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main.js
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/*!
* GENtle 2 - gentle ojbect
* Copyright (C) 2012 Magnus Manske
* MIT Licensed
@module gentle
*/
// TODO :
// ??? Maybe register API key for NCBI ajax access here : https://entrezajax.appspot.com/
/* Global variables :
* gentle (main.js)
* plugins (plugins.js)
*/
/**
gentle object containing core methods
@namespace
*/
//________________________________________________________________________________________
//
var gentle = {
fileTypeList : [ 'fasta' , 'genebank' , 'plaintext' , 'sybil' , 'cm5' , 'cm5_text', 'scf2json' ] ,
features : {} , //{ 'note':'Note' , 'gene':'Gene' , 'cds':'CDS' , 'promoter':'Promoter' , 'misc':'Misc' , 'protein_bind':'Protein binding site' } ,
sequences : [] ,
current_sequence_entry : undefined ,
main_sequence_canvas : undefined ,
is_mobile : false ,
is_in_dialog : false ,
storage : {} ,
/**
Initializes the gentle object.
*/
init : function () {
this.storage = new KeyValueStorage ( 'GENtle2' ) ;
this.storage.initialize ( function () {
if ( gentle_config.synbiota.show_designer ) $('#menu_tools_designer').show() ;
if(navigator.userAgent.match(/Android/i)) {
gentle.is_mobile = true ;
}
if(navigator.userAgent.match(/iPhone/i) || navigator.userAgent.match(/iPad/i)) {
gentle.is_mobile = true ;
}
gentle.is_chrome = navigator.userAgent.toLowerCase().indexOf('chrome') > -1;
window.onorientationchange = gentle.on_resize_event ;
$(window).bind('beforeunload', function(){
var confirmationMessage = "Did you mean to close this page? Files are saved locally automatically, but may not be stored in the cloud!";
//this Firefox trick only works for redirects, not for actual page closes.
/*if(/Firefox[\/\s](\d+)/.test(navigator.userAgent) && new Number(RegExp.$1) >= 4) {
if(confirm(confirmationMessage)) {
history.go();
} else {
window.setTimeout(function() {
window.stop();
}, 1);
}
} else {*/
return confirmationMessage;
//}
});
gentle.setMenuState ( 'edit_menu_undo' , false ) ;
gentle.setMenuState ( 'edit_menu_redo' , false ) ;
gentle.setMenuState ( 'edit_menu_cut' , false ) ;
gentle.setMenuState ( 'edit_menu_copy' , false ) ;
gentle.setMenuState ( 'edit_menu_paste' , false ) ;
gentle.setMenuState ( 'edit_menu_annotate' , false ) ;
gentle.setMenuState ( 'edit_menu_selection_info' , false ) ;
$('#toolbar_ul li.dropdown').each ( function ( k , v ) {
var id = $(v).attr('id') ;
if ( undefined === id ) return ;
gentle.sortMenu ( id ) ;
} ) ;
plugins.init() ;
if ( undefined === gentle_config ) {
gentle_config = { default_plugins : [] , deactivated_plugins : [] } ;
}
gentle.dragEntered = 0 ;
gentle.url_vars = {} ;
gentle.url_vars = gentle.getUrlVars ( gentle.url_vars ) ;
gentle.plugins = plugins ;
loadBaseData() ;
gentle.updateSequenceList() ;
if (window.File && window.FileReader && window.FileList && window.Blob) {
} else if ( gentle.is_mobile ) {
// Ignore iOS restrictions
} else if ( undefined !== getBlobBuilder() ) { // Otherwise, we have already warned...
gentle.addAlert ( 'error' , "This browser does not support reading local files. Try current <a href='https://www.mozilla.org/en-US/firefox/new/'>FireFox</a>, <a href='https://www.google.com/chrome/'>Google Chrome</a>, or similar." ) ;
}
$(window).bind('beforeunload', function(){ gentle.saveLocally () ; });
$(window).bind('unload', function(){ gentle.saveLocally () ; });
gentle.resizeMainDiv();
$(window)
.bind ( 'dragenter' , function ( evt ) {
gentle.dragEntered++ ;
if ( gentle.dragEntered == 1 ) $('#drop_zone').show() ;
} )
.bind ( 'dragleave' , function ( evt ) {
gentle.dragEntered-- ;
if ( gentle.dragEntered == 0 ) $('#drop_zone').hide() ;
} ) ;
$('#files').change ( gentle.handleFileSelect ) ;
$('#drop_zone') .bind('dragover',function(evt){gentle.markDropArea(evt,true)})
.bind('dragleave',function(evt){gentle.markDropArea(evt,false)})
.bind('drop',gentle.handleFileDrop) ;
gentle.loadLocally( function () {
plugins.loadPlugins() ;
if ( gentle.sequences.length == 0 ) gentle.showDefaultBlurb() ;
if ( gentle.url_vars.newsequence !== undefined ) gentle.startNewSequenceDialog() ;
} ) ;
$('#plasmidbox').hide();
gentle.topdisplaystyle = 'linear';
} ) ;
} ,
resizeMainDiv: function() {
$('#main').height ( $('body').height()-($('.navbar').height()+30) );
},
/**
Returns the "blessed" feature type string, or "misc"
@function
@param {string} s The feature type to be "blessed"
@return {string} The blessed type
*/
getFeatureType : function ( s ) {
var t = s.toLowerCase() ;
if ( undefined === cd.feature_types[t] ) return 'misc' ;
return t ;
} ,
addAlert : function ( type , message ) {
var h = '<div class="alert alert-' + type + '">' ;
h += '<a class="close" data-dismiss="alert">×</a>' ;
h += message ;
h += '</div>' ;
$('#gentle_alerts').append ( h ) ;
} ,
showDefaultBlurb : function () {
$("#main").load('public/templates/default_main.html', function(){
$('#main_blurb').css ( { overflow:'auto' } ) ;
// $('#main_blurb').width ( $('#main').width()/2 ) ;
$('#main_blurb').height ( $('#main').height() ) ;
$('#main_blurb').css ( { 'max-height' : $('#main').height() } ) ;
});
} ,
loadLocally : function ( callback ) {
var me = this ;
me.storage.hasItem('saved',function(hasit){
if ( !hasit ) {
gentle.loadLocalPlugins ( callback ) ;
return ;
}
// We cannot just assign the stored item, because of missing class methods
// Each sequence object needs to be reconstructed individually
me.storage.getItem('sequences',function(gi1){
var tmpseq = JSON.parse ( gi1 ) ;
gentle.sequences = [] ;
$.each ( tmpseq , function ( k , v ) {
if ( v.typeName == 'dna' ) {
var seq = new SequenceDNA () ;
seq.seedFrom ( v ) ;
gentle.sequences[k] = seq ;
} else if ( v.typeName == 'designer' ) {
var seq = new SequenceDesigner () ;
seq.seedFrom ( v ) ;
seq.typeName = 'designer' ;
gentle.sequences[k] = seq ;
} else if ( v.typeName == 'pcr' ) {
var seq = new SequencePCR () ;
seq.seedFrom ( v ) ;
seq.typeName = 'pcr' ;
gentle.sequences[k] = seq ;
} else {
console.log ( 'UNKNOWN LOCAL STORAGE SEQUENCE TYPENAME ' + v.typeName ) ;
}
} ) ;
// Now show last sequence, if any
gentle.current_sequence_entry === undefined ;
if ( gentle.sequences.length > 0 ) {
gentle.updateSequenceList() ;
me.storage.getItem('last_entry',function(gi2){
gentle.showSequence ( gi2 ) ;
} ) ;
}
gentle.loadLocalPlugins ( callback ) ;
} ) ;
} ) ;
} ,
loadLocalPlugins : function ( callback ) {
var me = this ;
me.storage.getItem('plugin_lists',function(plugin_list){
if ( plugin_list && object_length(plugin_list.all)>0 ) {
plugin_list = JSON.parse ( plugin_list ) ;
plugins.load_on_start = gentle_config.default_plugins ;
$.each ( plugin_list.all , function ( k , v ) { plugins.load_on_start.push ( k ) ; } ) ;
plugins.load_on_start = jQuery.unique ( plugins.load_on_start ) ;
plugins.deactivated = plugin_list.deactivated ;
plugins.loadPlugins();
} else {
plugins.load_on_start = gentle_config.default_plugins ;
}
callback();
} ) ;
} ,
/**
Wrapper around gentle.saveLocally(), might be wise to separate them for future use
*/
onThingsHaveChanged : function () {
this.saveLocally() ;
} ,
saveLocally : function () {
var me = this ;
gentle.updateCurrentSequenceSettings () ;
if ( gentle.sequences.length == 0 ) {
gentle.clearLocalStorage () ;
return ;
}
var tmp = [] ;
$.each ( gentle.sequences , function ( k , v ) {
tmp[k] = v.getStorageObject() ;
} ) ;
var s = JSON.stringify ( tmp ) ; // gentle.sequences
me.storage.setItem ( 'sequences' , s ) ;
me.storage.setItem ( 'last_entry' , gentle.current_sequence_entry ) ;
me.storage.setItem ( 'saved' , 'true' ) ;
var plugin_list = { all : {} , deactivated : {} } ;
$.each ( plugins.all , function ( k , v ) {
if ( v.url !== undefined ) plugin_list.all[v.url] = true;
} ) ;
$.each ( plugins.deactivated , function ( k , v ) {
plugin_list.deactivated[k] = true;
} ) ;
me.storage.setItem ( 'plugin_lists' , JSON.stringify(plugin_list) ) ;
} ,
setMenuState : function ( id , state ) {
if ( state ) {
$('#'+id).removeClass ( 'disabled btn-disabled' ) ;
//$('#'+id).show() ;
} else {
$('#'+id).addClass ( 'disabled btn-disabled' ) ;
//$('#'+id).hide() ;
}
// Show/hide entire edit menu
var show_edit_menu = $('#edit_menu ul a:not(.disabled)').length ;
if ( show_edit_menu > 0 ) $('#edit_menu').show() ;
else $('#edit_menu').hide() ;
} ,
sortMenu : function ( id ) {
var mylist = $($('#'+id+' ul').get(0)) ;
var listitems = mylist.children('li').get();
listitems.sort(function(a, b) {
var compA = $(a).attr('sort') || $(a).text().toUpperCase();
var compB = $(a).attr('sort') || $(b).text().toUpperCase();
return (compA < compB) ? -1 : (compA > compB) ? 1 : 0;
})
$.each(listitems, function(idx, itm) { mylist.append(itm); });
} ,
do_annotate : function () {
var sc = gentle.main_sequence_canvas ;
if ( sc === undefined ) return false ;
if ( sc.selections.length == 0 ) return ;
$("#selection_context_marker").remove();
// This should probably get its own file...
function submitTask () {
var ann = {
'_type' : $('#aad_type').val() ,
'_range' : [ { from:$('#aad_from').text()*1 , to:$('#aad_to').text()*1 } ] ,
'name' : $('#aad_name').val() ,
'desc' : $('#aad_desc').val()
} ;
sc.sequence.undo.addAction ( 'addAnnotation' , { label : 'add annotation' , editing : false , action : 'addAnnotation' , feature_id : sc.sequence.features.length , feature : clone ( ann ) } ) ;
sc.sequence.features.push ( ann ) ;
sc.recalc() ;
sc.show () ;
top_display.init() ;
if (gentle.main_sequence_canvas.plasmid_map){ gentle.main_sequence_canvas.plasmid_map.recalcAnnotations() ; gentle.main_sequence_canvas.plasmid_map.updateMap() ; }
$('#aad_annotation_dialog').modal('hide');
$('#aad_annotation_dialog').remove();
}
$('#aad_annotation_dialog').remove() ;
var dialogContainer = $("<div/>");
dialogContainer.load("public/templates/aad_annotation_dialog.html", function(){
gentle.is_in_dialog = true ;
sc.unbindKeyboard() ;
dialogContainer.appendTo("#all");
$('#aad_annotation_dialog').modal();
$('#aad_annotation_dialog').on('hidden' , function () {
gentle.is_in_dialog = false ;
sc.bindKeyboard() ;
});
$('#aad_from').text ( sc.selections[0].from+1 ) ;
$('#aad_to').text ( sc.selections[0].to+1 ) ;
var s = '';
var lastcat = '';
$.each ( gentle.features , function ( k , v ) {
var thiscat = cd.feature_types[k].category;
if(thiscat!= lastcat){
if (lastcat != ''){
s += "</optgroup>" ;
$('#aad_type').append ( s ) ;
s = '';
}
s += "<optgroup label="+thiscat+">" ;
lastcat = thiscat;
}
s += "<option value='"+k+"'" ;
if ( k == 'note' ) s += " selected" ;
s += ">"+v+"</option>" ;
} ) ;
s += "</optgroup>" ;
$('#aad_type').append ( s ) ;
$('#aad_name').focus() ;
$("#aad_annotation_form input[type=submit]").click(function(){submitTask();});
$("#aad_name").keypress(function(e) { if(e.keyCode === 13) submitTask(); });
});
return false ;
} ,
do_selection_info : function () {
var sc = gentle.main_sequence_canvas ;
if ( sc === undefined ) return false ;
if ( sc.selections.length == 0 ) return ;
$("#selection_context_marker").remove();
$('#selection_info_dialog').remove() ;
var dialogContainer = $("<div/>");
dialogContainer.load("public/templates/selection_info_dialog.html", function(){
gentle.is_in_dialog = true ;
sc.unbindKeyboard() ;
dialogContainer.appendTo("#all");
$('#selection_info_dialog').modal();
$('#selection_info_dialog').on('hidden' , function () {
gentle.is_in_dialog = false ;
sc.bindKeyboard() ;
});
var from = sc.selections[0].from;
var to = sc.selections[0].to;
var len = to - from + 1 ;
var s = sc.sequence.seq.substr ( from , len ) ;
$('#selection_info_length').html(len);
$('#selection_info_from').html(from+1);
$('#selection_info_to').html(to+1);
var tallies = { A: 0, C: 0, G: 0, T: 0 };
for (var i in s) {
if (typeof s[i] === 'string') {
if (!tallies[s[i]]) tallies[s[i]] = 0;
tallies[s[i]]++;
}
}
var syms = [];
for (var i in tallies) {
syms.push(i);
}
syms = syms.sort();
// http://www.geneinfinity.org/sp/sp_dnaprop.html
var mol_weight = (tallies['A'] * 313.2) + (tallies['C'] * 289.2) +
(tallies['G'] * 329.2) + (tallies['T'] * 304.2);
$('#selection_info_mol_weight').html(mol_weight.toFixed(2));
var h = '<table cellspacing=5 cellpadding=5>';
h += '<tr><th>Symbol</th>';
for (var i in syms) {
h += '<td>' + syms[i] + '</td>';
}
h += '</tr>';
h += '<tr><th>Frequency</th>';
for (var i in syms) {
h += '<td>' + tallies[syms[i]] + '</td>';
}
h += '</tr>';
h += '<tr><th>Percentage</th>';
for (var i in syms) {
var percent = 100.0 * tallies[syms[i]] / s.length;
h += '<td>' + percent.toFixed(2) + '</td>';
}
h += '</tr>';
var plot_height = 250;
h += '<tr valign=bottom><th></th>';
for (var i in syms) {
var height = Math.floor(plot_height * (tallies[syms[i]] / s.length));
var color = gentle_config.colors.DRuMS[syms[i]] || 'black';
h += '<td><div style="background-color:' + color + '; width: 50px; height: ' + height + 'px"></span></td>';
}
h += '</tr>';
h += '</table>';
$('#selection_info_tallies').html(h);
var AT = (tallies['A'] || 0) + (tallies['T'] || 0);
var CG = (tallies['C'] || 0) + (tallies['G'] || 0);
$('#selection_info_at_count').html(AT);
$('#selection_info_cg_count').html(CG);
$('#selection_info_at_percent').html((100.0 * AT / (AT + CG)).toFixed(2) + '%');
$('#selection_info_cg_percent').html((100.0 * CG / (AT + CG)).toFixed(2) + '%');
var graph_width = 400;
$('#selection_info_at_graph').css('width', Math.floor(graph_width * AT / (AT + CG)));
$('#selection_info_cg_graph').css('width', Math.floor(graph_width * CG / (AT + CG)));
});
return false ;
},
do_edit : function ( command ) {
if ( gentle.main_sequence_canvas === undefined ) return false ;
$("#selection_context_marker").remove();
var sc = gentle.main_sequence_canvas ;
var s = '' ;
var title = 'Copy/paste area' ;
if ( command == 'cut' || command == 'copy' ) {
s = gentle.main_sequence_canvas.cut_copy ( (command=='cut') ) ;
} else if ( command == 'paste' ) {
if ( !sc.edit.editing ) return false ; // Edit mode only
} else {
console.log ( "Unknown command " + command + " in gentle.do_edit" ) ;
return false ;
}
$('#ccp_dialog').remove() ;
var h = '' ;
h += '<div class="modal" id="ccp_dialog" style="display:none">' ;
h += '<div class="modal-header">' ;
h += '<a class="close" data-dismiss="modal">×</a>' ;
h += '<h3>' + title + '</h3>' ;
h += '</div>' ;
h += '<div class="modal-body">' ;
h += '<textarea id="paste_area" cols=60 rows=5 style="width:100%">' + s + '</textarea>' ;
if ( command == 'paste' ) h += '<input type="button" id="ccp_dialog_doit" value="Paste" />' ;
h += '</div>' ;
if ( !gentle.is_mobile ) {
h += '<div class="modal-footer">' ;
h += "<i>You can also use keyboard shortcuts for cut, copy, and paste without this dialog!</i>" ;
h += '</div>' ;
}
h += '</div>' ;
$('#all').append ( h ) ;
$('#ccp_dialog').modal() ;
$('#ccp_dialog').on('hidden' , function () {
sc.bindKeyboard() ;
} ) ;
$('#paste_area').focus() ;
$('#paste_area').select() ;
$(document).off ( 'copy keydown paste cut' ) ;
if ( command == 'paste' ) {
$('#ccp_dialog_doit').click ( function () {
var text = $('#paste_area').val() ;
var sc = gentle.main_sequence_canvas ;
$('#ccp_dialog').modal('hide') ;
$('#ccp_dialog').remove() ;
sc.doCheckedPaste ( sc , text ) ;
return false ;
} ) ;
}
return false ;
} ,
startAddSequenceDialog : function () {
$('#addSequenceDialog').remove() ;
var dialogContainer = $("<div/>");
dialogContainer.load("public/templates/add_sequence_dialog.html", function(){
var sc = gentle.main_sequence_canvas ;
if ( sc ) {
if ( sc.edit.editing ) {
sc.setEditMode ( false ) ;
sc.show() ;
}
sc.unbindKeyboard() ;
}
dialogContainer.appendTo("#all");
$('#addSequenceDialog').modal();
});
} ,
startNewSequenceDialog : function () {
$('#newSequenceDialog').remove() ;
var dialogContainer = $("<div/>");
dialogContainer.load("public/templates/new_sequence_dialog.html", function(){
var sc = gentle.main_sequence_canvas ;
if ( sc ) {
if ( sc.edit.editing ) {
sc.setEditMode ( false ) ;
sc.show() ;
}
sc.unbindKeyboard() ;
}
dialogContainer.appendTo("#all");
$('#newSequenceDialog').modal();
$('#new_sequence_entry').focus() ;
$('#new_sequence_name').inlineEditable({editingClass: 'inline-edited', onSaveCallback: function(val) {
console.log("you changed names:", val);
}});
});
} ,
createNewSequenceFromDialog : function () {
var text = $("#new_sequence_entry").val() ;
var title = $('#new_sequence_name').text() ;
if ( text == '' ) {
alert ( "In Soviet Russia, empty text parses YOU!" ) ;
return ;
}
// Determine file type
var found = false ;
$.each ( gentle.fileTypeList , function ( k , v ) {
var file = new window['FT_'+v]();
if ( file.checkText ( text ) ) { // End filetype search
found = true ;
return false ;
}
} ) ;
if ( found ) {
$("#newSequenceDialog").modal("hide").remove();
if (title != "Unnamed sequence" && gentle.main_sequence_canvas.sequence.name == "Unnamed sequence"){
gentle.main_sequence_canvas.sequence.name = title;
gentle.main_sequence_canvas.updateTitleBar() ;
}
} else {
alert ( "File type not recognised" ) ;
}
} ,
createNewSequenceForAlignment: function (sequence) {
var text = sequence;
if (text == '') {
alert("In Soviet Russia, empty text parses YOU!");
return;
}
var seq = new SequenceDNA('New Alignment', text);
gentle.addSequence(seq, true);
} ,
closeAllSequences : function () {
while ( gentle.sequences.length > 0 ) {
gentle.closeSequence ( 0 ) ;
}
} ,
closeCurrentSequence : function () {
gentle.closeSequence ( gentle.current_sequence_entry ) ;
gentle.onThingsHaveChanged() ;
} ,
closeSequence : function ( entry ) {
if ( entry === undefined ) return ;
gentle.main_sequence_canvas.onClose() ;
gentle.sequences.splice ( entry , 1 ) ;
gentle.updateSequenceList() ;
if ( gentle.sequences.length == 0 ) {
gentle.current_sequence_entry = undefined ;
gentle.clearLocalStorage () ;
$('#close_sequence').hide() ;
$('#topbox').html ( '' ) ;
$('#main').html ( '' ) ;
$('#sb_display_options').html ( '' ) ;
$('#position').html ( ' ' ) ;
$('#sequence_canvas_title_bar').html ( '' ) ;
// $('#right').html ( '' ) ;
$('#toolbar_ul .toolbar_plugin').remove() ;
gentle.showDefaultBlurb() ;
return ;
}
if ( entry == gentle.current_sequence_entry ) {
gentle.current_sequence_entry = gentle.current_sequence_entry - 1 ;
gentle.main_sequence_canvas.invalidated = true ;
} else if ( entry < gentle.current_sequence_entry ) gentle.current_sequence_entry-- ;
if ( gentle.current_sequence_entry < 0 ) gentle.current_sequence_entry = 0 ;
gentle.showSequence ( gentle.current_sequence_entry ) ;
} ,
clearLocalStorage : function () {
var me = this ;
// me.storage.clear() ; // Don't use, would nuke plugins
me.storage.removeItem('saved') ;
me.storage.removeItem('last_entry') ;
me.storage.removeItem('sequences') ;
} ,
updateCurrentSequenceSettings : function () {
if ( gentle.current_sequence_entry === undefined ) return ;
if ( gentle.main_sequence_canvas.invalidated ) return ;
gentle.sequences[gentle.current_sequence_entry].settings = gentle.main_sequence_canvas.getSettings() ;
// console.log ( "STORING : " + JSON.stringify ( gentle.sequences[gentle.current_sequence_entry].settings ) ) ;
} ,
handleSelectSequenceEntry : function ( entry ) {
gentle.updateCurrentSequenceSettings () ;
$('#close_sequence').show() ;
if ( gentle.current_sequence_entry !== undefined ){
gentle.main_sequence_canvas.onClose();
}
var sc = gentle.sequences[entry] ;
if ( sc === undefined ) return ; // Paranoia
if ( sc.typeName == 'designer' ) gentle.handleSelectSequenceEntryDesigner ( entry ) ;
else if ( sc.typeName == 'pcr' ) gentle.handleSelectSequenceEntryPCR ( entry ) ;
else gentle.handleSelectSequenceEntryDNA ( entry ) ; // Default
gentle.onThingsHaveChanged() ;
} ,
handleSelectSequenceEntryDesigner : function ( entry ) {
gentle.current_sequence_entry = entry ;
var html = "<div id='canvas_wrapper'>" ;
html += "</div>" ;
$('#main').html ( html ) ;
// Set up new top display
$('#top_zone').html('');
top_display = undefined ;
// Set up new sequence canvas
gentle.main_sequence_canvas = new SequenceCanvasDesigner ( gentle.sequences[entry] , 'sequence_canvas' ) ;
if ( $('#topbox').is(':visible') ) gentle.toggle_right_sidebar();
} ,
handleSelectSequenceEntryPCR : function ( entry ) {
gentle.current_sequence_entry = entry ;
var html = "<div id='canvas_wrapper'>" ;
html += "<canvas id='sequence_canvas'></canvas>" ;
html += "<canvas id='sequence_canvas_overlay'></canvas>" ;
html += "<div id='main_slider'></div>" ;
html += "</div>" ;
$('#main').html ( html ) ;
//if ( !gentle.is_mobile && !gentle.is_chrome ) $('#canvas_wrapper').attr ( 'contenteditable' , 'true' ) ;
$('#canvas_wrapper').height ( $('#main').height() - 20 ) ;
// Set up new top display
top_display = new TopDisplayDNA ( true ) ;
top_display.init() ;
// Set up new sequence canvas
gentle.main_sequence_canvas = new SequenceCanvasPCR ( gentle.sequences[entry] , 'sequence_canvas' ) ;
} ,
handleSelectSequenceEntryDNA : function ( entry ) {
gentle.current_sequence_entry = entry ;
var html = "<div id='canvas_wrapper'>" ;
html += "<canvas id='sequence_canvas'></canvas>" ;
html += "<canvas id='sequence_canvas_overlay'></canvas>" ;
html += "<div id='main_slider'></div>" ;
html += "</div>" ;
$('#main').html ( html ) ;
//if ( !gentle.is_mobile && !gentle.is_chrome ) $('#canvas_wrapper').attr ( 'contenteditable' , 'true' ) ;
$('#canvas_wrapper').height ( $('#main').height() - 20 ) ;
// Set up new top display
top_display = new TopDisplayDNA ( true ) ;
top_display.init() ;
// Set up new sequence canvas
gentle.main_sequence_canvas = new SequenceCanvasDNA ( gentle.sequences[entry] , 'sequence_canvas' ) ;
// Set up new plasmid map
gentle.main_sequence_canvas.plasmid_map = new PlasmidMapDialog ( true ) ;
gentle.main_sequence_canvas.plasmid_map.initMap() ;
} ,
getUrlVars : function ( def ) {
var vars = def , hash;
var hashes = window.location.href.slice(window.location.href.indexOf('?') + 1).split('&');
$.each ( hashes , function ( i , j ) {
var hash = j.split('=');
hash[1] += '' ;
vars[hash[0]] = decodeURI(hash[1]).replace(/_/g,' ');
} ) ;
return vars;
} ,
// File open/drop handlers
handleFileSelect : function ( evt ) {
$.each ( evt.target.files , function ( k , f ) { gentle.addLocalFile ( f ) } ) ;
$('#openFileFromDisk').modal ( 'hide' ) ;
} ,
handleFileDrop : function (evt) {
gentle.dragEntered = 0 ;
evt.originalEvent.stopPropagation();
evt.originalEvent.preventDefault();
$.each ( evt.originalEvent.dataTransfer.files , function ( k , f ) { gentle.addLocalFile ( f ) } ) ;
gentle.markDropArea(evt,false);
$('#drop_zone').hide() ;
} ,
markDropArea : function ( evt , mode ) {
evt.originalEvent.stopPropagation();
evt.originalEvent.preventDefault();
evt.originalEvent.dataTransfer.dropEffect = 'copy';
$('#drop_zone').css({'background-color':(mode?'#CCCCCC':'white')}) ;
} ,
fileLoaded : function ( f ) {
// $('#sb_log').append ( '<p>' + f.file.name + ' is ' + f.typeName + '</p>' ) ;
} ,
addLocalFile : function ( f ) {
// $('#sb_log').append ( '<p>Loading ' + f.name + '</p>' ) ;
// Determine file type
f.isIdentified = false ;
$.each ( gentle.fileTypeList , function ( k , v ) {
var file = new window['FT_'+v]();
file.checkFile ( f ) ;
} ) ;
} ,
addFileType : function ( type ) {
// TODO check if class exists and has necessary methods
// TODO check to avoid duplicate entries
gentle.fileTypeList.push ( type ) ;
} ,
toggle_display_settings : function () {
if ( $('#sb_display_options').is(':visible') ) {
$('#sb_display_options').dialog ( 'close' ) ;
} else {
// $('body').append("<div id='sb_display_options'></div>");
$('#sb_display_options').dialog ( { modal : false , width : 'auto' } ) ;
$('#sb_display_options').dialog('option', 'position', 'center');
}
} ,
toggle_loaded_sequences : function () {
if ( $('#sb_sequences_container').is(':visible') ) {
$('#sb_sequences_container').dialog ( 'close' ) ;
} else {
$('body').append("<div id='sb_sequences_container' style='display:none' title='Loaded sequences'><div id='sb_sequences_table_container'></div></div>");
gentle.updateSequenceList();
$('#sb_sequences_container').dialog ( {
modal:false , width:'auto' , maxWidth:1200 , height:'auto' ,
close : function () {
$('#sb_sequences_container').remove();
}
} ) ;
}
} ,
toggle_right_sidebar : function () {
var sc = gentle.main_sequence_canvas ;
if (gentle.topdisplaystyle == 'linear'){
$('#topbox').hide() ;
$('#plasmidbox').show() ;
$('#right_sidebar_icon').toggleClass('icon-asterisk').toggleClass('icon-chevron-right').attr('title', 'Hide Sidebar') ;
gentle.topdisplaystyle = 'circular' ;
console.log ("was linear, is circular") ;
}else if(gentle.topdisplaystyle == 'circular'){
gentle.tbw = $('#canvas_wrapper').css('right');
$('#canvas_wrapper').css ( { right : 0 } ) ;
$('#sequence_canvas_title_bar').css ( { right : 0 } ) ;
$('#plasmidbox').hide() ;
$('#right_sidebar_icon').toggleClass('icon-chevron-right').toggleClass('icon-chevron-left').attr('title', 'Show Linear Map') ;
gentle.topdisplaystyle = 'none' ;
console.log ("was circular, is none") ;
}else{
$('#canvas_wrapper').css ( { right : gentle.tbw } ) ;
$('#sequence_canvas_title_bar').css ( { right : gentle.tbw } ) ;
$('#topbox').show() ;
$('#right_sidebar_icon').toggleClass('icon-chevron-left').toggleClass('icon-asterisk').attr('title', 'Show Circular Map') ;
gentle.topdisplaystyle = 'linear' ;
console.log ("was none, is linear") ;
}
gentle.on_resize_event() ;
$('#zoombox').toggle ( $('#topbox').is(':visible') ) ;
} ,
delete_selection : function () {
var sc = gentle.main_sequence_canvas ;
$("#selection_context_marker").remove();
sc.deleteSelection();
} ,
startDesigner : function () {
if ( gentle.sequences.length == 0 ) {
alert ( "You need at least one DNA sequence open to start the Designer" ) ;
return ;
}
var use_existing ;
$.each ( gentle.sequences , function ( k , v ) {
if ( v.typeName == 'designer' ) use_existing = k ;
} ) ;
if ( undefined != use_existing ) {
gentle.handleSelectSequenceEntry ( use_existing ) ;
return ;
}
// Start new designed
var entry = gentle.sequences.length ;
var seq = gentle.sequences[gentle.current_sequence_entry].clone() ;
seq.typeName = 'designer' ;
gentle.addSequence ( seq , true ) ;
} ,
/* BEGIN Loaded sequences dialog functions */
addSequence : function ( sequence , show ) {
var seqid = gentle.sequences.length ;
gentle.sequences.push ( sequence ) ;
gentle.updateSequenceList () ;
if ( show ) gentle.showSequence ( seqid ) ;
return seqid ;
} ,
showSequence : function ( seqid ) {
seqid = parseInt ( seqid ) ; // Paranoia
gentle.handleSelectSequenceEntry ( seqid ) ;
$('.loaded_sequence_select_icon').hide() ;
$('#loaded_sequence_select_icon'+seqid).show() ;
} ,
updateSequenceList : function () {
var h = "<table class='table table-condensed'>" ;
h += "<thead><tr><th> </th><th>Type</th><th>Sequence</th><th>Action</th></tr></thead><tbody>" ;
$.each ( gentle.sequences , function ( seqid , seq ) {
var show_title = seq.name ;
var show_type = seq.typeName ;
if ( show_type == 'dna' ) show_type = show_type.toUpperCase() ;
else show_type = ucFirst ( show_type ) ;
h += "<tr onclick='gentle.showSequence(" + seqid + ");return false' style='cursor:pointer'><td>" ;
h += "<i class='icon-chevron-right loaded_sequence_select_icon' id='loaded_sequence_select_icon" + seqid + "'></i>" ;
h += "</td><td>" ;
h += show_type ;
h += "</td><td>" ;
h += show_title ;
h += "</td><td>" ;
h += "<button class='btn btn-danger' onclick='gentle.closeSequence(" + seqid + ")'>Close</button>" ;
h += "</td></tr>" ;
} ) ;
h += "</tbody></table>" ;
h += "<hr/><div style='text-align:right'><button class='btn btn-danger' onclick='gentle.closeAllSequences()'>Close all</button></div>" ;
if ( gentle.sequences.length == 0 ) {
h = "<i>No sequences loaded</i>" ;
}
$('#sb_sequences_table_container').html ( h ) ;
$('.loaded_sequence_select_icon').hide() ;
if ( undefined !== gentle.current_sequence_entry && gentle.current_sequence_entry < gentle.sequences.length ) {
$('#loaded_sequence_select_icon'+gentle.current_sequence_entry).show() ;
}
$( "sb_sequences_container" ).dialog( "option", "position", 'center' );
} ,
/* END Loaded sequences dialog functions */
do_start_pcr : function () {
var sc = gentle.main_sequence_canvas ;
if ( undefined === sc ) { console.log ( "No canvas" ) ; return ; }
if ( undefined === sc.sequence ) { console.log ( "No sequence" ) ; return ; }
// TODO paranoia checks
var template_sequence = sc.sequence ;
var start = sc.selections[0].from ;
var stop = sc.selections[0].to ;
var pcr = new SequencePCR ( template_sequence.name , template_sequence.seq ) ;
console.log("sequencePCR");
pcr.is_circular = template_sequence.is_circular ;
$.each ( (template_sequence.features||[]) , function ( k , v ) {
var o = clone ( v ) ;
o['_range'] = [] ;
$.each ( v['_range'] , function ( k2 , v2 ) {
o['_range'].push ( clone ( v2 ) ) ;
} ) ;
pcr.features.push ( o ) ;
} ) ;
pcr.undo.setSequence ( pcr ) ;
console.log("pcr.undo.setSequence (pcr)");
gentle.addSequence ( pcr , true ) ;
console.log("gentle.addSequence (pcr , true)");
pcr.addPrimer ( start , start+25 , false ) ;
console.log("pcr.addPrimer ( start , start+25 , false ) ;");
pcr.addPrimer ( stop-24 , stop , true ) ;
console.log("pcr.addPrimer ( stop-24 , stop , true ) ;");
return false ;
} ,
sequence_info : function () {
var sc = gentle.main_sequence_canvas ;
if ( undefined === sc ) return ;
gentle.sequence_info_dialog = new SequenceInfoDialogDNA ( sc ) ; // FIXME hardcoded for DNA
} ,
set_hover : function ( html ) {
$('#hoverbox').html ( html ) ;
} ,