute("onclick", "sorting('type')");
mycurrent_type_text.onclick = new Function("sorting('type');");
var mycurrent_type_text_content = document.createTextNode("FEATURE TYPE ");
var mycurrent_type_img_content = document.createElement("img");
if(sortOrderType== 1)
{
mycurrent_type_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowup.gif");
}
else if(sortOrderType == -1)
{
mycurrent_type_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowdown.gif");
}
else
{
mycurrent_type_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrownone.gif");
}
mycurrent_type_text.appendChild(mycurrent_type_text_content);
mycurrent_type_text.appendChild(mycurrent_type_img_content);
mycurrent_div_type.appendChild(mycurrent_type_text);
mycurrent_li.appendChild(mycurrent_div_type); // left_div_type, width_div_type, height_div
}
//------------------------------------------
// IDs
//------------------------------------------
if (show_col_id_temp == 1)
{
var mycurrent_div_id = document.createElement("div");
mycurrent_div_id.setAttribute("class", "gr_div gr_row_tittle");
mycurrent_div_id.setAttribute("className", "gr_div gr_row_tittle");
//mycurrent_div_id.setAttribute("style", "top:0px; left:" + left_div_id + "px; width:" + width_div_id + "px; height:" + height_div + "px;");
mycurrent_div_id.style.cssText = "top:0px; left:" + left_div_id + "px; width:" + width_div_id + "px; height:" + height_div + "px;";
var mycurrent_id_text = document.createElement("a");
mycurrent_id_text.setAttribute("class", "gr_text_02");
mycurrent_id_text.setAttribute("className", "gr_text_02");
//mycurrent_id_text.setAttribute("href", "");
//mycurrent_id_text.setAttribute("onclick", "sorting('id')");
mycurrent_id_text.onclick = new Function("sorting('id');");
var mycurrent_id_text_content = document.createTextNode("LABELS ");
mycurrent_id_text.appendChild(mycurrent_id_text_content);
mycurrent_div_id.appendChild(mycurrent_id_text);
mycurrent_li.appendChild(mycurrent_div_id); // left_div_id, width_div_id, height_div
}
//------------------------------------------
// FEATUREs
//------------------------------------------
var mycurrent_div_graphic = document.createElement("div");
mycurrent_div_graphic.setAttribute("class", "gr_div gr_row_tittle gr_cell_02");
mycurrent_div_graphic.setAttribute("className", "gr_div gr_row_tittle gr_cell_02");
//mycurrent_div_graphic.setAttribute("style", "top:0px; left:" + left_div_graphic + "px; width:" + width_div_graphic + "px; height:" + height_div + "px;");
mycurrent_div_graphic.style.cssText = "top:0px; left:" + left_div_graphic + "px; width:" + width_div_graphic + "px; height:" + height_div + "px;";
//var mycurrent_graphic_text = document.createElement("a");
var mycurrent_graphic_text = document.createElement("span");
mycurrent_graphic_text.setAttribute("class", "gr_text_02");
mycurrent_graphic_text.setAttribute("className", "gr_text_02");
//mycurrent_graphic_text.setAttribute("href", "");
var mycurrent_graphic_text_content = document.createTextNode("FEATURE ANNOTATONS ");
mycurrent_graphic_text.appendChild(mycurrent_graphic_text_content);
mycurrent_div_graphic.appendChild(mycurrent_graphic_text);
mycurrent_li.appendChild(mycurrent_div_graphic); // left_div_graphic, width_div_graphic, height_div
/*
//------------------------------------------
// VERSION
//------------------------------------------
if (show_col_warning == 1)
{
var mycurrent_div_warning = document.createElement("div");
mycurrent_div_warning.setAttribute("class", "gr_div gr_row_tittle");
mycurrent_div_warning.setAttribute("className", "gr_div gr_row_tittle");
mycurrent_div_warning.style.cssText = "top:0px; left:" + left_div_warning + "px; width:" + width_div_warning + "px; height:" + height_div + "px;";
var mycurrent_warning_text = document.createElement("a");
mycurrent_warning_text.setAttribute("class", "gr_text_02");
mycurrent_warning_text.setAttribute("className", "gr_text_02");
//mycurrent_warning_text.setAttribute("href", "");
//mycurrent_warning_text.setAttribute("onclick", "sorting('type')");
mycurrent_warning_text.onclick = new Function("sorting('version');");
var mycurrent_warning_text_content = document.createTextNode("");
var mycurrent_warning_img_content = document.createElement("img");
if(sortOrderVersion== 1)
{
mycurrent_warning_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/arrowup.gif");
}
else if(sortOrderVersion == -1)
{
mycurrent_warning_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/arrowdown.gif");
}
else
{
mycurrent_warning_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/arrownone.gif");
}
mycurrent_warning_text.appendChild(mycurrent_warning_text_content);
mycurrent_warning_text.appendChild(mycurrent_warning_img_content);
mycurrent_div_warning.appendChild(mycurrent_warning_text);
mycurrent_li.appendChild(mycurrent_div_warning); // left_div_type, width_div_type, height_div
}
*/
//------------------------------------------
// SERVERs
//------------------------------------------
if (show_col_server == 1)
{
var mycurrent_div_server = document.createElement("div");
mycurrent_div_server.setAttribute("class", "gr_div gr_row_tittle");
mycurrent_div_server.setAttribute("className", "gr_div gr_row_tittle");
//mycurrent_div_server.setAttribute("style", "top:0px; left:" + left_div_server + "px; width:" + width_div_server + "px; height:" + height_div + "px;");
mycurrent_div_server.style.cssText = "top:0px; left:" + left_div_server + "px; width:" + width_div_server + "px; height:" + height_div + "px;";
var mycurrent_server_text = document.createElement("a");
mycurrent_server_text.setAttribute("class", "gr_text_02");
mycurrent_server_text.setAttribute("className", "gr_text_02");
//mycurrent_server_text.setAttribute("href", "");
//mycurrent_server_text.setAttribute("onclick", "sorting('server')");
mycurrent_server_text.onclick = new Function("sorting('server');")
var mycurrent_server_text_content = document.createTextNode("SERVER NAME ");
var mycurrent_server_img_content = document.createElement("img");
if(sortOrderServer == 1)
{
mycurrent_server_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowup.gif");
}
else if(sortOrderServer == -1)
{
mycurrent_server_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrowdown.gif");
}
else
{
mycurrent_server_img_content.setAttribute("src", "http://www.gpcr.org/7tm/dasty2/client/img/arrownone.gif");
}
mycurrent_server_text.appendChild(mycurrent_server_text_content);
mycurrent_server_text.appendChild(mycurrent_server_img_content);
mycurrent_div_server.appendChild(mycurrent_server_text);
mycurrent_li.appendChild(mycurrent_div_server); // left_div_server, width_div_server, height_div
}
my_ul.appendChild(mycurrent_li);
div.appendChild(my_ul);
}
//------------------------------------------------------------------------------------------
// CREATE NON POSITIONAL FEATURE TABLE
//------------------------------------------------------------------------------------------
function createNPFeatureTable(featureXML_num, array, tagId, npf_num)
{
if(npf_num == 0)
{
// There are not positional features
}
else
{
var title_var = non_positional_features_coulmns;
/**
* The first time that a DAS source is loaded:
*/
var countNPF = dasty2.countNPF
if(countNPF == 0)
{
dasty2.countNPF++;
//Principio
var title = new Array();
title["type_category"] = "EVIDENCE (Category)";
title["type_data"] = "TYPE NAME";
title["type_id"] = "FEATURE TYPE";
//title["feature_id"] = "FEATURE ID";
title["feature_label"] = "LABEL";
title["note_data"] = "NOTE";
title["method_data"] = "METHOD";
title["score_data"] = "S.";
title["annotation_server"] = "SERVER NAME";
title["link_data"] = "";
title["version"] = "";
var title_width = new Array();
title_width["type_category"] = col_category_width;
title_width["type_data"] = col_type_width;
title_width["type_id"] = col_type_width;
title_width["feature_label"] = col_id_width;
title_width["note_data"] = "";
title_width["method_data"] = "";
title_width["score_data"] = 40;
title_width["annotation_server"] = col_server_width;
title_width["link_data"] = 5;
title_width["version"] = 5;
var mybody = document.getElementById(tagId);
var mytable = document.createElement("table");
mytable.setAttribute("id","non_positional_features");
mytable.setAttribute("class","sortable feature_table");
mytable.setAttribute("className","sortable feature_table");
mytable.style.cssText = "width:" + non_positional_feature_table_width + ";";
//mytable.setAttribute("class","sortable");
//mytable.setAttribute("className","sortable");
//var mythead = document.createElement('thead');
var mytbody = document.createElement('tbody');
mytbody.setAttribute("id","non_positional_features_tbody");
var mycurrent_row = document.createElement("tr");
mycurrent_row.setAttribute("class", "feature_table_row_title_decor");
mycurrent_row.setAttribute("className", "feature_table_row_title_decor");
for(var i = 0; i < title_var.length; i++)
{
var mycurrent_cell = document.createElement("th");
if(title_var[i] == "note_data" || title_var[i] == "link_data")
{
mycurrent_cell.setAttribute("class", "feature_table_cell_title_decor" + i + " unsortable");
mycurrent_cell.setAttribute("className", "feature_table_cell_title_decor" + i + " unsortable");
}
else
{
mycurrent_cell.setAttribute("class", "feature_table_cell_title_decor" + i);
mycurrent_cell.setAttribute("className", "feature_table_cell_title_decor" + i);
}
if(title_width[title_var[i]] != "")
{
mycurrent_cell.style.cssText = "width:" + title_width[title_var[i]] + "px;";
}
var content = document.createTextNode(title[title_var[i]]);
mycurrent_cell.appendChild(content);
mycurrent_row.appendChild(mycurrent_cell);
}
//mythead.appendChild(mycurrent_row);
mytbody.appendChild(mycurrent_row);
//mytable.appendChild(mythead);
mytable.appendChild(mytbody);
mybody.appendChild(mytable);
}
// Lo del medio
var mytbody = document.getElementById("non_positional_features_tbody");
var npfTypes = new Array();
var newType = false;
for(var j = 0; j < array.length; j++)
{
if (array[j]["start_data"]==0 && array[j]["end_data"]==0)
{ // non positional feature
newType = false;
if(typeof npfTypes[array[j]["type_id"]] == "undefined")
{
newType = true;
}
if(newType == true)
{
npfTypes[array[j]["type_id"]] = 0;
}
else
{
npfTypes[array[j]["type_id"]]++;
}
var mycurrent_row = document.createElement("tr");
var tr_name = "npf_item" + featureXML_num + "_" + array[j]["type_id"] + "_" + npfTypes[array[j]["type_id"]];
var tr_id_name = [];
tr_id_name.push(tr_name);
dasty2.IdlinesPerType.push([array[j]["type_id"], tr_id_name, 1]);
dasty2.IdlinesPerCategory.push([array[j]["type_category"], tr_id_name, 1]);
dasty2.IdlinesPerServer.push([array[j]["annotation_server"], tr_id_name, 1]);
mycurrent_row.setAttribute("id", tr_id_name);
mycurrent_row.style.cssText = "display: table-row;"; //display: block;
if(dasty2.decor_tr_npf == 0)
{
mycurrent_row.setAttribute("class", "feature_table_row_decor0");
mycurrent_row.setAttribute("className", "feature_table_row_decor0");
dasty2.decor_tr_npf++;
}
else
{
mycurrent_row.setAttribute("class", "feature_table_row_decor1");
mycurrent_row.setAttribute("className", "feature_table_row_decor1");
dasty2.decor_tr_npf--;
}
for(var i = 0; i < title_var.length; i++)
{
var mycurrent_cell = document.createElement("td");
//mycurrent_cell.setAttribute("class", "featuretable_cell_decor" + i);
//mycurrent_cell.setAttribute("className", "featuretable_cell_decor" + i);
if(title_var[i] == "link_data")
{
for(var w = 0; w < array[j][title_var[i]].length; w++)
{
var content = document.createElement("img");
content.setAttribute("src", "/site_media/js/dasty2/client/img/ico_info2.gif");
content.setAttribute("alt", array[j][title_var[i]][w]);
content.setAttribute("border","0");
var link_content = document.createElement("a");
link_content.setAttribute("target", "_featurelinks");
link_content.setAttribute("href", array[j]["link_href"][w]);
link_content.appendChild(content);
mycurrent_cell.appendChild(link_content);
}
}
else if(title_var[i] == "version")
{
for(var w = 0; w < array[j][title_var[i]].length; w++)
{
var content = document.createElement("img");
content.setAttribute("src", "/site_media/js/dasty2/client/img/checkmark.gif");
//content.setAttribute("alt", array[j][title_var[i]][w]);
content.setAttribute("border","0");
//var link_content = document.createElement("a");
//link_content.setAttribute("target", "_version");
//link_content.setAttribute("href", array[j]["link_href"][w]);
//link_content.appendChild(content);
mycurrent_cell.appendChild(content);
}
}
else if(title_var[i] == "note_data")
{
for(var w = 0; w < array[j][title_var[i]].length; w++)
{
var content = document.createTextNode(array[j][title_var[i]][w]);
mycurrent_cell.appendChild(content);
var br = document.createElement("br");
mycurrent_cell.appendChild(br);
}
}
else
{
var content = document.createTextNode(array[j][title_var[i]]);
mycurrent_cell.appendChild(content);
}
//title_width["link_data"] = 5;
//title["link_href"] = "LINK";
mycurrent_row.appendChild(mycurrent_cell);
}
mytbody.appendChild(mycurrent_row);
} // if (array[j]["start_data"]==0 && array[j]["end_data"]==0)
} // for(var j = 0; j < array.length; j++)
} //if(npf_num == 0)
}
/*
* data used for some of the javascript tree examples. share! :-)
*/
function create_ontology_tree()
{
// parseOntology(1, onto_path_type);
// parseOntology(2, onto_path_category);
}
/**
* Create Server Tree for the Server secction in the Ontology panel
*/
function create_server_tree()
{
var elementChecked = 2;
var server_tree_element = new Array;
server_tree_element[0] = new Array;
server_tree_element[0]['dataContainer'] = "Servers";
server_tree_element[0]['caption'] = "Servers";
server_tree_element[0]['isOpen'] = true;
server_tree_element[0]['isChecked'] = 2;
server_tree_element[0]['children'] = new Array;
for(var c = 0; c < dasty2.loadedDasSources.length; c++)
{
elementChecked = 2;
for(var n = 0; n < excluded_das_sources.length; n++)
{
if(excluded_das_sources[n].toLowerCase() == dasty2.loadedDasSources[c].toLowerCase())
{
elementChecked = 0;
}
}
server_tree_element[0]['children'][c] = new Array;
server_tree_element[0]['children'][c]['dataContainer'] = dasty2.loadedDasSources[c];
server_tree_element[0]['children'][c]['caption'] = dasty2.loadedDasSources[c];
server_tree_element[0]['children'][c]['isChecked'] = elementChecked;
server_tree_element[0]['children'][c]['onChangeCheckbox'] = display_ontology_servers;
server_tree_element[0]['children'][c]['onClick'] = "javascript:printOnSystemInformation('" + dasty2.loadedDasSources[c] + " DAS Source')";
}
server_tree = new Bs_Tree();
server_tree.imageDir = 'http://www.gpcr.org/7tm/dasty2/client/library/blueshoes46/components/tree/img/win98/';
server_tree.checkboxSystemImgDir = 'http://www.gpcr.org/7tm/dasty2/client/library/blueshoes46/components/checkbox/img/win2k_noBorder/';
server_tree.useCheckboxSystem = true;
server_tree.checkboxSystemWalkTree = 3;
server_tree.initByArray(server_tree_element);
server_tree.drawInto('display_maniputation_options3_server_div');
}
/**
* Hide or display ontology types on the graphic
*/
function display_ontology_servers(treeElement)
{
if(treeElement.isChecked == 2 || treeElement.isChecked == 0)
{
display_ontology(treeElement, "server");
}
}
function display_ontology_types(treeElement)
{
if(treeElement.isChecked == 2 || treeElement.isChecked == 0)
{
display_ontology(treeElement, "type");
}
}
function display_ontology_categories(treeElement)
{
if(treeElement.isChecked == 2 || treeElement.isChecked == 0)
{
display_ontology(treeElement, "category");
}
}
function display_ontology(treeElement, classification)
{
var linesPerClassification = lookForIdLines(treeElement.dataContainer, classification);
var display_block = 'block';
for(var j = 0; j < linesPerClassification[0].length; j++)
{
display_block = 'block';
//printOnTest("LINES: " + linesPerClassification[j]);
if(linesPerClassification[0][j].indexOf("npf_item") != -1)
{
if(browser_name != "Microsoft Internet Explorer")
{
display_block = "table-row";
}
}
var e=document.getElementById(linesPerClassification[0][j]);
var element_display = e.style.display;
if(treeElement.isChecked == 2 && element_display == 'none')
{
e.style.display = display_block;
var style_change = true;
if(typeof dasty2.line_id_name2[linesPerClassification[0][j]] != "undefined")
{
dasty2.line_id_name2[linesPerClassification[0][j]] = 1;
}
}
else if(treeElement.isChecked == 0 && element_display == display_block)
{
e.style.display = 'none';
var style_change = true;
if(typeof dasty2.line_id_name2[linesPerClassification[0][j]] != "undefined")
{
dasty2.line_id_name2[linesPerClassification[0][j]] = 0;
}
}
//printOnTest(linesPerClassification[j]);
}
var height_difference = parseInt((linesPerClassification[0].length - linesPerClassification[1]) * (height_graphic_feature + 7));
for(var j = 0; j < vertical_bars; j++)
{
if(treeElement.isChecked == 2 && style_change == true)
{
var new_height = parseInt(getPxHeightFromStyle("gr_scalebar_div_" + j)) + height_difference;
}
else if(treeElement.isChecked == 0 && style_change == true)
{
var new_height = parseInt(getPxHeightFromStyle("gr_scalebar_div_" + j)) - height_difference;
}
//printOnTest("gr_scalebar_div_" + j);
//printOnTest(getPxHeightFromStyle("gr_scalebar_div_" + j));
//printOnTest(new_height);
resize_height = document.getElementById("gr_scalebar_div_" + j);
resize_height.style.height = new_height + "px";
//resize_height.style.cssText = "height:" + new_height + "px";
//printOnTest(resize_height.style.height);
}
//dasty2.IdlinesPerType[treeElement.dataContainer].length
//
}
// TYPE name: dasty2.IdlinesPerType[w][0]
// Lines ID with one TYPE: dasty2.IdlinesPerType[w][1]
// CATEGORY name: dasty2.IdlinesPerType[w][2]
// Number of lines: dasty2.IdlinesPerType[w][3]
function lookForIdLines(target, classification)
{
var npf_item_perClassification = 0;
var idLines = [];
if(classification == "type")
{
for(var j = 0; j < dasty2.IdlinesPerType.length; j++)
{
if(dasty2.IdlinesPerType[j][0].toLowerCase() == target.toLowerCase())
{
for(var r = 0; r < dasty2.IdlinesPerType[j][2]; r++)
{
if(dasty2.IdlinesPerType[j][1][r].indexOf("npf_item") != -1)
{
npf_item_perClassification++;
}
idLines.push(dasty2.IdlinesPerType[j][1][r]);
}
}
}
}
else if(classification == "category")
{
for(var j = 0; j < dasty2.IdlinesPerCategory.length; j++)
{
var category_name = dasty2.IdlinesPerCategory[j][0].toLowerCase();
if(target == "")
{
if(category_name == target)
{
for(var r = 0; r < dasty2.IdlinesPerCategory[j][2]; r++)
{
if(dasty2.IdlinesPerCategory[j][1][r].indexOf("npf_item") != -1)
{
npf_item_perClassification++;
}
idLines.push(dasty2.IdlinesPerCategory[j][1][r]);
}
}
}
else
{
if(category_name.indexOf(target.toLowerCase()) > -1)
{
for(var r = 0; r < dasty2.IdlinesPerCategory[j][2]; r++)
{
if(dasty2.IdlinesPerCategory[j][1][r].indexOf("npf_item") != -1)
{
npf_item_perClassification++;
}
idLines.push(dasty2.IdlinesPerCategory[j][1][r]);
}
}
}
}
}
else if(classification == "server")
{
for(var j = 0; j < dasty2.IdlinesPerServer.length; j++)
{
if(dasty2.IdlinesPerServer[j][0].toLowerCase() == target.toLowerCase())
{
for(var r = 0; r < dasty2.IdlinesPerServer[j][2]; r++)
{
if(dasty2.IdlinesPerServer[j][1][r].indexOf("npf_item") != -1)
{
npf_item_perClassification++;
}
idLines.push(dasty2.IdlinesPerServer[j][1][r]);
}
}
}
}
//printOnTest(target + " / " +idLines + " / " + idLines.length);
return [idLines, npf_item_perClassification];
}
function printOnSystemInformation(message)
{
document.getElementById("system_information").innerHTML = message;
}
/**¨
* The algorithm go through the tree from the root to the leafs, when
* find a leaf calls the method isType to see if is a currently used type.
* If is not, the leaf is deleted.
* When all the leafs are deleted its parent is also deleted
* @return
* 0: if the element wasn't pruned
* 1: if the element was pruned
*
**/
function recursivePrune(elem){
var children=elem.getChildren();
var i=0;
for (i=0;i------------
temp_zoom_start:" + temp_zoom_start + " zoom_end:" + zoom_end + " zoom_width:" + zoom_width + " temp_zoom_end:" + temp_zoom_end + " seq_stop:" + seq_stop);
}
createAaDistanceList(num_of_bars, seq_width);
createPixelDistanceList(seq_width, left_div_graphic);
//alert(bar_px_distance_list);
var scalebar_ul = document.createElement("ul");
scalebar_ul.setAttribute("id", "gr_scalebar_ul");
scalebar_ul.setAttribute("class", "gr_scalebar");
scalebar_ul.setAttribute("className", "gr_scalebar");
//scalebar_ul.setAttribute("style", "width:" + width_ul + "px;");
scalebar_ul.style.cssText = "width:" + width_ul + "px;";
var scalebar_li = document.createElement("li");
scalebar_li.setAttribute("id", "gr_scalebar_li");
//scalebar_li.setAttribute("style", "height:" + tittle_height + "px;"); // tittle_height is gloabal!
scalebar_li.style.cssText = "height:" + tittle_height + "px;";
scalebar_ul.appendChild(scalebar_li);
return scalebar_ul;
}
function fillScaleBar()
{
if( zoom_end != 0)
{
var zoom_width = zoom_end - zoom_start;
var seq_width = zoom_width;
//alert(zoom_width);
}
else
{
var seq_start = sequence_info.sequence_start -1;
var seq_stop = sequence_info.sequence_stop;
var seq_width = seq_stop - seq_start;
}
var height_div = (dasty2.countVisibleLines * (height_graphic_feature + 7)) + (tittle_height * 2) + 1;
if(browser_name == "Microsoft Internet Explorer")
{
height_div = height_div + 3;
}
var scalebar = document.getElementById("gr_scalebar_li");
var div_width = setDivLength(seq_width);
for(var b = 0; b < bar_px_distance_list.length; b++)
{
//if(b == 0 || b == (bar_px_distance_list.length -1))
//{
// skip drawing
//}
//else
//{
// ----------------------------------------------------------------------------------
// POSITION BARS
// ----------------------------------------------------------------------------------
var scalebar_div_graphic = document.createElement("div");
//scalebar_div_graphic.setAttribute("class", "gr_div gr_row_0" + bg_color + " gr_cell_02");
scalebar_div_graphic.setAttribute("id", "gr_scalebar_div_" + b);
scalebar_div_graphic.setAttribute("class", "gr_div gr_scalebar_div");
scalebar_div_graphic.setAttribute("className", "gr_div gr_scalebar_div");
if( zoom_end != 0)
{
//scalebar_div_graphic.setAttribute("style", "top:0px; left:" + (bar_px_distance_list[b] - div_width + 1) + "px; width:" + div_width + "px; height:" + height_div + "px;");
scalebar_div_graphic.style.cssText = "top:0px; left:" + (bar_px_distance_list[b] - div_width + 1) + "px; width:" + div_width + "px; height:" + height_div + "px;";
}
else
{
//scalebar_div_graphic.setAttribute("style", "top:0px; left:" + (bar_px_distance_list[b] - div_width + 1) + "px; width:" + div_width + "px; height:" + height_div + "px;");
scalebar_div_graphic.style.cssText = "top:0px; left:" + (bar_px_distance_list[b] - div_width + 1) + "px; width:" + div_width + "px; height:" + height_div + "px;";
} // if( zoom_end != 0)
scalebar.appendChild(scalebar_div_graphic);
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
value:" + bar_px_distance_list[b] + " div:" + div_width);
//opa.innerHTML = (content_opa + "
------------
temp_zoom_start:" + temp_zoom_start + " zoom_end:" + zoom_end + " zoom_width:" + zoom_width + " temp_zoom_end:" + temp_zoom_end + " seq_stop:" + seq_stop);
// ----------------------------------------------------------------------------------
// POSITION NUMBERS
// ----------------------------------------------------------------------------------
var left_position = bar_px_distance_list[b] + 3;
var scalebar_position = document.createElement("span");
scalebar_position.setAttribute("class", "gr_scalebar_span");
scalebar_position.setAttribute("className", "gr_scalebar_span");
//scalebar_position.setAttribute("style", "top:0px; left:" + left_position + "px;");
scalebar_position.style.cssText = "top:0px; left:" + left_position + "px;";
var scalebar_position_content = document.createTextNode(bar_aa_distance_list[b]);
scalebar_position.appendChild(scalebar_position_content);
scalebar.appendChild(scalebar_position);
//} // if(b == 0 || b == (bar_px_distance_list.length -1))
} // for(var b = 0; b < bar_px_distance_list.length; b++)
}
function createAaDistanceList(num_of_bars, seq_width)
{
var num_of_bars_temp = num_of_bars;
if(seq_width < 16 && num_of_bars_temp > 4)
{
var num_of_bars = 4;
}
if(seq_width < 8 && num_of_bars_temp > 2)
{
var num_of_bars = 2;
}
var bar_aa_distance = (seq_width / num_of_bars);
//alert(bar_aa_distance);
var bar_aa_distance_correction = parseInt(bar_aa_distance/10);
//alert(bar_aa_distance_correction);
if(bar_aa_distance_correction > 0)
{
var bar_aa_distance_correction_value = parseInt(bar_aa_distance_correction.toString() + "0");
}
else
{
var bar_aa_distance_correction_value = parseInt(bar_aa_distance);
}
//bar_aa_distance_correction = bar_aa_distance;
//alert(bar_aa_distance_correction);
//var num_of_bars_correction = num_of_bars -1;
bar_aa_distance_list.push(1);
for(var b = 1; b < num_of_bars; b++)
{
bar_aa_distance_list.push(bar_aa_distance_correction_value * b);
}
bar_aa_distance_list.push(seq_width);
//alert(bar_aa_distance_list);
}
function createPixelDistanceList(seq_width, left_div_graphic)
{
for(var b = 0; b < bar_aa_distance_list.length; b++)
{
bar_px_distance_list.push(((width_div_graphic_correction * bar_aa_distance_list[b])/seq_width) + left_div_graphic);
// bar_px_distance_list.push(((width_div_graphic_correction * bar_aa_distance_list[b])/seq_width) + 1 + left_div_graphic);
}
if( zoom_end != 0)
{
if(zoom_start == 0 || zoom_start == 1)
{
// Don't add startZoom to bar_aa_distance_list
}
else
{
addZoomToBar_aa_distance_list();
}
}
}
function addZoomToBar_aa_distance_list()
{
//var aa_start = parseInt(zoom_start/10);
for(var b = 0; b < bar_aa_distance_list.length; b++)
{
// bar_aa_distance_list[b] = bar_aa_distance_list[b] + parseInt(aa_start.toString() + "0");
bar_aa_distance_list[b] = bar_aa_distance_list[b] + (zoom_start);
}
}
function setDivLength(seq_width)
{
var div_width_temp = width_div_graphic_correction / seq_width;
var div_width = 0;
if (div_width_temp < 1)
{
div_width = 1;
}
else
{
div_width = div_width_temp;
}
return div_width
}//------------------------------------------------------------------------------------------
// CREATE QUERY INFORMATION FIELD
//------------------------------------------------------------------------------------------
function createQueryInformationField(object, tagId)
{
var div = document.getElementById(tagId);
var a = document.createElement("span");
a.setAttribute("id", "display_query_id_title");
a.setAttribute("class", "title");
a.setAttribute("className", "title");
a.appendChild(document.createTextNode("Sequence ID: "));
div.appendChild(a);
var uniprot_link = document.createElement("a");
uniprot_link.setAttribute("target", "_uniprot");
uniprot_link.setAttribute("href", "http://beta.uniprot.org/uniprot/" + object["sequence_id"]);
var uniprot_acc = document.createTextNode(object["sequence_id"]);
uniprot_link.appendChild(uniprot_acc);
var b = document.createElement("span");
b.setAttribute("id", "display_query_id_content");
b.appendChild(uniprot_link);
div.appendChild(b);
var c = document.createElement("br");
div.appendChild(c);
var d = document.createElement("span");
d.setAttribute("id", "display_query_length_title");
d.setAttribute("class", "title");
d.setAttribute("className", "title");
d.appendChild(document.createTextNode("Sequence length: "));
div.appendChild(d);
var e = document.createElement("span");
e.setAttribute("id", "display_query_length_content");
e.appendChild(document.createTextNode(object["sequence_length"]));
div.appendChild(e);
document.getElementById('zoom_start_px').value = 1;
document.getElementById('zoom_end_px').value = object["sequence_length"];
}
////------------------------------------------------------------------------------------------
// CREATE SEQUENCE TEXT CONTENT
//------------------------------------------------------------------------------------------
function createSequenceField(tagId)
{
var sequenceDiv = document.createElement("div");
sequenceDiv.setAttribute("id", "display_seque_protein");
sequenceDiv.setAttribute("class", "sequence_format");
sequenceDiv.setAttribute("className", "sequence_format");
// sequenceDiv.setAttribute("onmouseup", "getSequenceRangeSelected(this)");
//sequenceDiv.appendChild(document.createTextNode(text));
document.getElementById(tagId).appendChild(sequenceDiv);
//highlightSequence(0, 0, sequence_limit); // this function will take the "sequence" global variable with the aa sequence
//makeRequest('xml/server_list.xml', 'serverListXML');
//makeStylesheetRequest();
sequenceDiv.innerHTML = sequence;//(new_sequence);
}
//// JavaScript Document
//------------------------------------------------------------------------------------------
// ZOOM SLIDE BAR
//------------------------------------------------------------------------------------------
function createSlideBar(width_ul, left_div_graphic, width_div_graphic)
{
var slidebar_ul = document.createElement("ul");
slidebar_ul.setAttribute("id", "gr_slidebar_ul");
slidebar_ul.setAttribute("class", "gr_slidebar");
slidebar_ul.setAttribute("className", "gr_slidebar");
//slidebar_ul.setAttribute("style", "width:" + width_ul + "px;");
//slidebar_ul.style.setAttribute('cssText', "width:" + width_ul + "px;");
slidebar_ul.style.cssText = "width:" + width_ul + "px;";
var slidebar_li = document.createElement("li");
slidebar_li.setAttribute("id", "gr_slidebar_li");
//slidebar_li.setAttribute("style", "height:" + tittle_height + "px;"); // tittle_height is gloabal!
//slidebar_li.style.setAttribute('cssText', "height:" + tittle_height + "px;");
slidebar_li.style.cssText = "height:" + tittle_height + "px;";
slidebar_ul.appendChild(slidebar_li);
var slidebar_div = document.createElement("div");
slidebar_div.setAttribute("id", "gr_slidebar_div_track");
//slidebar_div.setAttribute("style", "width:"+ width_div_graphic +"px;background-color:#E4E4E4;height:5px;position:relative;left:" + (left_div_graphic + 1) + "px;");
//slidebar_div.style.setAttribute('cssText', "width:"+ width_div_graphic +"px;background-color:#E4E4E4;height:5px;position:relative;left:" + (left_div_graphic + 1) + "px;");
slidebar_div.style.cssText = "width:"+ width_div_graphic +"px;background-color:#E4E4E4;height:5px;position:relative;left:" + (left_div_graphic + 1) + "px;display:none;";
slidebar_li.appendChild(slidebar_div);
var slidebar_div_thumb_01 = document.createElement("div");
slidebar_div_thumb_01.setAttribute("id", "gr_slidebar_div_thumb_01");
//slidebar_div_thumb_01.setAttribute("style", "cursor:e-resize;position:absolute;top:0;left:0;width:5px;height:10px;background-color:#f00;opacity:.70; filter: alpha(opacity=70);");
//slidebar_div_thumb_01.style.setAttribute('cssText', "cursor:e-resize;position:absolute;top:0;left:0;width:5px;height:10px;background-color:#f00;opacity:.70; filter: alpha(opacity=70);");
slidebar_div_thumb_01.style.cssText = "cursor:e-resize;position:absolute;top:0;left:0;width:5px;height:10px;background-color:#f00;opacity:.70; filter: alpha(opacity=70);";
slidebar_div.appendChild(slidebar_div_thumb_01);
var slidebar_div_thumb_02 = document.createElement("div");
slidebar_div_thumb_02.setAttribute("id", "gr_slidebar_div_thumb_02");
//slidebar_div_thumb_02.setAttribute("style", "cursor:w-resize;position:absolute;top:0;left:0;width:5px;height:10px;background-color:#f00;opacity:.70; filter: alpha(opacity=70);");
//slidebar_div_thumb_02.style.setAttribute('cssText', "cursor:w-resize;position:absolute;top:0;left:0;width:5px;height:10px;background-color:#f00;opacity:.70; filter: alpha(opacity=70);");
slidebar_div_thumb_02.style.cssText = "cursor:w-resize;position:absolute;top:0;left:0;width:5px;height:10px;background-color:#f00;opacity:.70; filter: alpha(opacity=70);";
slidebar_div.appendChild(slidebar_div_thumb_02);
//
return slidebar_ul;
}
function activateSlideBar(start_feature, end_feature, handle_start_id, handle_end_id, track_id, show_start_id, show_end_id)
{
var end_feature_temp = end_feature;
if(end_feature_temp == 0 || end_feature_temp == "")
{
start_feature = sequence_info.sequence_start;
end_feature = sequence_info.sequence_stop;
}
var slider = new Control.Slider([handle_start_id,handle_end_id],track_id,{
range:$R(parseInt(start_feature),parseInt(end_feature)), // start seq, end seq
sliderValue:[parseInt(start_feature),parseInt(end_feature)], // start seq, end seq
restricted:true,
//onSlide:function(v){document.getElementById(show_start_id).value = parseInt(v[0]); document.getElementById(show_end_id).value =parseInt(v[1]);}});
onSlide:function(v){v = v; document.getElementById(show_start_id).value = parseInt(v[0]); document.getElementById(show_end_id).value =parseInt(v[1]);}});
//onChange:function(v){$('debug6').innerHTML='Changed: '+ v[0]; $(name_debug).innerHTML='Changed: '+ v[1];}});
//onSlide:function(v){$('debug6').innerHTML='slide: '+ v},
//onChange:function(v){$('debug6').innerHTML='changed! '+v.inspect()}});
}
// JavaScript Document
//------------------------------------------------------------------------------------------
// Hide/Show columns in the graphic
//------------------------------------------------------------------------------------------
function define_graphic_column(column_name)
{
var plus_icon = "![](\"/site_media/js/dasty2/client/img/tick01.gif\")
";
var minus_icon = "![](\"/site_media/js/dasty2/client/img/notick01.gif\")
";
switch (column_name)
{
case "category" :
if(show_col_category == 1)
{
show_col_category = 0;
var icon = document.getElementById("menu_mo_img_category_column");
icon.innerHTML = minus_icon;
}
else
{
show_col_category = 1;
var icon = document.getElementById("menu_mo_img_category_column");
icon.innerHTML = plus_icon;
}
break;
case "method" :
if(show_col_method == 1)
{
show_col_method = 0;
var icon = document.getElementById("menu_mo_img_method_column");
icon.innerHTML = minus_icon;
}
else
{
show_col_method = 1;
var icon = document.getElementById("menu_mo_img_method_column");
icon.innerHTML = plus_icon;
}
break;
case "type" :
if(show_col_type == 1)
{
show_col_type = 0;
var icon = document.getElementById("menu_mo_img_type_column");
icon.innerHTML = minus_icon;
}
else
{
show_col_type = 1;
var icon = document.getElementById("menu_mo_img_type_column");
icon.innerHTML = plus_icon;
}
break;
case "server" :
if(show_col_server == 1)
{
show_col_server = 0;
var icon = document.getElementById("menu_mo_img_server_column");
icon.innerHTML = minus_icon;
}
else
{
show_col_server = 1;
var icon = document.getElementById("menu_mo_img_server_column");
icon.innerHTML = plus_icon;
}
break;
case "id" :
if(show_col_id == 1)
{
show_col_id = 0;
var icon = document.getElementById("menu_mo_img_id_column");
icon.innerHTML = minus_icon;
}
else
{
show_col_id = 1;
var icon = document.getElementById("menu_mo_img_id_column");
icon.innerHTML = plus_icon;
}
break;
}
sorting();
}
//------------------------------------------------------------------------------------------
// EXPANDING
//------------------------------------------------------------------------------------------
function expanding()
{
document.getElementById("system_information").innerHTML = "Dasty2 is modifying the columns of the graphic ...";
if(isExpanded == 0)
{
isExpanded = 1;
e=document.getElementById('id_column');
e.style.display = 'block';
var plus_icon = "![](\"http://www.gpcr.org/7tm/dasty2/client/tick01.gif\")
";
var icon = document.getElementById("menu_mo_img_expand");
icon.innerHTML = plus_icon;
if(expanded_feature_list.length == 0)
{
var row = 0;
for(var a = 0; a < new_feature_list_info2.length; a++)
{
if(new_feature_list_info2[a])
{
for(var b = 0; b < new_feature_list_info2[a].length; b++)
{
for(var c = 0; c < new_feature_list_info2[a][b]["features"].length; c++)
{
expanded_feature_list[row] = [];
//expanded_feature_list[row]["features"] = [];
expanded_feature_list[row]["features"] = [new_feature_list_info2[a][b]["features"][c]];
expanded_feature_list[row]["feature_group"] = new_feature_list_info2[a][b]["feature_group"];
expanded_feature_list[row]["method"] = new_feature_list_info2[a][b]["method"];
expanded_feature_list[row]["type"] = new_feature_list_info2[a][b]["type"];
expanded_feature_list[row]["category"] = new_feature_list_info2[a][b]["category"];
//expanded_feature_list[row]["feature_id"] = new_feature_list_info2[a][b]["feature_id"];
expanded_feature_list[row]["feature_label"] = new_feature_list_info2[a][b]["feature_label"];
expanded_feature_list[row]["server"] = new_feature_list_info2[a][b]["server"];
expanded_feature_list[row]["xmlnumber"] = a;
expanded_feature_list[row]["version"] = annotation_version[a];
//one_feature_list[row] = new_feature_list_info2[a][b];
//one_feature_list[row]["xmlnumber"] = a;
row++
} // for(var c = 0; c < new_feature_list_info2[a][b]["features"].length; c++)
} // for(var b = 0; b < new_feature_list_info2[a].length; b++)
} // if(new_feature_list_info2[a])
} // for(var a = 0; a < new_feature_list_info2.length; a++)
} // if(expanded_feature_list.length == 0)
var graphic_content = document.getElementById("display_graphic");
graphic_content.innerHTML = '';
createGraphic2(0, "display_graphic", sequence_info.sequence_start, sequence_info.sequence_stop, "expanding");
//Sortable.create('gr_list0',{ghosting:true,constraint:false}); // Simpler
Sortable.create('gr_list0', {onUpdate:function(){new Effect.Highlight('gr_list0', {startcolor:'#CCCCCC'});}});
}
else
{
isExpanded = 0;
e=document.getElementById('id_column');
e.style.display = 'none';
var minus_icon = "![](\"http://www.gpcr.org/7tm/dasty2/client/img/notick01.gif\")
";
var icon = document.getElementById("menu_mo_img_expand");
icon.innerHTML = minus_icon;
sorting();
}
document.getElementById("system_information").innerHTML = "... Dasty2 finished to modify the columns of the graphic.";
//--------------------------------
//for(var lu = 0; lu < expanded_feature_list.length; lu++)
//{
//var new_feature_list = expanded_feature_list;
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
new_feature_list[" + lu + "][features]: " + new_feature_list[lu]["features"] + "::::: new_feature_list[" + lu + "][feature_group]: " + new_feature_list[lu]["feature_group"] + "::::: new_feature_list[" + lu + "][type]: " + new_feature_list[lu]["type"] + new_feature_list[lu]["category"] + new_feature_list[lu]["server"] + new_feature_list[lu]["xmlnumber"]);
//}
}
//------------------------------------------------------------------------------------------
//PRINT FUNCTION
//------------------------------------------------------------------------------------------
function printOnTest(arg)
{
var opa = document.getElementById("display_test");
var content_opa = opa.innerHTML;
opa.innerHTML = (content_opa + "
------------
Test:" + arg);
}
//------------------------------------------------------------------------------------------
// FUNCTIONS TO HIGHLIGHT SEQUENCE AND STRUCTURE
//------------------------------------------------------------------------------------------
/**
* stores start position of a new highlight request
*/
function addPos(x){
//document.getElementById("output").innerHTML = x;
selStart = x;
}
/**
* highlight the structure as per highlighted sequence
*/
function highlightStru(x){
var segUniprot;
if (x>selStart){
segUniprot=new segment(sequence_info.sequence_id,selStart,x);
}else {
segUniprot=new segment(sequence_info.sequence_id,x,selStart);
}
var segPDB=extrapolateSegment(segUniprot);
if (segPDB!=null)
selectPDBResidues(segPDB.start,segPDB.end);
}
function highlightSequence(fstart, fend, aa_num_per_line, color)
{
fstart-=1;fend-=1;
for(var i=0;i=fstart)&&(i<=fend)){
spanBase.setAttribute("class","highlightSequence");
spanBase.style.color=color;
// spanBase.style.border-bottom="1px";
}else{
spanBase.setAttribute("class","");
spanBase.style.color="black";
// spanBase.style.border-bottom="1px";
}
}
/*
var start = fstart - 1;
var end = fend;
var span_start = "";
//var span_start = ""; // "";
//var span_start = ""; //opacity:0.2;background-color: border:#009933;
var span_end = "";
var aa_num = aa_num_per_line; // 60
//alert(sequence);
//TEST
var text = '';
var new_sequence = '';
//var regex = /\W+/g;
//var regex = /\n+/g;
text = sequence; // sequence is Global
//text = text.replace(regex,""); //commented, must discuss if essential. It interferes with highlight idea
//alert(text);
var count = 0;
var count2 = 0;
var control = 0;
while (count < text.length)
{
count2 = count + aa_num;
control = 0;
if(count <= start && start < count2)
{
if(count <= end && end < count2)
{
new_sequence = new_sequence + text.substring(count, start) + span_start + text.substring(start, end) + span_end + text.substring(end, count2) + "
";
}
else
{
new_sequence = new_sequence + text.substring(count, start) + span_start + text.substring(start, count2) + "
";
}
}
else
{
if(count <= end && end < count2)
{
new_sequence = new_sequence + text.substring(count, end) + span_end + text.substring(end, count2) + "
";
}
else
{
new_sequence = new_sequence + text.substring(count, count2) + "
";
}
}
count = count2;
}
*/
// var opa = document.getElementById("display_seque_protein");
// var content_opa = opa.innerHTML;
// opa.innerHTML = seq;//(new_sequence);
}
//
//------------------------------------------------------------------------------------------
// FUNCTION TO SHOW AND HIDE CONTENT
//------------------------------------------------------------------------------------------
function changeDisplayState(child, img_span, img_num)
{
//d=document.getElementById(father);
e=document.getElementById(child);
if (e.style.display == 'none' || e.style.display =="") {
e.style.display = 'block';
if( img_span == null || img_span == "")
{
// Do nothing
}
else
{
var img_display = document.getElementById(img_span);
img_display.innerHTML = "![](\"/7tm/dasty2/client/img/minus0")
";
}
} else {
e.style.display = 'none';
if( img_span == null || img_span == "")
{
// Do nothing
}
else
{
var img_display = document.getElementById(img_span);
img_display.innerHTML = "![](\"/7tm/dasty2/client/img/plus0")
";
}
}
}
//------------------------------------------------------------------------------------------
// CHECK AND PUT THE RIGHT +/- ICONS IN THE MAIN HTML PAGE
//------------------------------------------------------------------------------------------
function checkSectionIcons()
{
var plus_icon = "![](\"/7tm/dasty2/client/img/minus02.gif\")
";
var plus_icon_white = "![](\"/7tm/dasty2/client/img/minus01.gif\")
";
var display_query_box = document.getElementById("display_query_box_div");
var menu_query_box_img = document.getElementById("menu_query_box_img");
if (display_query_box.style.display == 'block')
{
menu_query_box_img.innerHTML = plus_icon;
}
var display_checking = document.getElementById("display_checking_div");
var menu_checking_img = document.getElementById("menu_checking_img");
if (display_checking.style.display == 'block')
{
menu_checking_img.innerHTML = plus_icon;
}
var display_server_checking = document.getElementById("display_server_checking_div");
var menu_server_checking_img = document.getElementById("menu_server_checking_img");
if (display_server_checking.style.display == 'block')
{
menu_server_checking_img.innerHTML = plus_icon;
}
var display_query = document.getElementById("display_query_div");
var menu_query_img = document.getElementById("menu_query_img");
if (display_query.style.display == 'block')
{
menu_query_img.innerHTML = plus_icon;
}
var display_seque = document.getElementById("display_seque_div");
var menu_seque_img = document.getElementById("menu_seque_img");
if (display_seque.style.display == 'block')
{
menu_seque_img.innerHTML = plus_icon;
}
var display_feature_details = document.getElementById("display_feature_details_div");
var menu_feature_details_img = document.getElementById("menu_feature_details_img");
if (display_feature_details.style.display == 'block')
{
menu_feature_details_img.innerHTML = plus_icon;
}
var display_maniputation_options = document.getElementById("display_maniputation_options_div");
var menu_maniputation_options_img = document.getElementById("menu_maniputation_options_img");
if (display_maniputation_options.style.display == 'block')
{
menu_maniputation_options_img.innerHTML = plus_icon;
}
var display_maniputation_options3 = document.getElementById("display_maniputation_options3_div");
var menu_maniputation_options3_img = document.getElementById("menu_maniputation_options3_img");
if (display_maniputation_options3.style.display == 'block')
{
menu_maniputation_options3_img.innerHTML = plus_icon;
//menu_maniputation_options2_img.innerHTML = plus_icon_white;
}
var display_maniputation_options3_type = document.getElementById("display_maniputation_options3_type_div");
var menu_maniputation_options3_type_img = document.getElementById("menu_maniputation_options3_type_img");
if (display_maniputation_options3_type.style.display == 'block')
{
menu_maniputation_options3_type_img.innerHTML = plus_icon;
//menu_maniputation_options2_img.innerHTML = plus_icon_white;
}
var display_maniputation_options3_category = document.getElementById("display_maniputation_options3_category_div");
var menu_maniputation_options3_category_img = document.getElementById("menu_maniputation_options3_category_img");
if (display_maniputation_options3_category.style.display == 'block')
{
menu_maniputation_options3_category_img.innerHTML = plus_icon;
//menu_maniputation_options2_img.innerHTML = plus_icon_white;
}
var display_maniputation_options3_server = document.getElementById("display_maniputation_options3_server_div");
var menu_maniputation_options3_server_img = document.getElementById("menu_maniputation_options3_server_img");
if (display_maniputation_options3_server.style.display == 'block')
{
menu_maniputation_options3_server_img.innerHTML = plus_icon;
//menu_maniputation_options2_img.innerHTML = plus_icon_white;
}
var display_graphic = document.getElementById("display_graphic_div");
var menu_graphic_img = document.getElementById("menu_graphic_img");
if (display_graphic.style.display == 'block')
{
menu_graphic_img.innerHTML = plus_icon;
}
var display_nonpositional = document.getElementById("display_nonpositional_div");
var menu_nonpositional_img = document.getElementById("menu_nonpositional_img");
if (display_nonpositional.style.display == 'block')
{
menu_nonpositional_img.innerHTML = plus_icon;
}
var display_test = document.getElementById("display_test_div");
var menu_test_img = document.getElementById("menu_test_img");
if (display_test.style.display == 'block')
{
menu_test_img.innerHTML = plus_icon;
}
} // function checkIcons()
//------------------------------------------------------------------------------------------
// CHECK AND PUT THE RIGHT +/- ICONS IN THE MANIPULATION OPTIONS
//------------------------------------------------------------------------------------------
function checkMoColumnIcons()
{
var plus_icon = "![](\"/7tm/dasty2/client/img/tick01.gif\")
";
var minus_icon = "![](\"/7tm/dasty2/client/img/notick01.gif\")
";
var mo_img_category_column = document.getElementById("menu_mo_img_category_column");
if (show_col_category == 1)
{
mo_img_category_column.innerHTML = plus_icon;
}
else
{
mo_img_category_column.innerHTML = minus_icon;
}
var mo_img_method_column = document.getElementById("menu_mo_img_method_column");
if (show_col_method == 1)
{
mo_img_method_column.innerHTML = plus_icon;
}
else
{
mo_img_method_column.innerHTML = minus_icon;
}
var mo_img_type_column = document.getElementById("menu_mo_img_type_column");
if (show_col_type == 1)
{
mo_img_type_column.innerHTML = plus_icon;
}
else
{
mo_img_type_column.innerHTML = minus_icon;
}
var mo_img_server_column = document.getElementById("menu_mo_img_server_column");
if (show_col_server == 1)
{
mo_img_server_column.innerHTML = plus_icon;
}
else
{
mo_img_server_column.innerHTML = minus_icon;
}
var mo_img_id_column = document.getElementById("menu_mo_img_id_column");
if (show_col_id == 1)
{
mo_img_id_column.innerHTML = plus_icon;
}
else
{
mo_img_id_column.innerHTML = minus_icon;
}
if (show_popup == 2)
{
var menu_mo_img_popups = document.getElementById("menu_mo_img_popups");
menu_mo_img_popups.innerHTML = plus_icon;
}
//if(show_popup == 0)
//{
//var mo_img_popup_no = document.getElementById("menu_mo_img_popup_no");
//mo_img_popup_no.innerHTML = radio_icon;
//}
//else if(show_popup == 1)
//{
//var mo_img_popup_mouseover = document.getElementById("menu_mo_img_popup_mouseover");
//mo_img_popup_mouseover.innerHTML = radio_icon;
//}
//else
//{
//var mo_img_popup_mouseclick = document.getElementById("menu_mo_img_popup_mouseclick");
//mo_img_popup_mouseclick.innerHTML = radio_icon;
//}
} // function checkIcons()
//------------------------------------------------------------------------------------------
// FUNCTION TO FIND DOTS
//------------------------------------------------------------------------------------------
function isDot(s)
{
var dot;
var i;
var u = String(s);
loop:
for (i = 0; i < u.length; i++)
{
if (u[i] == ".") {
dot = "true";
break loop;
} else {
dot = "false";
}
}
if (dot == "false") { return false; } else { return true; }
}
//
//------------------------------------------------------------------------------------------
// IS NUMERIC
//------------------------------------------------------------------------------------------
function isNumeric(x)
{
var RegExp = /^(-)?(\d*)(\.?)(\d*)$/; // Note: this WILL allow a number that ends in a decimal: -452.
// compare the argument to the RegEx
// the 'match' function returns 0 if the value didn't match
var result = x.match(RegExp);
if (result==null) result=false;
return result;
}
//------------------------------------------------------------------------------------------
// Getting window size and scroll bars position
//------------------------------------------------------------------------------------------
// by http://www.softcomplex.com/docs/get_window_size_and_scrollbar_position.html
function f_clientWidth() {
return f_filterResults (
window.innerWidth ? window.innerWidth : 0,
document.documentElement ? document.documentElement.clientWidth : 0,
document.body ? document.body.clientWidth : 0
);
}
function f_clientHeight() {
return f_filterResults (
window.innerHeight ? window.innerHeight : 0,
document.documentElement ? document.documentElement.clientHeight : 0,
document.body ? document.body.clientHeight : 0
);
}
function f_scrollLeft() {
return f_filterResults (
window.pageXOffset ? window.pageXOffset : 0,
document.documentElement ? document.documentElement.scrollLeft : 0,
document.body ? document.body.scrollLeft : 0
);
}
function f_scrollTop() {
return f_filterResults (
window.pageYOffset ? window.pageYOffset : 0,
document.documentElement ? document.documentElement.scrollTop : 0,
document.body ? document.body.scrollTop : 0
);
}
function f_filterResults(n_win, n_docel, n_body) {
var n_result = n_win ? n_win : 0;
if (n_docel && (!n_result || (n_result > n_docel)))
n_result = n_docel;
return n_body && (!n_result || (n_result > n_body)) ? n_body : n_result;
}
//------------------------------------------------------------------------------------------
// PRELOAD IMAGES
//------------------------------------------------------------------------------------------
// http://elouai.com/javascript-preload-images.php
//------------------------------------------------------------------------------------------
function MM_preloadImages() { //v3.0
var d=document; if(d.images){ if(!d.MM_p) d.MM_p=new Array();
var i,j=d.MM_p.length,a=MM_preloadImages.arguments; for(i=0; iCargo and JMol by Fernando Fernando@softlech.com
//------------------------------------------------------------------------------------------
/**
* Initialize the Jmol Applet and load (so far hardcoded) a .pdb file
*/
function iniStructPanel(){
if (alignments==null)
{
//document.getElementById("applet").innerHTML="WARNING:Dasty2 could not find PDBs associated to this protein ID";
document.getElementById("display_protstru_div").innerHTML="
Dasty2 could not find PDBs associated to this protein ID on the 'biojavapdbuniprot' DAS aligment server
";
return;
}
else
{
document.getElementById("display_protstru_div").innerHTML=""
}
var divDd=document.getElementById("dropdown");
if (divDd!=null){
var select=document.createElement("select");
select.setAttribute("id","PDBlist");
//select.setAttribute("size","4"); // Rafael
select.size = 4;
//select.setAttribute("onchange","changeStructure(this);"); // Rafael
select.onchange = function() {changeStructure(this);};
var fileNames= getPDBfileNames();
for (i=0;i0){
if(alignments[0].blocks!=null){
segmentPDB=alignments[0].blocks[0].segments[0];
segmentUniprot=alignments[0].blocks[0].segments[1];
}
}
}
}
}
/**
* Private function to erase the spaces at the end and at the beggining of a String
*/
function trim(cadena){
var i=0;
for(i=0; i=0; i=cadena.length-1) {
if(cadena.charAt(i)==" ")
cadena=cadena.substring(0,i);
else
break;
}
return cadena;
}
/**
* Private function to get the initial jmol script to load a model
*/
function getJmolLoadScript() {
if (PDBid!="") {
var script ="load "+path_pdb_files+PDBid+".pdb; select all; cartoon on; wireframe off; spacefill off; color chain;";
return script;
}
alert("error in pdb file");
return null;
}
/**
* Public function. Call when selecting a range of PDB residues is needed
* @params: - start: first PDB residue to select, - end: final PDB residue to select
*/
function selectPDBResidues(start, end){
var divDd=document.getElementById("dropdown");
if (divDd!=null){
jmolScriptWait('selectionHalos ON');
var scr='select '+start+'-'+end;
if (structureChain!="")
scr=scr+':'+structureChain;
jmolScriptWait(scr);
}
}
/**
* Public Function. Call when selecting the region of a anotation is needed
* @params: - feature_row: , - feature_xmlnumber:
*/
function selectAnotationRegion(feature_row, feature_xmlnumber){
var objectTest = [];
objectTest = feature_info[feature_xmlnumber];
var segUniprot=new segment(sequence_info.sequence_id,objectTest[feature_row]["start_data"],objectTest[feature_row]["end_data"]);
var segPDB=extrapolateSegment(segUniprot);
if (segPDB!=null)
selectPDBResidues(segPDB.start,segPDB.end);
}
/**
* ON DEVELOPMENT
* Public Function. Get the value of some sequence position in the structure
* @params: - sequencePosition: Integer value for a position in the sequence.
* @return: Integer value for the position in the structure.
*/
function getValueInStructure(sequencePosition){
//TODO: call the alignment to get the value of some sequence position in the structure
var PDBList=document.getElementById("PDBlist");
if (PDBList!=null){
var PDBname=PDBList.value;
var structurePosition=extrapolatePosition(sequencePosition, PDBname);
return structurePosition;
}
}
/*
* ON DEVELOPMENT
* Public Function. get the number of the limits of a selection in the sequence DIV
* @params: - sequenceDiv: The DIV element in dasty, where a sequence is showed
*/
function getSequenceRangeSelected(sequenceDiv){
var tags=sequenceDiv.getElementsByTagName("*");
var salida='selecciono secuencia';
for (i=0; iUniprot Region: "+segmentUniprot.start+" To:"+segmentUniprot.end;
}
var div3=document.getElementById("Applet_Size");
div3.innerHTML="";
div3.appendChild(createDivOfSize());
}
function createDivOfSize(){
var div=document.createElement("div");
var small=document.createElement("input");
small.setAttribute("type","button");
small.setAttribute("value","Small");
small.setAttribute("onclick","changeAppletSize(330,330)");
div.appendChild(small);
var medium=document.createElement("input");
medium.setAttribute("type","button");
medium.setAttribute("value","Medium");
medium.setAttribute("onclick","changeAppletSize(600,600)");
div.appendChild(medium);
var large=document.createElement("input");
large.setAttribute("type","button");
large.setAttribute("value","Large");
large.setAttribute("onclick","changeAppletSize(800,800)");
div.appendChild(large);
return div;
}
function changeAppletSize(width, height){
var applet=document.getElementById("jmolApplet0");
applet.setAttribute("width",width);
applet.setAttribute("height",height);
var div=document.getElementById("display_protstru_div");
//div.setAttribute("width",width+100);
var div_width = width+20;
var div_height = height+120;
//div.style.cssText = "width:" + div_width + "px; height:" + div_height + "px;";
div.style.cssText = "width:" + div_width + "px;";
}
function printArray(array){
var texto="L="+array.length+" >";
var k=0;
for(k=0;k
//------------------------------------------------------------------------------
//
// start_dasty(0)
//
// Makes Dasty2 independent from the URL. You need to tell dasty2 what default
// configuration values you want to use. Use set_query to define them ...
// set_query('P05067', 'BioSapiens', 3, 'index.html'). Recommended option if you
// embed dasty2 in your own web site.
//------------------------------------------------------------------------------
//
// start_dasty(1)
//
// Dasty2 check first the attributes from the URL. Recomended!
//------------------------------------------------------------------------------
//
// start_dasty(2)
//
// Use it for redirections
//------------------------------------------------------------------------------
function start_dasty(url_control)
{
dasty_url_control = url_control;
query_id_null = 0; // "0" means that query ID is not null
if(url_control == 0)
{
start_globals();
}
else if(url_control == 1)
{
start_url();
}
else
{
//createDastyURLNewID('');
DastyRedirector();
}
}
// Use this function in body load when start_dasty(0) and when the serach module is hidden or off.
// onLoad="set_query('P05067', 'BioSapiens', 3), start_dasty(0);"
function set_query(q_id, q_label, q_timeout, q_template)
{
query_id = "";
filterLabel = "";
timeout = 3;
dasty_mainpage_name = "";
default_query_parameters();
if( q_id == null || q_id == "") { query_id = default_query_id; } else { query_id = q_id; };
if( q_label == null || q_label == "") { filterLabel = default_filterLabel; } else { filterLabel = q_label; };
if( q_id == null || q_id == "") { timeout = default_timeout; } else { timeout = q_timeout; };
if( q_template == null || q_template == "") { dasty_mainpage_name = default_dasty_mainpage_name; } else { filterLabel = template; };
}
function start_url()
{
query_id = "";
filterLabel = "";
timeout = 3;
dasty_mainpage_name = findDastyHtmlPageName('page_name') + "." + findDastyHtmlPageName('ext_name');
configuration();
//dasty_mainpage_name = findDastyHtmlPageName('page_name') + "." + findDastyHtmlPageName('ext_name');
default_query_parameters();
setDastyURLParam();
//if(dasty_mainpage_name.indexOf("interactorview") != -1)
//{
//populate_interactorview();
//}
// Query parameter keys : by Antony
// var QueryParamKeys = {
//id: "q",
//registryServer: "registry",
//registryLabel: "label",
//logLevel: "l",
//timeout: "t"
//};
}
function start_globals()
{
MM_preloadImages("/site_media/js/dasty2/client/img/blast_icon.gif", "/site_media/js/dasty2/client/css/window/mac_os_x/B.png", "/site_media/js/dasty2/client/css/window/mac_os_x/B_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/BL.png", "/site_media/js/dasty2/client/css/window/mac_os_x/BL_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/BR.png", "/site_media/js/dasty2/client/css/window/mac_os_x/BR_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/close.gif", "/site_media/js/dasty2/client/css/window/mac_os_x/L.png", "/site_media/js/dasty2/client/css/window/mac_os_x/L_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/maximize.gif", "/site_media/js/dasty2/client/css/window/mac_os_x/minimize.gif", "/site_media/js/dasty2/client/css/window/mac_os_x/R.png", "/site_media/js/dasty2/client/css/window/mac_os_x/R_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/T.png", "/site_media/js/dasty2/client/css/window/mac_os_x/T_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/TL.png", "/site_media/js/dasty2/client/css/window/mac_os_x/TL_Main.png", "/site_media/js/dasty2/client/css/window/mac_os_x/TR.png", "/site_media/js/dasty2/client/css/window/mac_os_x/TR_Main.png");
ontologyPrefix = ["GO:", "BS:", "ECO:", "MOD:", "SO:"];
browser_name = navigator.appName;
browser_version = navigator.appVersion;
// feature_url roperties: id, url, state, XML_num, general_order
// [].state => / 1 => have features / 2 => do not have features / 3 => Warning /
dasty_mainpage_name = findDastyHtmlPageName('page_name') + "." + findDastyHtmlPageName('ext_name');
configuration();
//dasty_mainpage_name = findDastyHtmlPageName('page_name') + "." + findDastyHtmlPageName('ext_name');
default_query_parameters();
if (typeof query_id == "undefined") { query_id = default_query_id; };
if (typeof filterLabel == "undefined") { filterLabel = default_filterLabel; };
if (typeof timeout == "undefined") { timeout = default_timeout; };
checkSectionIcons();
checkMoColumnIcons();
/*
// Set up a windows observer, check ou debug window to get messages
var myObserver = {
onClose: function(eventName, pdbWin) {
debug(eventName + " on " + pdbWin.getId())
if(pdbWin.getId() == "pdbWin")
{
printOnTest("ok");
changeStructure();
}
}
}
Windows.addObserver(myObserver);
*/
//------------------------------------------------------------------------------------------
// NECESSARY GLOBAL VARIABLES USED BY DASTY2
//------------------------------------------------------------------------------------------
dasty2 = new Object;
http_request = false;
// CREATED_IN: ajax.js // USED_IN: parse_sequence.js, parse_sequece.js, parse_serverlist.js, parse_stylesheet.js, request_xml.js
feature_http_request = [];
// CREATED_IN: request_xml.js // USED_IN: parse_feature.js
feature_info = [];
// CREATED_IN: parse_feature.js // USED_IN: create_graphic.js, create_feature_details.js
annotation_version = [];
stylesheet_properties_info = [];
// CREATED_IN: parse_stylesheet.js // USED_IN: create_graphics.js
//type_counter = [];
// CREATED_IN: parse_feature.js // USED_IN: create_graphic.js
//category_counter = [];
// CREATED_IN: parse_features.js // USED_IN: No yet!!!
new_feature_list_info = [];
new_feature_list_info2 = [];
// CREATED_IN: reorganize_types.js // USED_IN: create_graphic.js
sequence = '';
// CREATED_IN: parse_sequence.js // USED_IN: functions.js => highlightSequence()
//sequence_info = [];
sequence_info = new Object();
selStart = 1; // stores selection starting position
useHighlight = true; // if true, sequence will be transformed to support highlight technique
// CREATED_IN: parse_sequence.js // USED_IN:
//das_server = '';
// CREATED_IN: request_features.js // USED_IN: parse_feature.js
//featureXML_num = -1;
// CREATED_IN: request_features.js // USED_IN: request_xmls.js, parse_feature.js
bg_color = 1;
// CREATED_IN: global.js // USED_IN: create_graphic.js
one_feature_list = [];
expanded_feature_list = [];
sortOrderType = 0;
sortOrderMethod = 0;
sortOrderCategory = 0;
sortOrderServer = 0;
sortOrderVersion = 0;
zoom_start = 0;
zoom_end = 0;
show_graphic_tittle_temp = 1; // boolean 0/1. 0=no / 1=yes
show_scale_bar_temp = 1; // boolean 0/1. 0=no / 1=yes
show_slide_bar_temp = 1;
features_row_number = 0;
width_div_graphic_correction = 0;
bar_aa_distance_list = [];
bar_px_distance_list = [];
isExpanded = 0; // boolean 0/1. 0=no / 1=yes
//display = "free";
//standby = [];
count_displayed_groups = 0;
elements_http_request = [];
//das_registry_label = [];
progress_bar_width = getPxWidthFromStyle("progress_bar_empty");
servers_count = 0;
server_checking = "";
warning_count = 0;
no_feature_results_count = 0;
feature_results_count = 0;
results_XML_order = [];
popup_num = 0;
dasty2.loadedDasSources = [];
dasty2.excludedDasSources = [];
dasty2.loadedDasSources_temp = [];
dasty2.firstRequestNumber = 0;
dasty2.validFirstSources = [];
dasty2.typesLoaded = []; // It seems it is not beeing used. Try "dasty2.typesLoaded2".
dasty2.categoriesLoaded = [];
dasty2.IdlinesPerType = [];
dasty2.IdlinesPerCategory =[];
dasty2.IdlinesPerServer = [];
dasty2.temporalTree =[];
dasty2.temporalArray =[];
dasty2.line_id_name2 = new Array(); // Hash
dasty2.line_id_name2_length = 0;
dasty2.countVisibleLines = 0;
dasty2.firstTimeSortByType = true;
dasty2.typesLoaded2 = [];
dasty2.countIdType = [];
dasty2.countNPF = 0;
dasty2.decor_tr_npf = 0;
//PDB CHAIN
structureChain="";
segmentUniprot=null;
segmentPDB=null;
//------------------------------------------------------------------------------------------
// START APPLICATION
//------------------------------------------------------------------------------------------
//alert(filterLabel);
//alert(query_id);
//alert(timeout);
document.getElementById("system_information").innerHTML = "... please be patient, Dasty2 is loading data from the DAS servers";
document.getElementById("progress_bar_1").innerHTML = "";
document.getElementById("progress_bar_2").style.width = 0;
document.getElementById('feature_id_box').value = query_id;
document.getElementById("graphic_width_px").value = graphic_width;
filterLabel = filterLabel.replace(/%20/g, " ")
ajax();
} // function start_globals()
//------------------------------------------------------------------------------------------
// GROUPING
//------------------------------------------------------------------------------------------
function grouping(featureXML_num, type_counter, segment_start, segment_stop)
{
new_feature_list_info2[featureXML_num] = [];
for(var a = 0; a < type_counter.length; a++)
{
lookforSameIdType(featureXML_num, type_counter[a][1]);
}
createGraphic2(featureXML_num, "display_graphic", segment_start, segment_stop, "grouping");
//alert(new_feature_list_info2[featureXML_num].length);
//for(var lu = 0; lu < new_feature_list_info2[featureXML_num].length; lu++)
// {
// var new_feature_list = new_feature_list_info2[featureXML_num];
// var opa = document.getElementById("display_test");
// var content_opa = opa.innerHTML;
// opa.innerHTML = (content_opa + "
------------
new_feature_list[" + lu + "][features]: " + new_feature_list[lu]["features"] + "::::: new_feature_list[" + lu + "][feature_group]: " + new_feature_list[lu]["feature_group"] + "::::: new_feature_list[" + lu + "][type]: " + new_feature_list[lu]["type"] + new_feature_list[lu]["category"] + new_feature_list[lu]["server"]);
// }
}//------------------------------------------------------------------------------------------
// Create arrays "fids" and "same_fids" to be able to group features in the graphic.
//------------------------------------------------------------------------------------------
function lookforSameIdType(featureXML_num, type_counter)
{
//----------------------------------------------------------------------------------
// Look for features of the same feature ID and put this info in fids
// fids = [feature_id, [ids]]
//----------------------------------------------------------------------------------
var same_fids = []; // rows in fids with more than one feature id.
var fids = []; // feature ids
var feature_row_num = 0;
var add_fids = 0;
var add_same_fids = 0;
var tcounter = type_counter; // example: type_counter[0][1]; number of features rows for one type
var finfo = feature_info[featureXML_num];
//alert(finfo[0]["feature_id"]);
for(var i = 0; i < tcounter.length; i++)
{
feature_row_num = tcounter[i];
fids_length = fids.length;
if (fids_length == 0)
{
fids[fids_length] = [];
fids[fids_length][0] = finfo[feature_row_num]["feature_id"];
fids[fids_length][1] = [];
fids[fids_length][1].push(feature_row_num);
}
else
{
add_fids = 0;
for(var m = 0; m < fids_length; m++)
{
if(fids[m][0] == finfo[feature_row_num]["feature_id"])
{
fids[m][1].push(feature_row_num);
add_fids = 1;
//----------------------------------------------------------------------------------
// Get same_fids
// same_fids = [fids rows where there is more than one feature ID]
//----------------------------------------------------------------------------------
same_fids_length = same_fids.length;
if (same_fids_length == 0)
{
same_fids[same_fids_length] = m;
}
else
{
add_same_fids = 0;
for(var e = 0; e < same_fids_length; e++)
{
if(same_fids[e] == m) {add_same_fids = 1;}
}
if(add_same_fids == 0) {same_fids[same_fids_length] = m;}
}
//----------------------------------------------------------------------------------
}
}
if(dasty2_grouping == false) // RC. 03.05.08
{
same_fids = [];
add_fids = 0;
}
if(add_fids == 0)
{
fids[fids_length] = [];
fids[fids_length][0] = finfo[feature_row_num]["feature_id"];
fids[fids_length][1] = [];
fids[fids_length][1].push(feature_row_num);
}
}
}
//reorganizeIdTypes(finfo, fids, same_fids);
organizeIdTypes(featureXML_num, fids, same_fids);
//for(var lu = 0; lu < fids.length; lu++)
//{
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
fids[" + lu +"][0]:" + fids[lu][0] + " fids[" + lu +"][0]:" + fids[lu][1]);
//}
//for(var lu = 0; lu < same_fids.length; lu++)
//{
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
same_fids[" + lu + "]:" + same_fids[lu]);
//}
} // JavaScript Document
//------------------------------------------------------------------------------------------
// REQUEST INFORMATION FROM DIFFERENT XML SPECIFIYING A LOCAL URL.
//------------------------------------------------------------------------------------------
function newid(id, label)
{
//var labelName = "";
//if(label == null || label == ""){labelName = default_filterLabel} else {labelName = label};
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
info: " + document.getElementById(label) );
var new_feature_id = document.getElementById(id).value;
if(document.getElementById(label) == null)
{
filterLabel = default_filterLabel;
}
else
{
filterLabel = document.getElementById(label).value;
}
//var new_feature_label = document.getElementById(label).value;
//var display_query = document.getElementById("display_query");
//display_query.innerHTML = "";
//var display_seque = document.getElementById("display_seque");
//display_seque.innerHTML = "";
//var display_server_checking = document.getElementById("display_server_checking");
//display_server_checking.innerHTML = "";
//var display_feature_details = document.getElementById("display_feature_details");
//display_feature_details.innerHTML = "";
//var display_graphic = document.getElementById("display_graphic");
//display_graphic.innerHTML = "";
//var display_nonpositional = document.getElementById("display_nonpositional");
//display_nonpositional.innerHTML = "";
//var display_test = document.getElementById("display_test");
//display_test.innerHTML = "";
query_id = new_feature_id;
//filterLabel = new_feature_label;
if (dasty_url_control == 0)
{
var display_query = document.getElementById("display_query");
display_query.innerHTML = "";
var display_seque = document.getElementById("display_seque");
display_seque.innerHTML = "";
var display_server_checking = document.getElementById("display_server_checking");
display_server_checking.innerHTML = "";
var display_feature_details = document.getElementById("display_feature_details");
display_feature_details.innerHTML = "";
var display_ontology_types = document.getElementById("display_maniputation_options3_type_div");
display_graphic.innerHTML = "";
var display_ontology_types = document.getElementById("display_maniputation_options3_category_div");
display_graphic.innerHTML = "";
var display_graphic = document.getElementById("display_graphic");
display_graphic.innerHTML = "";
var display_nonpositional = document.getElementById("display_nonpositional");
display_nonpositional.innerHTML = "";
var display_test = document.getElementById("display_test");
display_test.innerHTML = "";
start_globals();
}
else
{
document.location.href = createDastyURL();
}
}
////------------------------------------------------------------------------------------------
// reorganize features ID in Types
//------------------------------------------------------------------------------------------
function organizeIdTypes(featureXML_num, fids, same_fids)
{
//------------------------------------------------------------------------------------------
// put the features with the same ID in the same line
//------------------------------------------------------------------------------------------
//alert("fids[0][1]:" + fids[0][1]);
//alert("same_fids:" + same_fids);
//alert("array:" + array[1]["feature_id"]);
var do_push = 0;
var non_same_fids = [];
var new_feature_list = [];
var line = [];
var line_length = 0;
var eline_length = 0;
var start_end = [];
var con_eline01 = 0;
var con_eline02 = 0;
var con_eline = 0;
var feature_included = 0;
var con_line = 0;
var array_row_num = 0;
var nfl_length =0;
var last_c = 0;
var line_id_name = [];
var line_name = "";
var lineIdValue = 1;
var finfo = feature_info[featureXML_num];
// new_feature_list_info = [];
//new_feature_list_info2 = [];
//------------------------------------------------------------------------------------------
// create an array with the features with the same id (same feature group id)
//------------------------------------------------------------------------------------------
for(var i = 0; i < same_fids.length; i++)
{
new_feature_list[i] = [];
new_feature_list[i]["line"] = i;
new_feature_list[i]["features"] = []; // FEATURES: Contains references to the features for the array "feature_info"
new_feature_list[i]["feature_group"] = 1; // FEATURE GROUP: boolean "1/0". "1" means feature with the same ID o group
new_feature_list[i]["type"] = finfo[fids[same_fids[i]][1][0]]["type_id"]; // TYPE
new_feature_list[i]["type_data"] = finfo[fids[same_fids[i]][1][0]]["type_data"]; // TYPE
new_feature_list[i]["category"] = finfo[fids[same_fids[i]][1][0]]["type_category"]; // CATEGORY
new_feature_list[i]["method"] = finfo[fids[same_fids[i]][1][0]]["method_data"]; // METHOD
//new_feature_list[i]["feature_id"] = finfo[fids[same_fids[i]][1][0]]["feature_id"]; // ID
new_feature_list[i]["feature_label"] = finfo[fids[same_fids[i]][1][0]]["feature_label"]; // ID
new_feature_list[i]["server"] = finfo[fids[same_fids[i]][1][0]]["annotation_server"]; // SERVER
new_feature_list[i]["registry_uri"] = finfo[fids[same_fids[i]][1][0]]["annotation_server_uri"]; // SERVER ID (REGISTRY URI)
new_feature_list[i]["version"] = annotation_version[finfo[fids[same_fids[i]][1][0]]["xmlnumber"]]; // ANNOTATION VERSION boolean "1/0". "1" means the feature file has the same version than the sequence file.
for(var a = 0; a < fids[same_fids[i]][1].length; a++)
{
new_feature_list[i]["features"].push(fids[same_fids[i]][1][a]);
}
line_name = "gr_item" + featureXML_num + "_" + new_feature_list[i]["type"] + "_" + new_feature_list[i]["line"];
line_id_name.push(line_name);
for(var n = 0; n < excluded_das_sources.length; n++)
{
if(excluded_das_sources[n].toLowerCase() == new_feature_list[0]["server"].toLowerCase())
{
lineIdValue = 0;
}
}
dasty2.line_id_name2[line_name] = lineIdValue;
dasty2.line_id_name2_length++;
}
if(same_fids.length > 0)
{
dasty2.IdlinesPerType.push([new_feature_list[0]["type"], line_id_name, line_id_name.length]);
dasty2.IdlinesPerCategory.push([new_feature_list[0]["category"], line_id_name, line_id_name.length]);
dasty2.IdlinesPerServer.push([new_feature_list[0]["server"], line_id_name, line_id_name.length]);
}
line_id_name = [];
//add_new_type = 0;
//------------------------------------------------------------------------------------------
// create an array with the feature id that are not reapeted => non_same_fids
//------------------------------------------------------------------------------------------
for(var i = 0; i < fids.length; i++)
{
do_push = 0;
for(var a = 0; a < same_fids.length; a++)
{
if(i == same_fids[a]) { do_push = 1; }
}
if(do_push == 0)
{
non_same_fids.push(i);
}
}
//------------------------------------------------------------------------------------------
// look for the rest of features IDs, check their ends and starts and try to overlap in the same line if possible
//------------------------------------------------------------------------------------------
for(var i = 0; i < non_same_fids.length; i++)
{
array_row_num = fids[non_same_fids[i]][1][0];
if (i == 0)
{
line[i] = [];
line[i].push(array_row_num);
start_end[i] = [];
start_end[i][0] = []; // START DATA
start_end[i][0].push(finfo[array_row_num]["start_data"]);
start_end[i][1] = []; // END DATA
start_end[i][1].push(finfo[array_row_num]["end_data"]);
}
else // (i == 0)
{
con_line = 0;
line_length = line.length;
line_loop:
for(var a = 0; a < line_length; a++)
{
con_eline = 0;
con_eline01 = 0;
con_eline02 = 0;
eline_length = line[a].length;
for(var b = 0; b < eline_length; b++)
{
start01 = finfo[array_row_num]["start_data"];
start02 = start_end[a][0][b];
end01 = finfo[array_row_num]["end_data"];
end02 = start_end[a][1][b];
con_eline01 = end02 - start01;
con_eline02 = end01 - start02;
if(con_eline01 < 0) { con_eline++ }
if(con_eline02 < 0) { con_eline++ }
}
if(con_eline == eline_length)
{ // include in the line
line[a].push(array_row_num);
start_end[a][0].push(finfo[array_row_num]["start_data"]);
start_end[a][1].push(finfo[array_row_num]["end_data"]);
break line_loop;
}
else
{ // not include in the line
con_line++;
}
} // for(var a = 0; a < line_length; a++)
if(con_line == line_length)
{ // include new line
line[line_length] = [];
line[line_length].push(array_row_num);
start_end[line_length] = [];
start_end[line_length][0] = []; // START DATA
start_end[line_length][0].push(finfo[array_row_num]["start_data"]);
start_end[line_length][1] = []; // END DATA
start_end[line_length][1].push(finfo[array_row_num]["end_data"]);
}
} // if (i == 0)
} // for(var i = 0; i < non_same_fids.length; i++)
//------------------------------------------------------------------------------------------
// concatenate "new_feature_list" with "line"
//------------------------------------------------------------------------------------------
nfl_length = new_feature_list.length;
for(var i = 0; i < line.length; i++)
{
new_feature_list[i+nfl_length] = [];
new_feature_list[i+nfl_length]["line"] = i+nfl_length;
new_feature_list[i+nfl_length]["features"] = []; // Contains references to the features for the array "feature_info"
new_feature_list[i+nfl_length]["feature_group"] = 0; // boolean. 1 mean feature with the same ID o group
new_feature_list[i+nfl_length]["type"] = finfo[fids[non_same_fids[i]][1][0]]["type_id"]; // TYPE ID
new_feature_list[i+nfl_length]["type_data"] = finfo[fids[non_same_fids[i]][1][0]]["type_data"]; // TYPE DATA
new_feature_list[i+nfl_length]["method"] = finfo[fids[non_same_fids[i]][1][0]]["method_data"]; // CATEGORY
new_feature_list[i+nfl_length]["category"] = finfo[fids[non_same_fids[i]][1][0]]["type_category"]; // CATEGORY
//new_feature_list[i+nfl_length]["feature_id"] = finfo[fids[non_same_fids[i]][1][0]]["feature_id"]; // ID
new_feature_list[i+nfl_length]["feature_label"] = finfo[fids[non_same_fids[i]][1][0]]["feature_label"]; // ID
new_feature_list[i+nfl_length]["server"] = finfo[fids[non_same_fids[i]][1][0]]["annotation_server"]; // SERVER
new_feature_list[i+nfl_length]["registry_uri"] = finfo[fids[non_same_fids[i]][1][0]]["annotation_server_uri"]; // SERVER ID (REGISTRY URI)
new_feature_list[i+nfl_length]["version"] = annotation_version[finfo[fids[non_same_fids[i]][1][0]]["xmlnumber"]]; // ANNOTATION VERSION
for(var a = 0; a < line[i].length; a++)
{
new_feature_list[i+nfl_length]["features"].push(line[i][a]);
}
line_name = "gr_item" + featureXML_num + "_" + new_feature_list[i+nfl_length]["type"] + "_" + new_feature_list[i+nfl_length]["line"];
line_id_name.push(line_name);
for(var n = 0; n < excluded_das_sources.length; n++)
{
if(excluded_das_sources[n].toLowerCase() == new_feature_list[nfl_length]["server"].toLowerCase())
{
lineIdValue = 0;
}
}
dasty2.line_id_name2[line_name] = lineIdValue;
dasty2.line_id_name2_length++;
}
if(line_id_name.length > 0)
{
dasty2.IdlinesPerType.push([new_feature_list[nfl_length]["type"], line_id_name, line_id_name.length]);
dasty2.IdlinesPerCategory.push([new_feature_list[nfl_length]["category"], line_id_name, line_id_name.length]);
dasty2.IdlinesPerServer.push([new_feature_list[nfl_length]["server"], line_id_name, line_id_name.length]);
}
for(var b = 0; b < new_feature_list.length; b++)
{
new_feature_list_info2[featureXML_num].push(new_feature_list[b]);
}
//create_graphic2("display_graphic", segment_start, segment_stop);
} // function reorganizeIdTypes(array) // Fernando's code to get started with pasing alignments
var testing = false, // used for testing
alignments = new Array(), // array of parsed alignments
nalignments = 0; // number of alignments
/**
* called with url of alignment file to load and parse
*/
function parseAlignment(url){
loadAlignment(url);
}
// <------------- definition of an alignment -------------->
/**
* defines an alignObject contained withing an alignment
* @params: accessionid,type,dbsource: attributes of the alignmentObject
* header,title,description: this three are properties of alignObjectDetail for a PDB
*/
function alignObject(accessionid,type,dbsource,header,title,description){
this.accessionid = accessionid;
this.type = type;
this.dbsource = dbsource;
this.header = header;
this.title =title;
this.description = description;
}
/**
* defines a segment contained withing an alignment block
* @params: objid: intObjectId, start: start attribute, end: end attribute
*/
function segment(objid,start,end){
this.objid = objid;
this.start = start;
this.end = end;
}
/**
* Compare 2 segments and return a boolean
*/
segment.prototype.equals=function(segm){
if ((this.objid==segm.objid)&&(this.start==segm.start)&&(this.end==segm.end)){
return true;
}
return false;
}
/**
* defines a block contained withing an alignment
* @params: order: blockOrder attribute, segments: segments found in block
*/
function block(order,segments){
this.order = order;
this.segments = segments;
}
/**
* defines an alignment
* @params: atype: alignType attribute, blocks: blocks found in the alignment
*/
function alignment(atype,alignObjects,blocks){
this.atype = atype;
this.alignObjects = alignObjects;
this.blocks = blocks;
}
// <------------ Loading and Parsing --------------->
/**
* parse the xml alignment file received in doc
*/
function doParseAligment(doc){
var alignElms = doc.documentElement.getElementsByTagName("alignment");
if (alignElms.length==0){
alignments=null;
}
if(testing){
document.getElementById("nalgn").innerHTML = alignElms.length;
}
adata = document.getElementById("algdata");
var s = "";
for(var i=0;iStart: '+segPDB.start+'
End: '+segPDB.end;
}
adata.innerHTML = listAlignments()+extra;
}
}
/**
* parse an xml alignObject
*/
function parseAlignObject(obj){
accessionid = obj.attributes.getNamedItem("dbAccessionId").value;
type = obj.attributes.getNamedItem("type").value;
dbsrc = obj.attributes.getNamedItem("dbSource").value;
adetails = new Array();ndets = 0;header="";title="";descr="";
for(var k=0;k0)
{
property = detail.attributes.getNamedItem("property").value; // printOnTest("type:"+type+" ,prop:"+property);
switch(property){
case "header":
header = getNodeData(detail);
break;
case "title":
title = getNodeData(detail);
break;
case "molecule description":
descr = getNodeData(detail);
break;
}
}
}
}
return new alignObject(accessionid,type,dbsrc,header,title,descr);
}
/**
* return content if text node, empty string otherwise
*/
function getNodeData(node){
if(!node.hasChildNodes)
return "";
for(var j=0;j0)
{
intObjectId = segm.attributes.getNamedItem("intObjectId").value;
start = segm.attributes.getNamedItem("start").value;
end = segm.attributes.getNamedItem("end").value;
segments[nsegms++] = new segment(intObjectId,start,end);
}
}
}
return new block(blockOrder,segments);
}
function listAlignments(){
s = "";
for(i=0;iAlignmentType: "+alignments[i].atype+"
";
if(alignments[i].blocks!=null)
for(j=0;j";
for(k=0;k";
}
}
if(alignments[i].alignObjects!=null)
for(j=0;j";
s+="......type: "+alignments[i].alignObjects[j].type+"
";
s+="......dbsource: "+alignments[i].alignObjects[j].dbsource+"
";
s+="......header: "+alignments[i].alignObjects[j].header+"
";
s+="......title: "+alignments[i].alignObjects[j].title+"
";
s+="......description: "+alignments[i].alignObjects[j].description+"
";
}
}
return s;
}
/**
* Assume that a block has the segment[0] as the PDB segment and the segment[1] as the Uniprot segment
* then go through the alignments to get the PDB segment which is with the Uniprot segment.
* Return null if it doesn't have a match.
*/
function segmentUniprot2segmentPDB(segmentUniprot){
for(i=0;i0){
if(alignments[0].blocks!=null){
term= alignments[0].blocks[0].segments[1].start - alignments[0].blocks[0].segments[0].start;
top=alignments[0].blocks[0].segments[0].end;
bottom=alignments[0].blocks[0].segments[0].start;
}
}
}
if (1>position-term)
return bottom;
if (position-term>top)
return top;
return position-term;
}
function extrapolateSegment(segmentQuery){
var term=0;
var top=0
var bottom=0
var entro=false;
// segmentUniprot=null;
// segmentPDB=null;
if ((segmentUniprot!=null)&&(segmentPDB!=null)){
var segmentResult;
segmentResult= new segment();
segmentResult.objid=segmentPDB.objid;
if ((Math.round(segmentQuery.start)Math.round(segmentUniprot.end))&&(Math.round(segmentQuery.end)>Math.round(segmentUniprot.end))){
segmentResult.start=0;
segmentResult.end=0;
}else{
if (Math.round(segmentQuery.start)Math.round(segmentUniprot.end)){
segmentResult.end=segmentPDB.end;
} else{
segmentResult.end=segmentQuery.end - (segmentUniprot.end - segmentPDB.end);
}
}
return segmentResult;
}
return null;
}
/**
* load the xml alignment file from the server
*/
function loadAlignment(url){
var http_request = false;
if (window.XMLHttpRequest) {
http_request = new XMLHttpRequest();
if (http_request.overrideMimeType) { http_request.overrideMimeType('text/xml');} // Rafa
} else if (window.ActiveXObject) { // IE.
try {
http_request = new ActiveXObject("Msxml2.XMLHTTP");
} catch (e) {
try {
http_request = new ActiveXObject("Microsoft.XMLHTTP");
} catch (e) {}
}
}
http_request.open('GET', url, true);
http_request.onreadystatechange = function(){
if (http_request.readyState == 4) {
if (http_request.status == 200) {
if(http_request.responseText && testing)
document.getElementById("xmlalgn").value= http_request.responseText;
//if(http_request.responseXML && http_request.responseXML.contentType=="text/xml") // Rafa
if(http_request.responseXML){
doParseAligment(http_request.responseXML);
//Only load the applet and the dropdown after parse the alignment
iniStructPanel();
}else
alert("wrong type alignment");
}else
alert("wrong code");
}
}
http_request.send(null);
}
/**
* get an array of the parsed structure with the name of the pdb's files
*/
function getPDBfileNames(){
var fileNames = new Array();
for(i=0;iDas Registry warning:
" + excep.firstChild.data + "
Dasty2 could not load data from the servers";
}
else
{
createLabelOptions(das_registry_label, "feature_label_list_select");
if(serverCount == 0)
{
document.getElementById("system_information").innerHTML = "Das Registry warning:
Dasty2 did not find protein sequence annotation server for this label. Please chose another label.";
}
else
{
makeSequenceRequest();
}
}
//makeFeatureRequest();
} else {
alert('There was a problem with the request.');
} //if (http_request.status == 200)
}
}
//------------------------------------------------------------------------------------------
// CREATE LABELS IN SEARCH FIELD
//------------------------------------------------------------------------------------------
function createLabelOptions(das_registry_label, tagId)
{
var div = document.getElementById("feature_label_list");
var content = "";
content = content + " ";
div.innerHTML = content;
}
//
//function createLabelOptions(das_registry_label, tagId)
//{
//for ( var i = 0; i < das_registry_label.length; i++ )
//{
//var form_select = document.getElementById("feature_label_list_select");
//var content_form_select = form_select.innerHTML;
//form_select.innerHTM = (content_form_select + " ");
//}
//}
//------------------------------------------------------------------------------------------
// "PASRSE A FEATURE XML AND POPULATE GRAPHIC AND NP TABLE"
//------------------------------------------------------------------------------------------
function parseFeatureXML(featureXML_num) {
if (feature_http_request[featureXML_num].readyState == 4) {
if (feature_http_request[featureXML_num].status == 200) {
document.getElementById("system_information").innerHTML = "... loading features from " + feature_url[featureXML_num].id;
// DRAWING PROGRESS BAR
servers_count++;
var percentage = parseInt(servers_count*100/feature_url.length);
if(percentage == 100)
{
allSourcesLoaded = true;
}
progBar(percentage);
var npf_num = 0; // Count number of non positional features
var row_num = 0;
var update = 0;
var type_counter = [];
var tc_length = 0;
feature_info[featureXML_num] = [];
var parsing_error = 0;
var url = feature_url[featureXML_num].url;
feature_url[featureXML_num].XML_num = featureXML_num;
feature_url[featureXML_num].general_order = servers_count;
var firstRequestNumberTemp = dasty2.firstRequestNumber;
var xmldoc = feature_http_request[featureXML_num].responseXML;
var excep = xmldoc.getElementsByTagName('exception').item(0);
if (excep != null)
{
warning_count++;
var server_checking = document.getElementById("display_server_checking").innerHTML;
document.getElementById("display_server_checking").innerHTML = server_checking + "
" + servers_count + ".- " + feature_url[featureXML_num].id + " ... Warning: " + excep.firstChild.data.slice(0,40) + "...";
feature_url[featureXML_num].state = 3;
}
var tf = xmldoc.getElementsByTagName('FEATURE').item(0);
if (tf != null)
{
results_XML_order[feature_results_count] = featureXML_num;
feature_results_count++;
var server_checking = document.getElementById("display_server_checking").innerHTML;
document.getElementById("display_server_checking").innerHTML = server_checking + "
" + servers_count + ".- " + feature_url[featureXML_num].id + " ... have feature annotations.";
feature_url[featureXML_num].state = 1;
//feature_url[featureXML_num].results_order = feature_results_count;
var gff_node = xmldoc.getElementsByTagName('GFF').item(0);
// var opa = document.getElementById("display_test");
// var content_opa = opa.innerHTML;
// opa.innerHTML = (content_opa + "
------------
tf:" + tf);
var gff_attrs = gff_node.attributes;
gff_loop:
for(var g=gff_attrs.length-1; g>=0; g--)
{
if (gff_attrs[g].name == 'version') { var gff_version = gff_attrs[g].value; }
else if (gff_attrs[g].name == 'href') { var gff_href = gff_attrs[g].value; };
}
// var opa = document.getElementById("display_test");
// var content_opa = opa.innerHTML;
// opa.innerHTML = (content_opa + "
------------
gff_href:" + gff_href);
var segment_node = gff_node.childNodes;
segment_loop:
for (var s = 0; s < segment_node.length; s++)
{
if (segment_node[s].nodeName == 'SEGMENT')
{
//var segment_data = segment_node[s].firstChild.data;
var segment_attrs = segment_node[s].attributes;
for(var i=segment_attrs.length-1; i>=0; i--)
{
if (segment_attrs[i].name == 'id') { var segment_id = segment_attrs[i].value; }
else if (segment_attrs[i].name == 'version')
{
var segment_version = segment_attrs[i].value;
if(segment_version == sequence_info.sequence_version)
{
annotation_version[featureXML_num] = 1; // ok
}
else
{
annotation_version[featureXML_num] = 0; // different
}
}
else if (segment_attrs[i].name == 'start')
{
//if(segment_attrs[i].value == '')
//{
var segment_start = sequence_info.sequence_start;
//} // sequence_info is glogal!
//else
//{ var segment_start = segment_attrs[i].value;}
}
else if (segment_attrs[i].name == 'stop')
{
//if(segment_attrs[i].value == '' || segment_attrs[i].value == '-1')
//{
var segment_stop = sequence_info.sequence_stop;
//} // sequence_info is glogal!
//else
//{
//var segment_stop = segment_attrs[i].value;
//}
}
}
var feature_node = segment_node[s].childNodes;
feature_loop:
for (var f = 0; f < feature_node.length; f++)
{
var feature_id = '';
var feature_label = '';
var type_data = '';
var type_id = '';
var type_category = '';
var method_data = '';
var method_id = '';
var start_data = '';
var end_data = '';
var score_data = '';
var orientation_data = '';
var phase_data = '';
var note_data = [];
var link_data = [];
var link_href = [];
var group_id = '';
if (feature_node[f].nodeName == 'FEATURE')
{
//var segment_data = segment_node[s].firstChild.data;
var feature_attrs = feature_node[f].attributes;
for(var i=feature_attrs.length-1; i>=0; i--)
{
if (feature_attrs[i].name == 'id') { feature_id = feature_attrs[i].value; }
else if (feature_attrs[i].name == 'label') { feature_label = feature_attrs[i].value; };
}
// Exception for "http://cathwww.biochem.ucl.ac.uk:9000/das/cath_pdb/"
if(feature_id == "Query_failed") { break feature_loop; parsing_error = 1; }
var feature_child_node = feature_node[f].childNodes;
feature_child_loop:
for (var c = 0; c < feature_child_node.length; c++)
{
if (feature_child_node[c].nodeName == 'TYPE')
{
if(feature_child_node[c].firstChild == null)
{
//var type_data = "";
var type_data_temp = "";
type_data = "";
}
else
{
//var type_data = feature_child_node[c].firstChild.data;
var type_data_temp = feature_child_node[c].firstChild.data;
type_data = feature_child_node[c].firstChild.data;
}
var feature_child_attrs = feature_child_node[c].attributes;
for(var i=feature_child_attrs.length-1; i>=0; i--)
{
if (feature_child_attrs[i].name == 'id')
{
type_id = feature_child_attrs[i].value;
if (type_data_temp == "")
{
type_data = type_id;
}
//if (type_data_temp.toLowerCase() == type_id.toLowerCase() || type_data_temp == "" )
//{
// // do nothing
//}
//else
//{
// type_data = type_data_temp + " (" + type_id + ")";
//}
}
else if (feature_child_attrs[i].name == 'category')
{
type_category = feature_child_attrs[i].value;
}
} // for(var i=feature_child_attrs.length-1; i>=0; i--)
/**
* Create an list of non redundant types
*/
//if(type_id != "")
//{
var typesLoadedLength = dasty2.typesLoaded.length;
var typeDuplicated = 0;
for(var w = 0; w < typesLoadedLength; w++)
{
if(dasty2.typesLoaded[w].toUpperCase() == type_id.toUpperCase())
{
typeDuplicated = 1;
}
}
if(typeDuplicated == 0)
{
dasty2.typesLoaded.push(type_id);
}
//}
/**
* Create an list of non redundant categories
*/
//if(type_category != "")
//{
var categoriesLoadedLength = dasty2.categoriesLoaded.length;
var categoryDuplicated = 0;
for(var w = 0; w < categoriesLoadedLength; w++)
{
if(dasty2.categoriesLoaded[w].toUpperCase() == type_category.toUpperCase())
{
categoryDuplicated = 1;
}
}
if(categoryDuplicated == 0)
{
dasty2.categoriesLoaded.push(type_category);
}
//}
}
else if (feature_child_node[c].nodeName == 'METHOD')
{
if(feature_child_node[c].firstChild == null)
{
var method_data_temp = "";
method_data = "";
}
else
{
method_data = feature_child_node[c].firstChild.data;
var method_data_temp = feature_child_node[c].firstChild.data;
}
//var method_data = feature_child_node[c].firstChild.data;
var feature_child_attrs = feature_child_node[c].attributes;
for(var i=feature_child_attrs.length-1; i>=0; i--)
{
if (feature_child_attrs[i].name == 'id')
{
method_id = feature_child_attrs[i].value;
if (method_data_temp == "")
{
method_data = method_id;
}
if (method_data_temp.toLowerCase() == method_id.toLowerCase() || method_data_temp == "" )
{
// do nothing
}
else
{
method_data = method_data_temp + " (" + method_id + ")";
}
}
}
}
else if (feature_child_node[c].nodeName == 'START')
{
start_data = feature_child_node[c].firstChild.data;
}
else if (feature_child_node[c].nodeName == 'END')
{
end_data = feature_child_node[c].firstChild.data;
}
else if (feature_child_node[c].nodeName == 'SCORE')
{
if(feature_child_node[c].firstChild == null)
{
score_data = "0.0";
}
else
{
score_data = feature_child_node[c].firstChild.data;
}
}
else if (feature_child_node[c].nodeName == 'ORIENTATION')
{
orientation_data = feature_child_node[c].firstChild.data;
}
else if (feature_child_node[c].nodeName == 'PHASE')
{
phase_data = feature_child_node[c].firstChild.data;
}
else if (feature_child_node[c].nodeName == 'NOTE')
{
note_data.push(feature_child_node[c].firstChild.data);
}
else if (feature_child_node[c].nodeName == 'LINK')
{
link_data.push(feature_child_node[c].firstChild.data);
var feature_child_attrs = feature_child_node[c].attributes;
for(var i=feature_child_attrs.length-1; i>=0; i--)
{
if (feature_child_attrs[i].name == 'href') { link_href.push(feature_child_attrs[i].value); };
}
}
else if (feature_child_node[c].nodeName == 'GROUP')
{
var feature_child_attrs = feature_child_node[c].attributes;
for(var i=feature_child_attrs.length-1; i>=0; i--)
{
if (feature_child_attrs[i].name == 'id') { group_id = feature_child_attrs[i].value; };
}
}
// FOR feature_child_loop
}
//} // if(feature_id != "Query_failed")
//if(type_category) { /* defined */ } else { var type_category = ''; }
var feature_row = {feature_id: feature_id, feature_label: feature_label, type_data: type_data, type_id: type_id, type_category: type_category, method_data: method_data, method_id: method_id, start_data: start_data, end_data: end_data, score_data: score_data, orientation_data: orientation_data, phase_data: phase_data, note_data: note_data, link_data: link_data, link_href: link_href, group_id: group_id, annotation_server: feature_url[featureXML_num].id, annotation_server_uri: feature_url[featureXML_num].registry_uri, xmlnumber: featureXML_num };
//feature_info[row_num] = feature_row;
feature_info[featureXML_num][row_num] = feature_row;
if (start_data==0 && end_data==0)
{
npf_num++;
}
if (start_data == 0 && end_data ==0)
{ // non positional feature
} else {
//----------------------------------------------------------------------------------
// ARRAY THAT SAYS WHERE A "type" IS HAPPENING IN THE "feature_info" ARRAY
//----------------------------------------------------------------------------------
tc_length = type_counter.length;
if(tc_length == 0)
{
type_counter[0] = [];
type_counter[0][0] = type_id;
type_counter[0][1] = [];
type_counter[0][1] = [row_num];
}
tc_update = 0;
for(var h = 0; h < tc_length; h++)
{
if(type_counter[h][0] == type_id)
{
type_counter[h][1].push(row_num);
tc_update = 1;
}
}
if(tc_update == 0 && tc_length != 0)
{
type_counter[tc_length] = [];
type_counter[tc_length][0] = type_id;
type_counter[tc_length][1] = [];
type_counter[tc_length][1] = [row_num];
}
} // finish => if (start_data == 0 && end_data ==0)
row_num++;
// IF 'FEATURE'
}
// FOR feature_loop
}
}
}
if(parsing_error == 0)
{
createNPFeatureTable(featureXML_num, feature_info[featureXML_num], "display_nonpositional", npf_num);
grouping(featureXML_num, type_counter, segment_start, segment_stop);
if(firstRequestNumberTemp <= dasty2.validFirstSources.length)
{
if(firstRequestNumberTemp == dasty2.validFirstSources.length)
{
dasty2.firstRequestNumber++;
makeFeatureRequest2();
}
else
{
makeFeatureRequest(dasty2.firstRequestNumber);
}
}
}
else
{
createGraphic2(featureXML_num, "display_graphic", 0, 0, "noresults");
if(firstRequestNumberTemp <= dasty2.validFirstSources.length)
{
if(firstRequestNumberTemp == dasty2.validFirstSources.length)
{
dasty2.firstRequestNumber++;
makeFeatureRequest2();
}
else
{
makeFeatureRequest(dasty2.firstRequestNumber);
}
}
}
} // if (tf != "null" && tf != "" && tf != null)
else
{
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
tf:" + tf);
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
featureXML_num:" + featureXML_num);
if (excep == null)
{
no_feature_results_count++;
var server_checking = document.getElementById("display_server_checking").innerHTML;
document.getElementById("display_server_checking").innerHTML = server_checking + "
" + servers_count + ".- " + feature_url[featureXML_num].id + " ... do not have feature annotations available.";
feature_url[featureXML_num].state = 2;
}
createGraphic2(featureXML_num, "display_graphic", 0, 0, "noresults");
if(firstRequestNumberTemp <= dasty2.validFirstSources.length)
{
if(firstRequestNumberTemp == dasty2.validFirstSources.length)
{
dasty2.firstRequestNumber++;
makeFeatureRequest2();
}
else
{
makeFeatureRequest(dasty2.firstRequestNumber);
}
}
} // if (tf != "null" && tf != "" && tf != null)
} else {
alert('There was a problem with the request: Parse feature');
} // if (feature_http_request[featureXML_num].status == 200)
} // if (feature_http_request[featureXML_num].readyState == 4)
//alert(standby.length);
} // function parseFeatureXML()
//
// Fernando's code to get started with parsing ontologies
var testing = false; // used for testing
/**
* called with url of ontology file to load and parse
* @params: otype: ontology to parse (either 1 for type or 2 for category)
*/
function parseOntology(otype,url){
loadOntology(otype,url);
}
// <------------ Loading and Parsing --------------->
/**
* parse the xml ontology file received in doc
*/
function doParseOntology(doc,otype){
//Preparing the arrays of types and categories. The graphic must be loaded
dasty2.temporalArray=[];
dasty2.temporalArray2=[];
dasty2.leaves=[];
if(otype==1){
//Types
dasty2.temporalArray2=dasty2.typesLoaded;
}else{
//Categories
dasty2.temporalArray2=dasty2.categoriesLoaded;
}
for(var i=0;i
if(xmlterm.childNodes[j].nodeName == "def"){
for(var h=0;h
if(is_definition == false){
definition = "Description not available";
}
// <- Rafael
if(isobsolete==0){
if(isroot!=null && isroot==1){
this.rootptr = 0;
this.terms[0] = addTerm(id,name,relations,otype,definition);
this.termsidx[id] = 0;
}else{
if(this.rootptr==-1){
this.terms[0]= new Array();
this.terms[this.nterms] = addTerm(id,name,relations,otype,definition);
this.rootptr = 0;
}else{
this.terms[this.nterms] = addTerm(id,name,relations,otype,definition);
}
this.termsidx[id] = this.nterms++;
}
}
}
}
/**
* return a new term in Tree component format
* @params: id=term id, name = term name, relations = relations found for the term
*/
function addTerm(id,name,relations,otype,definition){
term = new Array();
term['dataContainer'] = id;
term['caption'] = name;
term['visible'] = false;
term['relations'] = relations;
term['onClick'] = "javascript:printOnSystemInformation('" + id + "; " + definition + "')";
if(otype==1)
term['onChangeCheckbox'] = display_ontology_types;
else
term['onChangeCheckbox'] = display_ontology_categories;
return term;
}
/**
* return content if text node, empty string otherwise
*/
function getNodeData(node){
if(!node.hasChildNodes)
return "";
for(var j=0;j0){
for(j=0;j";
if(t['children']!=null){
for(var j=0;jTermId: "+this.terms[i]['dataContainer']+"
";
if(this.terms[i]['relations']!=null)
for(j=0;j";
}
}
return s;
}
/**
* display ontology for testing purposes
*/
doParseOntology.prototype.showOntologyTree = function(ontoType){
if(ontoType==1){
t = new Bs_Tree();
t.imageDir = 'http://www.gpcr.org/7tm/dasty2/client/library/blueshoes46/components/tree/img/win98/';
t.checkboxSystemImgDir = 'http://www.gpcr.org/7tm/dasty2/client/library/blueshoes46/components/checkbox/img/win2k_noBorder/';
t.useCheckboxSystem = true;
//t.useAutoSequence = false;
t.checkboxSystemWalkTree = 3;
t.initByArray(this.terms);
//prune(t,dasty2.typesLoaded,ontoType);
t.drawInto('display_maniputation_options3_type_div');
//Close Ontology terms (nodes) in the tree
// This does not work. Probably because the tree takes some time to load and
// when this script tries to access is still too early.
/*
var termArray = ['binding_site','polypeptide_region'];
for(i=0;i"+seqDataArray[i]+"";
if ((i+1)%sequence_limit==0){
seq +="
";
}
}
return seq;
}
function parseSequenceXML() {
//sequence_info = [];
//alert(http_request.readyState);
if (http_request.readyState == 4) {
if (http_request.status == 200) {
document.getElementById("system_information").innerHTML = "... loading sequence information from the Reference Server";
var xmldoc = http_request.responseXML;
var excep = xmldoc.getElementsByTagName('exception').item(0);
var root_node = xmldoc.getElementsByTagName('DASSEQUENCE').item(0);
if(root_node)
{
if (root_node.hasChildNodes())
// So, first we check if the object is not empty, if the object has child nodes
{
var children = root_node.childNodes;
sequence_loop:
for (var j = 0; j < children.length; j++)
{
if (children[j].nodeName == 'SEQUENCE')
{
if(useHighlight)
{
sequence = transformSeqData(children[j].firstChild.data);
}
else
{
sequence = children[j].firstChild.data;
}
var sequence_attrs = children[j].attributes;
for(var i=sequence_attrs.length-1; i>=0; i--)
{
if (sequence_attrs[i].name == 'id') { var sequence_id = sequence_attrs[i].value; }
else if (sequence_attrs[i].name == 'version') { var sequence_version = sequence_attrs[i].value; }
else if (sequence_attrs[i].name == 'start') { var sequence_start = sequence_attrs[i].value; }
else if (sequence_attrs[i].name == 'stop') { var sequence_stop = sequence_attrs[i].value; }
else if (sequence_attrs[i].name == 'moltype') { var sequence_moltype = sequence_attrs[i].value; };
}
var sequence_length = sequence_stop - (parseInt(sequence_start) - 1);
//insertElement("div", "display_query_id", "display_query", sequence_id);
//insertElement("div", "display_query_length", "display_query", sequence_length);
//insertElement("div", "display_seque_sequence2", "display_seque", sequence);
var sequence_row = {sequence: sequence, sequence_id: sequence_id, sequence_version: sequence_version, sequence_start: sequence_start, sequence_stop: sequence_stop, sequence_moltype: sequence_moltype, sequence_length: sequence_length };
//sequence_info.push(sequence_row); //Convert to object!
sequence_info = sequence_row;
//alert(sequence_info.sequence_stop);
createQueryInformationField(sequence_info, "display_query");
//createSequenceField(sequence, "display_seque");
createSequenceField("display_seque");
break sequence_loop;
}
}
}
} // if(root_node)
if (excep != null)
{
document.getElementById("system_information").innerHTML = "Das Reference Server warning:
" + excep.firstChild.data + "
Dasty2 could not load data from the servers";
}
else
{
makeStylesheetRequest();
}
} else {
alert('There was a problem with the request.');
}
}
}
////------------------------------------------------------------------------------------------
// "PASRSE A STYLESHEET XML"
//------------------------------------------------------------------------------------------
function parseStylesheetXML() {
if (http_request.readyState == 4) {
if (http_request.status == 200) {
document.getElementById("system_information").innerHTML = "... loading stylesheet from the server";
var xmldoc = http_request.responseXML;
var excep = xmldoc.getElementsByTagName('exception').item(0);
var category_node = xmldoc.getElementsByTagName('CATEGORY').item(0);
if(category_node)
{
var category_attrs = category_node.attributes;
for(var g=category_attrs.length-1; g>=0; g--)
{
if (category_attrs[g].name == 'id') { var category_id = category_attrs[g].value; }
}
var type_node = category_node.childNodes;
type_loop:
for (var s = 0; s < type_node.length; s++)
{
if (type_node[s].nodeName == 'TYPE')
{
var type_attrs = type_node[s].attributes;
for(var i=type_attrs.length-1; i>=0; i--)
{
if (type_attrs[i].name == 'id') { var type_id = type_attrs[i].value; }
}
var glyph_node = type_node[s].childNodes;
glyph_loop:
for (var gl = 0; gl < glyph_node.length; gl++)
{
if (glyph_node[gl].nodeName == 'GLYPH')
{
var shape_node = glyph_node[gl].childNodes;
shape_loop:
for (var f = 0; f < shape_node.length; f++)
{
if (shape_node[f].nodeName == 'ARROW' || shape_node[f].nodeName =='ANCHORED_ARROW' || shape_node[f].nodeName =='BOX' || shape_node[f].nodeName =='CROSS' || shape_node[f].nodeName =='EX' || shape_node[f].nodeName =='HIDDEN' || shape_node[f].nodeName =='LINE' || shape_node[f].nodeName =='SPAN' || shape_node[f].nodeName =='TEXT' || shape_node[f].nodeName =='TOOMANY' || shape_node[f].nodeName =='TRIANGLE' || shape_node[f].nodeName =='PRIMERS')
{
var shape_nodeName = shape_node[f].nodeName;
var color_node = shape_node[f].childNodes;
color_loop:
for (var c = 0; c < color_node.length; c++)
{
if (color_node[c].nodeName == 'FGCOLOR')
{
var fgcolor_data = color_node[c].firstChild.data;
}
else if (color_node[c].nodeName == 'BGCOLOR')
{
var bgcolor_data = color_node[c].firstChild.data;
}
} // FOR color_loop
// TEST
// var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
// opa.innerHTML = (content_opa + "
BF:" + fgcolor_data + " BG:" + bgcolor_data + " TYPEID:" + type_id);
var stylesheet_properties = {type_id: type_id, shape_nodeName: shape_nodeName, fgcolor_data: fgcolor_data, bgcolor_data: bgcolor_data};
stylesheet_properties_info.push(stylesheet_properties);
} // IF 'SHAPE'
} // FOR shape_loop
} // IF 'SHAPE'
} // FOR shape_loop
}
}
} // if(category_node)
if (excep != null)
{
document.getElementById("system_information").innerHTML = "" + stylesheet_url[0][0] + " Das Stylesheet warning:
" + excep.firstChild.data + "
Dasty2 could not load data from the servers";
}
else
{
makeFeatureRequest();
}
} else {
alert('There was a problem with the request.');
}
//makeRequest('xml/features2_c.xml', 'featureXML');
//makeRequest('xml/fea_A4_Human.xml', 'featureXML');
//makeRequest('xml/fea_A4_Human_short.xml', 'featureXML');
//makeRequest('xml/fea_A4_Human_mod2.xml', 'featureXML');
//alert("hello");
//makeFeatureRequest();
}
}
//// JavaScript Document
function feature_mouse_action(posX, posY, feature_title, feature_xmlnumber, feature_row, action)
{
if(action == 'mouseover')
{
createFeatureDetails(feature_row, feature_xmlnumber);
if (isPDBVisible==true){
selectAnotationRegion(feature_row, feature_xmlnumber);
}
if(show_popup == 1)
{
//var rafa = document.getElementById('__tooltip__');
//rafa.style.display = "none";
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
unique_id: " + unique_id + " / show_popup: " + show_popup);
}
}
else if(action == 'mouseclick')
{
if(show_popup == 2)
{
createFeatureDetails(feature_row, feature_xmlnumber);
win2(posX, posY, feature_title);
//TooltipManager = null;
//TooltipManager.tooltipWindow.removeEventListener('mouseover',arguments.callee,false);
//var rafa = document.getElementById('Pfam-B_2235_529');
//rafa.removeEventListener('mouseover',arguments.callee,false);
//removeEventListener('click',arguments.callee,false);
}
}
}
function win2(setX, setY, feature_id)
{
//var scrollbar_height = f_scrollTop();
var newX = setX - 14;
//var newY = setY + height_graphic_feature - 2;
var newY = setY + height_graphic_feature + 2;
var feature_content = document.getElementById('display_feature_details').innerHTML;
popup_num = popup_num + 1;
//Windows.closeAll();
//var win = new Window('window_id_' + popup_num, {className: "mac_os_x", title: feature_id});
var win = new Window('window_id_' + popup_num, {className: "mac_os_x", title: feature_id, width:260, height:170});
win.keepMultiModalWindow=false;
//win.getContent().innerHTML = "Constraint inside page !!
";
win.getContent().innerHTML = feature_content;
win.setDestroyOnClose();
//win.setHTMLContent(html)
//win.setContent('display_feature_details', false, false)
win.toFront();
//win.showCenter();
//win.setConstraint(true, {left:0, right:0});
win.setLocation(newY, newX);
win.show();
}
function pdbOnWindow(div_id)
{
var pdbWin = new Window('pdbWin', {className: "mac_os_x", title: "PROTEIN STRUCTURE", hideEffect:Element.hide, showEffect:Element.show, maximizable: false, resizable: true, zIndex:9999});
pdbWin.setContent(div_id, true, true);
pdbWin.setDestroyOnClose();
pdbWin.show();
//changeStructure();
}
/*
contentWin = new Window({maximizable: false, resizable: false, hideEffect:Element.hide, showEffect:Element.show, minWidth: 10, destroyOnClose: true}) contentWin.setContent('test_content', true, true) contentWin.show();
function openModalDialog() {
debug($('modal_window_content'))
var win = new Window('modal_window', {className: "dialog", title: "Ruby on Rails",top:100, left:100, width:300, height:200, zIndex:150, opacity:1, resizable: true})
//win.getContent().innerHTML = "Hi"
win.setContent("select")
win.setDestroyOnClose();
win.show(true);
}
function pdbOnWindow(div_id)
{
var pdbWin = new Window('pdbWin', {className: "mac_os_x", maximizable: false, resizable: true, hideEffect:Element.hide, showEffect:Element.show, minWidth: 10);
pdbWin.setContent(div_id);
setDestroyOnClose();
pdbWin.show();
}
*/
//TooltipManager.init("tooltip", {url: "tooltip_ajax.html", options: {method: 'get'}}, {showEffect: Element.show, hideEffect: Element.hide});
//TooltipManager.addHTML("tooltip1", "tooltip_content2");
//TooltipManager.addAjax("tooltip2", {url: "tooltip_ajax.html", options: {method: 'get'}});
//TooltipManager.addURL("tooltip3", "tooltip_url.html", 200, 300);
function define_popups()
{
if(show_popup == 2)
{
show_popup = 1;
var minus_icon = " ";
var icon = document.getElementById("menu_mo_img_popups");
icon.innerHTML = minus_icon;
}
else
{
show_popup = 2;
var plus_icon = " ";
var icon = document.getElementById("menu_mo_img_popups");
icon.innerHTML = plus_icon;
}
}
// JavaScript Document
function progBar(percentage)
{
//alert(percentage);
var total_px = parseInt(progress_bar_width*percentage/100);
if (total_px <= progress_bar_width )
{
if (total_px > 40){document.getElementById("progress_bar_1").innerHTML = percentage + "%";}
document.getElementById("progress_bar_2").style.width = total_px + "px";
}
}
function getPxWidthFromStyle(TagId)
{
var width = document.getElementById(TagId).style.width;
var width_value = width.split("px");
return width_value[0];
}
function getPxHeightFromStyle(TagId)
{
var height = document.getElementById(TagId).style.height;
var height_value = height.split("px");
return height_value[0];
}//------------------------------------------------------------------------------------------
// MAKE A SEQUENCE REQUESTS
//------------------------------------------------------------------------------------------
function makeSequenceRequest()
{
makeRequest(sequence_url[0][1], 'sequenceXML'); // sequence_url is Global!
}
//
//------------------------------------------------------------------------------------------
// MAKE A STYLESHEET REQUESTS
//------------------------------------------------------------------------------------------
// I Should retrieve one stylesheet by Annotation server. By now I just will recover the uniprot one.
function makeStylesheetRequest()
{
makeRequest(stylesheet_url[0][1], 'styleSheetXML'); // stylesheet_url is Global!
}
//
//------------------------------------------------------------------------------------------
// MAKE A DAS REGISTRY REQUESTS
//------------------------------------------------------------------------------------------
function makeDasRegistryRequest()
{
makeRequest(das_registry_url, 'dasRegistryXML'); // stylesheet_url is Global!
}
//
//------------------------------------------------------------------------------------------
// MAKE SEVERAL FEATURE REQUESTS
//------------------------------------------------------------------------------------------
function makeFeatureRequest(requestNumber)
{
dasty2.validFirstSources = lookForSpecificSources(first_das_source);
//printOnTest(dasty2.validFirstSources);
if(dasty2.validFirstSources.length > 0)
{
if(typeof requestNumber == "undefined")
{
var requestNumberTemp = 0;
}
else
{
var requestNumberTemp = requestNumber;
} //if(requestNumber == null || requestNumber = '')
dasty2.firstRequestNumber = requestNumberTemp + 1;
var featureXML_num = dasty2.validFirstSources[requestNumberTemp];
var url = feature_url[featureXML_num].url;
makeRequest(url, 'featureXML', featureXML_num);
}
else
{ dasty2.firstRequestNumber++;
makeFeatureRequest2();
} //if(first_das_source.length > 0)
}
// Look for specific source names in the Source array file "feature_url"
function lookForSpecificSources(sources)
{
var sourceFound = [];
for(var i = 0; i < sources.length; i++)
{
for(var h = 0; h < feature_url.length; h++)
{
//printOnTest(feature_url[h].id.toLowerCase() + " " + sources[i].toLowerCase());
if(feature_url[h].id.toLowerCase() == sources[i].toLowerCase())
{
sourceFound.push(h);
}
}
}
return sourceFound;
}
function makeFeatureRequest2()
{
// RCJ: Make a aligment request
if (isPDBVisible==true){
parseAlignment(uniprot_pdb_alignment);
}
// RCJ: Make multiple feature request leaving out sources in "first_das_source"
for(var h = 0; h < feature_url.length; h++)
{
duplicated = 0;
for(var i = 0; i < first_das_source.length; i++)
{
if(feature_url[h].id.toLowerCase() == first_das_source[i].toLowerCase())
{
duplicated = 1;
}
}
if(duplicated == 0)
{
var featureXML_num = h;
var url = feature_url[featureXML_num].url;
makeRequest(url, 'featureXML', featureXML_num);
}
}
}
//------------------------------------------------------------------------------------------
// REQUEST INFORMATION FROM DIFFERENT XML SPECIFIYING A LOCAL URL.
//------------------------------------------------------------------------------------------
function makeRequest(url, xml_type, featureXML_num)
{
//alert("fn:" + featureXML_num);
if (xml_type=='sequenceXML')
{
http_request.open('GET', url, true);
http_request.onreadystatechange = parseSequenceXML;
http_request.send(null);
}
else if (xml_type=='featureXML')
{
ajax_feature(featureXML_num);
//feature_http_request[featureXML_num] = http_request;
//feature_http_request[featureXML_num].onreadystatechange = parseFeatureXML;
feature_http_request[featureXML_num].onreadystatechange = function()
{
parseFeatureXML(featureXML_num);
};
feature_http_request[featureXML_num].open('GET', url, true);
feature_http_request[featureXML_num].send(null);
//alert("featureXML_num: " + featureXML_num);
}
else if (xml_type=='serverListXML')
{
http_request.open('GET', url, true);
http_request.onreadystatechange = parseServerListXML;
http_request.send(null);
}
else if (xml_type=='styleSheetXML')
{
http_request.open('GET', url, true);
http_request.onreadystatechange = parseStylesheetXML;
http_request.send(null);
}
else if (xml_type=='dasRegistryXML')
{
http_request.open('GET', url, true);
http_request.onreadystatechange = parseDasRegistryXML;
http_request.send(null);
//ajax_elements("das_registry");
//elements_http_request["das_registry"].open('GET', url, true);
//elements_http_request["das_registry"].onreadystatechange = parseDasRegistryXML;
//elements_http_request["das_registry"].send(null);
};
} // JavaScript Document
//------------------------------------------------------------------------------------------
// SORTING
//------------------------------------------------------------------------------------------
function sorting(sortby)
{
if(one_feature_list.length == 0 && isExpanded == 0)
{
var row = 0;
for(var a = 0; a < new_feature_list_info2.length; a++)
{
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
new_feature_list_info2[a]: " + new_feature_list_info2[a]);
if(new_feature_list_info2[a])
{
for(var b = 0; b < new_feature_list_info2[a].length; b++)
{
one_feature_list[row] = new_feature_list_info2[a][b];
one_feature_list[row]["xmlnumber"] = a;
row++
}
} // if(new_feature_list_info2[a])
}
//for(var lu = 0; lu < one_feature_list.length; lu++)
//{
//var new_feature_list = one_feature_list;
//var opa = document.getElementById("display_test");
//var content_opa = opa.innerHTML;
//opa.innerHTML = (content_opa + "
------------
new_feature_list[" + lu + "][features]: " + new_feature_list[lu]["features"] + "::::: new_feature_list[" + lu + "][feature_group]: " + new_feature_list[lu]["feature_group"] + "::::: new_feature_list[" + lu + "][type]: " + new_feature_list[lu]["type"] + new_feature_list[lu]["category"] + new_feature_list[lu]["server"] + new_feature_list[lu]["xmlnumber"]);
//}
} //if(one_feature_list.length == 0 && isExpanded == 0)
if (sortby)
{
document.getElementById("system_information").innerHTML = "Dasty2 is sorting the graphic by " + sortby + " ...";
//alert("zoom beggining");
/* NOT NECESSARY BECAUSE SORTING INCLUDED IN THE GRAPHIC
//------------------------------------------------
// DRAW +/- ICON
//------------------------------------------------
var img_display_type = document.getElementById("menu_mo_img_type");
var img_display_category = document.getElementById("menu_mo_img_category");
var img_display_server = document.getElementById("menu_mo_img_server");
var img_display_version = document.getElementById("menu_mo_img_version");
var minus_icon = "![](\"img/noradio01.gif\")
";
var plus_icon = "![](\"img/radio01.gif\")
";
if(sortby == "type")
{
img_display_type.innerHTML = plus_icon; img_display_category.innerHTML = minus_icon;
img_display_server.innerHTML = minus_icon; img_display_version.innerHTML = minus_icon;
}
else if (sortby == "category")
{
img_display_type.innerHTML = minus_icon; img_display_category.innerHTML = plus_icon;
img_display_server.innerHTML = minus_icon; img_display_version.innerHTML = minus_icon;
}
else if (sortby == "server")
{
img_display_type.innerHTML = minus_icon; img_display_category.innerHTML = minus_icon;
img_display_server.innerHTML = plus_icon; img_display_version.innerHTML = minus_icon;
}
else if (sortby == "version")
{
img_display_type.innerHTML = minus_icon; img_display_category.innerHTML = minus_icon;
img_display_server.innerHTML = minus_icon; img_display_version.innerHTML = plus_icon;
}
*/
//-------------------------------------------------
// ASC DES by Type
//-------------------------------------------------
if(sortOrderType == -1)
{
sortOrderType = 1; // Descending
sortOrderType2 = -1;
}
else
{
sortOrderType = -1; // Ascending
sortOrderType2 = 1;
}
//-------------------------------------------------
// ASC DES by Method
//-------------------------------------------------
if(sortOrderMethod == -1)
{
sortOrderMethod = 1; // Descending
sortOrderMethod2 = -1;
}
else
{
sortOrderMethod = -1; // Ascending
sortOrderMethod2 = 1;
}
//-------------------------------------------------
// ASC DES by Category
//-------------------------------------------------
if(sortOrderCategory == -1)
{
sortOrderCategory = 1; // Descending
sortOrderCategory2 = -1;
}
else
{
sortOrderCategory = -1; // Ascending
sortOrderCategory2 = 1;
}
//-------------------------------------------------
// ASC DES by Server
//-------------------------------------------------
if(sortOrderServer == -1)
{
sortOrderServer = 1; // Descending
sortOrderServer2 = -1;
}
else
{
sortOrderServer = -1; // Ascending
sortOrderServer2 = 1;
}
//-------------------------------------------------
// ASC DES by Version
//-------------------------------------------------
if(sortOrderVersion == -1)
{
sortOrderVersion = -1; // Ascending
sortOrderVersion2 = 1;
}
else
{
sortOrderVersion = 1; // Descending
sortOrderVersion2 = -1;
}
//---------------------------------------------------------------------
// SORT "one_feature_list" by "sortby". Sort by indicate a colum number
//---------------------------------------------------------------------
if(isExpanded == 0)
{
sortCompactArray(sortby);
}
else
{
sortExpandedArray(sortby);
}
}
resetSortingVariables(sortby);
var graphic_content = document.getElementById("display_graphic");
graphic_content.innerHTML = '';
if(isExpanded == 0)
{
createGraphic2(0, "display_graphic", sequence_info.sequence_start, sequence_info.sequence_stop, "sorting");
}
else
{
createGraphic2(0, "display_graphic", sequence_info.sequence_start, sequence_info.sequence_stop, "expanding");
}
//Sortable.create('gr_list0',{ghosting:true,constraint:false}); // Simpler
Sortable.create('gr_list0', {onUpdate:function(){new Effect.Highlight('gr_list0', {startcolor:'#CCCCCC'});}});
if (sortby) { document.getElementById("system_information").innerHTML = "... Dasty2 finished to sort the graphic by " + sortby + ""; }
} // function sorting(sortby)
function sortCompactArray(sortby)
{
switch (sortby)
{
case "type" :
one_feature_list.sort(sortByType);
break;
case "method" :
one_feature_list.sort(sortByMethod);
break;
case "category" :
one_feature_list.sort(sortByCategory);
break;
case "server" :
one_feature_list.sort(sortByServer);
break;
case "version" :
one_feature_list.sort(sortByVersion);
break;
}
} // function sortArray(column)
function sortExpandedArray(sortby)
{
switch (sortby)
{
case "type" :
expanded_feature_list.sort(sortByType);
break;
case "method" :
expanded_feature_list.sort(sortByType);
break;
case "category" :
expanded_feature_list.sort(sortByCategory);
break;
case "server" :
expanded_feature_list.sort(sortByServer);
break;
case "version" :
expanded_feature_list.sort(sortByVersion);
break;
}
} // function sortArray(column)
function sortByType(a, b)
{
var x = a.type.toLowerCase();
var y = b.type.toLowerCase();
return ((x < y) ? sortOrderType : ((x > y) ? sortOrderType2 : 0));
} // function sortByType(a, b)
function sortByMethod(a, b)
{
var x = a.method.toLowerCase();
var y = b.method.toLowerCase();
return ((x < y) ? sortOrderMethod : ((x > y) ? sortOrderMethod2 : 0));
} // function sortByType(a, b)
function sortByCategory(a, b)
{
var x = a.category.toLowerCase();
var y = b.category.toLowerCase();
return ((x < y) ? sortOrderCategory : ((x > y) ? sortOrderCategory2 : sortByType(a, b)));
} // function sortByCategory(a, b)
function sortByServer(a, b)
{
var x = a.server.toLowerCase();
var y = b.server.toLowerCase();
return ((x < y) ? sortOrderServer : ((x > y) ? sortOrderServer2 : sortByType(a, b)));
} // function sortByServer(a, b)
function sortByVersion(a, b)
{
var x = a.version;
var y = b.version;
return ((x < y) ? sortOrderVersion : ((x > y) ? sortOrderVersion2 : sortByServer(a, b)));
} // function sortByVersion(a, b)
function resetSortingVariables(sortby)
{
if(sortby != "type") {sortOrderType = 0}
if(sortby != "method") {sortOrderMethod = 0}
if(sortby != "category") {sortOrderCategory = 0}
if(sortby != "server") {sortOrderServer = 0}
if(sortby != "version") {sortOrderVersion = 0}
}
//-----------------------------------------------------
// Get url parameters
//-----------------------------------------------------
// FROM: http://www.11tmr.com/11tmr.nsf/d6plinks/MWHE-695L9Z
// Modified by Rafael Jimenez to get 2 formats
function getURLParam(strParamName)
{
var strReturn = "";
var strHref = document.location.href;
if ( strHref.indexOf("?") > -1 )
{
var strQueryString = strHref.substr(strHref.indexOf("?")).toLowerCase();
if ( strHref.indexOf("&") > -1 )
{
var aQueryString = strQueryString.split("&");
}
else if ( strHref.indexOf(":") > -1 )
{
var aQueryString = strQueryString.split(":");
}
for ( var iParam = 0; iParam < aQueryString.length; iParam++ )
{
if (
aQueryString[iParam].indexOf(strParamName + "=") > -1 )
{
var aParam = aQueryString[iParam].split("=");
strReturn = aParam[1];
break;
}
}
}
return strReturn;
}
//-----------------------------------------------------
// Get the 3 posible different url parameters for Dasty
//-----------------------------------------------------
function getDastyURLParam(param01, param02, param03)
{
var param = "";
var url_param01 = getURLParam(param01); // Dasty2
var url_param02 = getURLParam(param02); // Dasty1 by Biosapiens
var url_param03 = getURLParam(param03); // Dasty1 by Dasty1
if(url_param01 == null || url_param01 == "")
{
if(url_param02 == null || url_param02 == "")
{
if(url_param03 == null || url_param03 == "")
{
param = null;
}
else
{
param = url_param03.toUpperCase();
}
}
else
{
param = url_param02.toUpperCase();
}
}
else
{
param = url_param01.toUpperCase();
}
return param;
}
//-----------------------------------------------------
// If the URL is not right create a right one and
// start Dasty2
//-----------------------------------------------------
function setDastyURLParam(redirection)
{
var count_null = 0;
//var query_id_null_temp = query_id_null;
if(typeof(query_id_null) == "undefined")
{
query_id_null = 0;
}
// label
var url_label = getDastyURLParam("label", "display", "dis");
if(url_label == null || url_label == "")
{
filterLabel = default_filterLabel;
count_null++;
}
else
{
filterLabel = url_label;
}
// id
var url_id = getDastyURLParam("q", "id", "ID");
if( url_id == null || url_id == "")
{
query_id = default_query_id;
if( default_query_id == null || default_query_id == "")
{
query_id_null = 1;
}
else
{
count_null++;
}
}
else
{
query_id = url_id;
}
// timeout
var url_timeout = getDastyURLParam("t", "t", "t");
if(url_timeout == null || url_timeout == "")
{
timeout = default_timeout;
count_null++;
}
else
{
timeout = url_timeout;
}
if(query_id_null == 0 || redirection == "redirection")
{
// Correct URL if it is not complete otherwise start Dasty2.
if(count_null > 0 || redirection == "redirection")
{
//alert(createDastyURL() + " / " + count_null);
document.location.href = createDastyURL()
}
else
{
start_globals();
}
}
else
{
start_globals();
}
}
//-----------------------------------------------------
// Create Dasty URL
//-----------------------------------------------------
function createDastyURL(newId)
{
if(newId)
{
query_id = newId;
}
var new_url = dasty_mainpage_name + "?q=" + query_id + "&label=" + filterLabel + "&t=" + timeout;
return new_url;
}
//-----------------------------------------------------
// Create Dasty URL
//-----------------------------------------------------
function createDastyURLNewID(newId)
{
if (dasty_url_control == 0)
{
query_id = newId;
var display_query = document.getElementById("display_query");
display_query.innerHTML = "";
var display_seque = document.getElementById("display_seque");
display_seque.innerHTML = "";
var display_server_checking = document.getElementById("display_server_checking");
display_server_checking.innerHTML = "";
var display_feature_details = document.getElementById("display_feature_details");
display_feature_details.innerHTML = "";
var display_graphic = document.getElementById("display_graphic");
display_graphic.innerHTML = "";
var display_nonpositional = document.getElementById("display_nonpositional");
display_nonpositional.innerHTML = "";
var display_test = document.getElementById("display_test");
display_test.innerHTML = "";
start_globals();
}
else
{
document.location.href = createDastyURL(newId);
}
}
//-----------------------------------------------------
// Redirect pages with other names to index.html
//-----------------------------------------------------
function DastyRedirector()
{
//configuration();
//default_query_parameters()
//dasty_mainpage_name = "display.html";
//query_id = getURLParam("ID");
//filterLabel = getURLParam("dis");
//timeout = getURLParam("t");
//query_id = "";
//filterLabel = "";
//timeout = 3;
//default_filterLabel = "BioSapiens";
//default_query_id = "P05067";
//default_timeout = 3;
setDastyURLParam("redirection");
//if(query_id == null || query_id == "") {query_id = default_query_id;}
//if(filterLabel == null || filterLabel == "") {filterLabel = default_filterLabel;}
//if(timeout == null || timeout == "") {timeout = default_timeout;}
//document.location.href = createDastyURL();
}
function findDastyHtmlPageName(option)
{
var strHref = document.location.href;
var protocol = document.location.protocol;
var strHref_http = strHref.split(protocol + "//");
var url_dir = strHref_http[1].split("/");
var url_dir_count = url_dir.length;
var url_page = url_dir[url_dir_count - 1];
var url_page_name = url_page.split(".");
var dasty_page_name = url_page_name[0];
if(url_page_name.indexOf("?") > -1)
{
var url_page_ext = url_page_name[1].split("?");
var dasty_ext_name = url_page_ext[0];
}
else if(url_page_name.indexOf("&") > -1)
{
var url_page_ext = url_page_name[1].split("&");
var dasty_ext_name = url_page_ext[0];
}
else if(url_page_name.indexOf("#") > -1)
{
var url_page_ext = url_page_name[1].split("#");
var dasty_ext_name = url_page_ext[0];
}
else
{
var dasty_ext_name = url_page_name[1]
}
if(option == 'ext_name')
{
return dasty_ext_name;
}
else if(option == 'page_name')
{
return dasty_page_name;
}
else
{
return dasty_page_name;
}
}
//-----------------------------------------------------
// Old function createDastyURL()
//-----------------------------------------------------
/*
function createDastyURL()
{
var strHref = document.location.href;
var strQueryString = strHref.split("?");
var url = strQueryString[0];
if(url[url.length -1] == "/")
{
var url_options = dasty_mainpage_name + "?q=" + query_id + "&label=" + filterLabel + "&t=" + timeout;
}
else
{
var url_options = "?q=" + query_id + "&label=" + filterLabel + "&t=" + timeout;
}
var new_url = url + url_options;
return new_url;
}
*/
//-----------------------------------------------------
//-----------------------------------------------------
// Old function DastyRedirector(file)
//-----------------------------------------------------
/**
* Dasty 1.0 redirector.
*
* Requires:
* - DastyConfig.js
*
* @author Antony Quinn
* @version $Id$
* Modified by Rafel Jimenez
* The modified version don't require DastyConfig.js
*/
/**
* Redirects URLs of the form:
* content?ID=:dis=