',
@@ -138,16 +126,7 @@ var PageLayoutView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({
].join('');
},
- hideSidePanels : function(){
- if( this.left ){
- this.left.hide();
- }
- if( this.right ){
- this.right.hide();
- }
- },
-
- toString : function(){ return 'PageLayoutView'; }
+ toString : function() { return 'PageLayoutView' }
});
// ============================================================================
diff --git a/client/galaxy/scripts/layout/scratchbook.js b/client/galaxy/scripts/layout/scratchbook.js
index 296657a684c..695686e361e 100644
--- a/client/galaxy/scripts/layout/scratchbook.js
+++ b/client/galaxy/scripts/layout/scratchbook.js
@@ -1,84 +1,51 @@
-// dependencies
-define(["mvc/ui/ui-frames"], function(Frames) {
-
/** Frame manager uses the ui-frames to create the scratch book masthead icon and functionality **/
-var GalaxyFrame = Backbone.View.extend({
- // base element
- el_main: 'body',
-
- // frame active/disabled
- active: false,
-
- // button active
- button_active: null,
-
- // button load
- button_load : null,
-
- // initialize
- initialize : function(options) {
- options = options || {};
-
- // add to masthead menu
+define([ 'mvc/ui/ui-frames' ], function( Frames ) {
+return Backbone.View.extend({
+ initialize : function( options ) {
var self = this;
-
- // create frames
- this.frames = new Frames.View({
- visible: false,
- });
-
- // add activate icon
- this.button_active = new GalaxyMastheadIcon({
+ options = options || {};
+ this.frames = new Frames.View({ visible : false });
+ this.setElement( this.frames.$el );
+ this.buttonActive = options.collection.add({
icon : 'fa-th',
tooltip : 'Enable/Disable Scratchbook',
- onclick : function() { self._activate(); },
+ onclick : function() {
+ self.active = !self.active;
+ self.buttonActive.set({
+ toggle : self.active,
+ show_note : self.active,
+ note_cls : self.active && 'fa fa-check'
+ });
+ !self.active && self.frames.hide();
+ },
onbeforeunload : function() {
- if (self.frames.length() > 0) {
- return "You opened " + self.frames.length() + " frame(s) which will be lost.";
+ if ( self.frames.length() > 0 ) {
+ return 'You opened ' + self.frames.length() + ' frame(s) which will be lost.';
}
}
});
-
- // add load icon
- this.button_load = new GalaxyMastheadIcon({
- icon : 'fa-eye',
- tooltip : 'Show/Hide Scratchbook',
- onclick : function(e) {
- if (self.frames.visible) {
- self.frames.hide();
- } else {
- self.frames.show();
- }
- },
- with_number : true
+ this.buttonLoad = options.collection.add({
+ icon : 'fa-eye',
+ tooltip : 'Show/Hide Scratchbook',
+ show_note : true,
+ visible : false,
+ onclick : function( e ) {
+ self.frames.visible ? self.frames.hide() : self.frames.show();
+ }
});
-
- // add to masthead
- if( options.masthead ){
- options.masthead.append(this.button_active);
- options.masthead.append(this.button_load);
- }
-
- // create
- this.setElement(this.frames.$el);
-
- // append to main
- $(this.el_main).append(this.$el);
-
- // refresh menu
- this.frames.setOnChange(function() {
- self._refresh();
+ this.frames.on( 'add remove', function() {
+ this.visible && this.length() == 0 && this.hide();
+ self.buttonLoad.set( { 'note': this.length(), 'visible': this.length() > 0 } );
+ }).on( 'show hide ', function() {
+ self.buttonLoad.set( { 'toggle': this.visible, 'icon': this.visible && 'fa-eye' || 'fa-eye-slash' } );
});
- this._refresh();
},
- /**
- * Add a dataset to the frames.
- */
- add_dataset: function(dataset_id) {
+ /** Add a dataset to the frames */
+ addDataset: function( dataset_id ) {
var self = this;
- require(['mvc/dataset/data'], function(DATA) {
- var dataset = new DATA.Dataset({ id: dataset_id });
+ require([ 'mvc/dataset/data' ], function( DATA ) {
+ var dataset = new DATA.Dataset( { id : dataset_id } );
$.when( dataset.fetch() ).then( function() {
// Construct frame config based on dataset's type.
var frame_config = {
@@ -87,44 +54,36 @@ var GalaxyFrame = Backbone.View.extend({
// HACK: For now, assume 'tabular' and 'interval' are the only
// modules that contain tabular files. This needs to be replaced
// will a is_datatype() function.
- is_tabular = _.find(['tabular', 'interval'], function(data_type) {
- return dataset.get('data_type').indexOf(data_type) !== -1;
+ is_tabular = _.find( [ 'tabular', 'interval' ] , function( data_type ) {
+ return dataset.get( 'data_type' ).indexOf( data_type ) !== -1;
});
// Use tabular chunked display if dataset is tabular; otherwise load via URL.
- if (is_tabular) {
- var tabular_dataset = new DATA.TabularDataset(dataset.toJSON());
- _.extend(frame_config, {
- type: 'other',
+ if ( is_tabular ) {
+ var tabular_dataset = new DATA.TabularDataset( dataset.toJSON() );
+ _.extend( frame_config, {
content: function( parent_elt ) {
DATA.createTabularDatasetChunkedView({
- model: tabular_dataset,
- parent_elt: parent_elt,
- embedded: true,
- height: '100%'
+ model : tabular_dataset,
+ parent_elt : parent_elt,
+ embedded : true,
+ height : '100%'
});
}
});
}
else {
- _.extend(frame_config, {
- type: 'url',
- content: Galaxy.root + 'datasets/' +
- dataset.id + '/display/?preview=True'
+ _.extend( frame_config, {
+ url: Galaxy.root + 'datasets/' + dataset.id + '/display/?preview=True'
});
}
-
- self.add(frame_config);
-
+ self.add( frame_config );
});
});
-
},
- /**
- * Add a trackster visualization to the frames.
- */
- add_trackster_viz: function(viz_id) {
+ /** Add a trackster visualization to the frames. */
+ addTrackster: function(viz_id) {
var self = this;
require(['viz/visualization', 'viz/trackster'], function(visualization, trackster) {
var viz = new visualization.Visualization({id: viz_id});
@@ -155,7 +114,6 @@ var GalaxyFrame = Backbone.View.extend({
id: d.dataset_id
};
});
-
view = ui.create_visualization(view_config,
latest_revision.config.viewport,
latest_revision.config.view.drawables,
@@ -163,183 +121,37 @@ var GalaxyFrame = Backbone.View.extend({
false);
}
};
-
self.add(frame_config);
});
});
},
- /**
- * Add and display a new frame/window based on options.
- */
- add: function(options){
- // open new tab
- if (options.target == '_blank'){
- window.open(options.content);
- return;
- }
-
- // reload entire window
- if (options.target == '_top' || options.target == '_parent' || options.target == '_self'){
- window.location = options.content;
- return;
- }
-
- // validate
- if (!this.active){
- // fix url if main frame is unavailable
- var $galaxy_main = $(window.parent.document).find('#galaxy_main');
- if (options.target == 'galaxy_main' || options.target == 'center'){
- if ($galaxy_main.length === 0){
- var href = options.content;
- if (href.indexOf('?') == -1)
+ /** Add and display a new frame/window based on options. */
+ add: function( options ) {
+ if ( options.target == '_blank' ) {
+ window.open( options.url );
+ } else if ( options.target == '_top' || options.target == '_parent' || options.target == '_self' ) {
+ window.location = options.url;
+ } else if ( !this.active ) {
+ var $galaxy_main = $( window.parent.document ).find( '#galaxy_main' );
+ if ( options.target == 'galaxy_main' || options.target == 'center' ){
+ if ( $galaxy_main.length === 0 ){
+ var href = options.url;
+ if ( href.indexOf( '?' ) == -1 )
href += '?';
else
href += '&';
href += 'use_panels=True';
window.location = href;
} else {
- $galaxy_main.attr('src', options.content);
+ $galaxy_main.attr( 'src', options.url );
}
} else
- window.location = options.content;
-
- // stop
- return;
- }
-
- // add to frames view
- this.frames.add(options);
- },
-
- // activate/disable panel
- _activate: function (){
- // check
- if (this.active){
- // disable
- this.active = false;
-
- // toggle
- this.button_active.untoggle();
-
- // hide panel
- this.frames.hide();
+ window.location = options.url;
} else {
- // activate
- this.active = true;
-
- // untoggle
- this.button_active.toggle();
- }
- },
-
- // update frame counter
- _refresh: function(){
- // update on screen counter
- this.button_load.number(this.frames.length());
-
- // check
- if(this.frames.length() === 0)
- this.button_load.hide();
- else
- this.button_load.show();
-
- // check
- if (this.frames.visible) {
- this.button_load.toggle();
- } else {
- this.button_load.untoggle();
+ this.frames.add( options );
}
}
});
-/** Masthead icon **/
-var GalaxyMastheadIcon = Backbone.View.extend({
- // icon options
- options:{
- id : '',
- icon : 'fa-cog',
- tooltip : '',
- with_number : false,
- onclick : function() { alert ('clicked') },
- onunload : null,
- visible : true
- },
-
- // location identifier for masthead class
- location: 'iconbar',
-
- // initialize
- initialize: function (options){
- // read in defaults
- if (options)
- this.options = _.defaults(options, this.options);
-
- // add template for icon
- this.setElement($(this._template(this.options)));
-
- // configure icon
- var self = this;
- $(this.el).find('.icon').tooltip({title: this.options.tooltip, placement: 'bottom'})
- .on('mouseup', self.options.onclick);
-
- // visiblity
- if (!this.options.visible)
- this.hide();
- },
-
- // show
- show: function(){
- $(this.el).css({visibility : 'visible'});
- },
-
- // show
- hide: function(){
- $(this.el).css({visibility : 'hidden'});
- },
-
- // switch icon
- icon: function (new_icon){
- // update icon class
- $(this.el).find('.icon').removeClass(this.options.icon)
- .addClass(new_icon);
-
- // update icon
- this.options.icon = new_icon;
- },
-
- // toggle
- toggle: function(){
- $(this.el).addClass('toggle');
- },
-
- // untoggle
- untoggle: function(){
- $(this.el).removeClass('toggle');
- },
-
- // set/get number
- number: function(new_number){
- $(this.el).find('.number').text(new_number);
- },
-
- // fill template icon
- _template: function (options){
- var tmpl = '
' +
- '
';
- if (options.with_number)
- tmpl+= '
';
- tmpl += '
';
-
- // return template
- return tmpl;
- }
-});
-
-// return
-return {
- GalaxyFrame: GalaxyFrame,
- GalaxyMastheadIcon: GalaxyMastheadIcon
-};
-
});
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
index ba0afb5ca11..a962b2ce90e 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
@@ -209,9 +209,8 @@ var DatasetListItemEdit = _super.extend(
$links.click( function( ev ){
if( Galaxy.frame && Galaxy.frame.active ){
Galaxy.frame.add({
- title : "Visualization",
- type : "url",
- content : $( this ).attr( 'href' )
+ title : 'Visualization',
+ url : $( this ).attr( 'href' )
});
ev.preventDefault();
ev.stopPropagation();
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index 8d425fcda4f..1bc08d38795 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -161,7 +161,7 @@ var DatasetListItemView = _super.extend(
displayBtnData.onclick = function( ev ){
if (Galaxy.frame && Galaxy.frame.active) {
// Add dataset to frames.
- Galaxy.frame.add_dataset(self.model.get('id'));
+ Galaxy.frame.addDataset(self.model.get('id'));
ev.preventDefault();
}
};
diff --git a/client/galaxy/scripts/mvc/ui/ui-frames.js b/client/galaxy/scripts/mvc/ui/ui-frames.js
index 9d7e58037e4..9a83a7fc332 100644
--- a/client/galaxy/scripts/mvc/ui/ui-frames.js
+++ b/client/galaxy/scripts/mvc/ui/ui-frames.js
@@ -1,302 +1,170 @@
-// dependencies
+/** Scratchbook viewer */
define([], function() {
-
-// frame manager
var View = Backbone.View.extend({
- // defaults inputs
- options: {
- // default frame size
- frame: {
+ defaultOptions: {
+ frame: { // default frame size in cells
cols : 6,
rows : 3
},
-
- // maximum number of rows
- rows: 1000,
-
- // cell size in px
- cell: 130,
-
- // margin
- margin: 5,
-
- // scroll speed
- scroll: 5,
-
- // minimum top
- top_min: 40,
-
- // maximum number of frames
- frame_max: 9,
-
- // visible
- visible: true,
-
- // onchange
- onchange: null
+ rows : 1000, // maximum number of rows
+ cell : 130, // cell size in px
+ margin : 5,
+ scroll : 5, // scroll speed
+ top_min : 40, // top margin
+ frame_max : 9, // maximum number of frames
+ visible : true, // initial visibility
},
- // number of columns
- cols: 0,
+ cols : 0, // number of columns
+ top : 0, // scroll/element top
+ top_max : 0, // viewport scrolling state
+ frame_z : 0, // frame z-index
+ frame_counter : 0, // frame counter
+ frame_uid : 0,
+ frame_list : {}, // list of all frames
+ frame_shadow : null,
+ visible : false,
+ event : {},
- // scroll/element top
- top: 0,
-
- // viewport scrolling state
- top_max: 0,
-
- // frame z-index
- frame_z : 0,
-
- // frame counter
- frame_counter: 0,
-
- // frame counter
- frame_counter_id: 0,
-
- // frame list
- frame_list: [],
-
- // frame shadow
- frame_shadow: null,
-
- // frame panel visible
- visible: null,
-
- // initialize
- initialize : function(options) {
- // add to masthead menu
+ initialize : function( options ) {
var self = this;
-
- // read in defaults
- if (options) {
- this.options = _.defaults(options, this.options);
- }
-
- // set visibility
+ this.options = _.defaults( options || {}, this.defaultOptions );
this.visible = this.options.visible;
-
- // initialize top
this.top = this.top_max = this.options.top_min;
+ this.setElement( $( '
' ).addClass( 'galaxy-frame' ) );
+ this.$el.append( $( '
' ).addClass( 'frame-background' ) );
+ this.$el.append( $( '
' ).addClass( 'frame-menu frame-scroll-up fa fa-chevron-up fa-2x' ) );
+ this.$el.append( $( '
' ).addClass( 'frame-menu frame-scroll-down fa fa-chevron-down fa-2x' ) );
+ this.$el.append( $( '
' ).addClass( 'frame-shadow corner' ).attr( 'id', 'frame-shadow' ) );
- // create
- this.setElement(this._template());
-
- // load background
- $(this.el).append(this._templateBackground());
-
- // load menu buttons
- $(this.el).append(this._templateMenu());
-
- // load to main frame
- $(this.el_main).append($(this.el));
-
- //
- // define shadow frame
- //
- var id_shadow = '#frame-shadow';
-
- // add shadow template
- $(this.el).append(this._templateShadow(id_shadow.substring(1)));
-
- // initialize frame
+ // initialize shadow to guiding drag/resize events
this.frame_shadow = {
- id : id_shadow,
+ id : '#frame-shadow',
screen_location : {},
grid_location : {},
grid_rank : null,
grid_lock : false
};
-
- // initialize size
- this._frameResize(this.frame_shadow, {width: 0, height: 0});
-
- // add shadow to frame list
- this.frame_list[id_shadow] = this.frame_shadow;
+ this._frameResize( this.frame_shadow, { width: 0, height: 0 } );
+ this.frame_list[ '#frame-shadow' ] = this.frame_shadow;
// initialize panel
+ this.visible ? this.show() : this.hide();
this._panelRefresh();
+ $( window ).resize( function() { self.visible && self._panelRefresh() } );
+ },
- // apply visibility
- if (!this.visible) {
- this.hide();
- } else {
- this.show();
- }
-
- // catch window resize event
- var self = this;
- $(window).resize(function () {
- if (self.visible)
- self._panelRefresh();
- });
+ /** Render */
+ render: function() {
+ this.$( '.frame-scroll-up' ) [ this.top != this.options.top_min && 'show' || 'hide' ]();
+ this.$( '.frame-scroll-down')[ this.top != this.top_max && 'show' || 'hide' ]();
},
/**
* Adds and displays a new frame.
*
* options:
- * type: 'url' or 'other' ; if 'url', 'content' is treated as a URL and loaded into an iframe;
- * if 'other', content is treated as a function or raw HTML. content function is passed a single
- * argument that is the frame's content DOM element
- * content: the content to be loaded into the frame.
+ * url : loaded into an iframe
+ * content : content is treated as a function or raw HTML, function is passed a single
+ * argument that is the frame's content DOM element
*/
- add: function(options) {
- // frame default options
- var frameOptions = {
- title: '',
- content: null,
- target: '',
- type: null
- };
+ add: function( options ) {
+ if ( this.frame_counter >= this.options.frame_max ) {
+ Galaxy.modal.show( {
+ title : 'Warning',
+ body : 'You have reached the maximum number of allowed frames (' + this.options.frame_max + ').',
+ buttons : { 'Close' : function() { Galaxy.modal.hide() } }
+ });
- // read in defaults
- if (options) {
- options = _.defaults(options, frameOptions);
} else {
- options = frameOptions;
- }
+ var frame_id = '#frame-' + ( this.frame_uid++ );
+ if ( $ ( frame_id ).length !== 0 ) {
+ Galaxy.modal.show( {
+ title : 'Error',
+ body : 'This frame already exists. This page might contain multiple frame managers.',
+ buttons : { 'Close' : function() { Galaxy.modal.hide() } }
+ });
+ } else {
+ // initialize new frame elements
+ this.top = this.options.top_min;
+ var $frame_el = $( this._frameTemplate( frame_id.substring( 1 ), options.title ) );
+ var $frame_content = $frame_el.find( '.f-content' );
+ this.$el.append( $frame_el );
- // check for content
- if(!options.content) {
- return;
- }
+ // configure content
+ if ( options.url ) {
+ $frame_content.append(
+ $ ( '
' ).addClass( 'f-iframe' )
+ .attr( 'scrolling', 'auto' )
+ .attr( 'src', options.url + ( options.url.indexOf( '?' ) === -1 ? '?' : '&' ) + 'widget=True' )
+ );
+ } else if ( options.content ) {
+ _.isFunction( options.content ) ? options.content( $frame_content ) : $frame_content.append( options.content );
+ }
- // check for number of frames
- if (this.frame_counter >= this.options.frame_max) {
- alert("You have reached the maximum number of allowed frames (" + this.options.frame_max + ").");
- return;
- }
+ // construct a new frame
+ var frame = {
+ id : frame_id,
+ screen_location : {},
+ grid_location : {},
+ grid_rank : null,
+ grid_lock : false
+ };
- // generate frame identifier
- var frame_id = '#frame-' + (this.frame_counter_id++);
+ // set dimensions
+ options.width = this._toPixelCoord( 'width', this.options.frame.cols );
+ options.height = this._toPixelCoord( 'height', this.options.frame.rows );
- // check if frame exists
- if ($(frame_id).length !== 0) {
- alert("This frame already exists. This page might contain multiple frame managers.");
- return;
- }
-
- // reset top
- this.top = this.options.top_min;
-
- // append
- var $frame_el = null;
- if (options.type === 'url') {
- $frame_el = $(this._templateFrameUrl(frame_id.substring(1), options.title, options.content));
- } else if (options.type === 'other') {
- $frame_el = $(this._templateFrame(frame_id.substring(1), options.title));
-
- // Load content into frame.
- var content_elt = $frame_el.find('.f-content');
- if (_.isFunction(options.content)) {
- options.content(content_elt);
+ // set default z-index and add to ui and frame list
+ this.frame_z = parseInt( $( frame.id ).css( 'z-index' ) );
+ this.frame_list[ frame_id ] = frame;
+ this.frame_counter++;
+ this._frameResize( frame, { width: options.width, height: options.height } );
+ this._frameInsert( frame, { top: 0, left: 0 }, true );
+ !this.visible && this.show();
+ this.trigger( 'add' );
}
- else {
- content_elt.append(options.content);
- }
- }
- $(this.el).append($frame_el);
-
- // construct a new frame
- var frame = {
- id : frame_id,
- screen_location : {},
- grid_location : {},
- grid_rank : null,
- grid_lock : false
- };
-
- // set dimensions
- options.width = this._toPixelCoord('width', this.options.frame.cols);
- options.height = this._toPixelCoord('height', this.options.frame.rows);
-
- // default z-index
- this.frame_z = parseInt($(frame.id).css('z-index'));
-
- // add to frame list
- this.frame_list[frame_id] = frame;
-
- // increase frame counter
- this.frame_counter++;
-
- // resize
- this._frameResize(frame, {width: options.width, height: options.height});
-
- // place frame
- this._frameInsert(frame, {top: 0, left: 0}, true);
-
- // show frames if hidden
- if (!this.visible) {
- this.show();
}
},
- // show panel
+ /** Remove a frame */
+ del: function( frame_id ) {
+ var self = this;
+ var $frame = this.$( frame_id );
+ $frame.fadeOut( 'fast', function() {
+ $frame.remove();
+ delete self.frame_list[ frame_id ];
+ self.frame_counter--;
+ self._panelRefresh( true );
+ self._panelAnimationComplete();
+ self.trigger( 'remove' );
+ });
+ },
+
+ /** Show panel */
show: function() {
- // show
this.visible = true;
-
- // show
- this.$el.find(".frame").fadeIn('fast');
-
- // hide shadow
- this.$el.find(this.frame_shadow.id).hide();
-
- // show background
- this.$el.find(".frame-background").show();
-
- // show panel
- this._panelRefresh();
-
- // refresh
- this._menuRefresh();
+ this.$el.fadeIn( 'fast' );
+ this.trigger( 'show' );
},
- // hide panel
+ /** Hide panel */
hide: function() {
- // make sure that no event is currently processing
- if (this.event.type !== null)
- return;
-
- // hide
- this.visible = false;
-
- // hide
- this.$el.find(".frame").fadeOut('fast');
-
- // hide background
- this.$el.find(".frame-background").hide();
-
- // hide menu
- this.$el.find(".frame-menu").hide();
-
- // refresh
- this._menuRefresh();
+ if ( !this.event.type ) {
+ this.visible = false;
+ this.$el.fadeOut('fast', function() { $( this ).hide() });
+ this.trigger( 'hide' );
+ }
},
- // length
+ /** Returns the number of frames */
length: function() {
return this.frame_counter;
},
- // set onchange event
- setOnChange: function(callback) {
- this.options.onchange = callback;
- },
-
/*
EVENT HANDLING
*/
-
- // event
- event: {
- type : null,
- target : null,
- xy : null
- },
-
- // events
events: {
// global frame events
'mousemove' : '_eventFrameMouseMove',
@@ -314,337 +182,175 @@ var View = Backbone.View.extend({
'mousedown .f-pin' : '_eventFrameLock'
},
- // drag start
- _eventFrameMouseDown: function (e) {
- // skip if event is already active
- if (this.event.type !== null) {
- return;
- }
-
- // check for drag event
- if ($(e.target).hasClass('f-header') || $(e.target).hasClass('f-title')) {
- this.event.type = 'drag';
- }
-
- // check for resize event
- if ($(e.target).hasClass('f-resize')) {
- this.event.type = 'resize';
- }
-
- // skip if no event has to be handled
- if (this.event.type === null) {
- return;
- }
-
- // prevent
- e.preventDefault();
-
- // identify frame
- this.event.target = this._frameIdentify(e.target);
-
- // check if frame is locked
- if (this.event.target.grid_lock) {
- this.event.type = null;
- return;
- }
-
- // backup event details
- this.event.xy = {
- x: e.originalEvent.pageX,
- y: e.originalEvent.pageY
- };
-
- // prepare drag/resize
- this._frameDragStart(this.event.target);
- },
-
- // mouse move event
- _eventFrameMouseMove: function (e) {
- // check
- if (this.event.type != 'drag' && this.event.type != 'resize') {
- return;
- }
-
- // current position
- var event_xy_new = {
- x : e.originalEvent.pageX,
- y : e.originalEvent.pageY
- };
-
- // position delta
- var event_xy_delta = {
- x : event_xy_new.x - this.event.xy.x,
- y : event_xy_new.y - this.event.xy.y
- };
-
- // update
- this.event.xy = event_xy_new;
-
- // object position / size
- var p = this._frameScreen (this.event.target);
-
- // resize event
- if (this.event.type == 'resize') {
- // update
- p.width += event_xy_delta.x;
- p.height += event_xy_delta.y;
-
- // check size
- var min_dim = this.options.cell - this.options.margin - 1;
- p.width = Math.max(p.width, min_dim);
- p.height = Math.max(p.height, min_dim);
-
- // apply resize to frame
- this._frameResize(this.event.target, p);
-
- // break down to grid coordinates
- p.width = this._toGridCoord('width', p.width) + 1;
- p.height = this._toGridCoord('height', p.height) + 1;
-
- // transfer back to pixels
- p.width = this._toPixelCoord('width', p.width);
- p.height = this._toPixelCoord('height', p.height);
-
- // apply
- this._frameResize(this.frame_shadow, p);
-
- // fix position
- this._frameInsert(this.frame_shadow, {
- top : this._toGridCoord('top', p.top),
- left : this._toGridCoord('left', p.left)
- });
- }
-
- // drag event
- if (this.event.type == 'drag') {
- // update
- p.left += event_xy_delta.x;
- p.top += event_xy_delta.y;
-
- // apply
- this._frameOffset(this.event.target, p);
-
- // get location of shadow
- var l = {
- top : this._toGridCoord('top', p.top),
- left : this._toGridCoord('left', p.left)
- };
-
- // increase priority of current frame
- if (l.left !== 0) {
- l.left++;
+ /** Start drag/resize event */
+ _eventFrameMouseDown: function ( e ) {
+ if ( !this.event.type ) {
+ if ( $( e.target ).hasClass( 'f-header' ) || $( e.target ).hasClass( 'f-title' ) ) {
+ this.event.type = 'drag';
+ }
+ if ( $( e.target ).hasClass( 'f-resize' ) ) {
+ this.event.type = 'resize';
+ }
+ if ( this.event.type ) {
+ e.preventDefault();
+ this.event.target = this._frameIdentify( e.target );
+ if ( this.event.target.grid_lock ) {
+ this.event.type = null;
+ return;
+ }
+ this.event.xy = {
+ x: e.originalEvent.pageX,
+ y: e.originalEvent.pageY
+ };
+ this._frameDragStart( this.event.target );
}
-
- // fix position
- this._frameInsert(this.frame_shadow, l);
}
},
- // mouse up
- _eventFrameMouseUp: function (e) {
- // check
- if (this.event.type != 'drag' && this.event.type != 'resize') {
- return;
- }
+ /** Processes drag/resize events */
+ _eventFrameMouseMove: function ( e ) {
+ if ( this.event.type ) {
+ // get mouse motion and delta
+ var event_xy_new = {
+ x : e.originalEvent.pageX,
+ y : e.originalEvent.pageY
+ };
+ var event_xy_delta = {
+ x : event_xy_new.x - this.event.xy.x,
+ y : event_xy_new.y - this.event.xy.y
+ };
+ this.event.xy = event_xy_new;
- // stop
- this._frameDragStop(this.event.target);
+ // get current screen position and size of frame
+ var p = this._frameScreen ( this.event.target );
- // reset event
- this.event.type = null;
- },
-
- // drag start
- _eventFrameClose: function (e) {
- // check
- if (this.event.type !== null) {
- return;
- }
-
- // prevent
- e.preventDefault();
-
- // get frame
- var frame = this._frameIdentify(e.target);
- var self = this;
-
- // fade out
- $(frame.id).fadeOut('fast', function() {
- // remove element
- $(frame.id).remove();
-
- // remove from dictionary
- delete self.frame_list[frame.id];
-
- // reduce frame counter
- self.frame_counter--;
-
- // reload
- self._panelRefresh(true);
-
- // refresh scroll state once all animations completed
- self._panelAnimationComplete();
-
- // hide if no frames left
- if (self.visible && self.frame_counter == 0)
- self.hide();
- });
- },
-
- // drag start
- _eventFrameLock: function (e) {
- // check
- if (this.event.type !== null) {
- return;
- }
-
- // prevent
- e.preventDefault();
-
- // get frame
- var frame = this._frameIdentify(e.target);
-
- // check
- if (frame.grid_lock) {
- // unlock
- frame.grid_lock = false;
-
- // remove class
- $(frame.id).find('.f-pin').removeClass('toggle');
- $(frame.id).find('.f-header').removeClass('f-not-allowed');
- $(frame.id).find('.f-title').removeClass('f-not-allowed');
- $(frame.id).find('.f-resize').show();
- $(frame.id).find('.f-close').show();
- } else {
- // lock
- frame.grid_lock = true;
-
- // add class
- $(frame.id).find('.f-pin').addClass('toggle');
- $(frame.id).find('.f-header').addClass('f-not-allowed');
- $(frame.id).find('.f-title').addClass('f-not-allowed');
- $(frame.id).find('.f-resize').hide();
- $(frame.id).find('.f-close').hide();
+ // drag/resize event
+ if ( this.event.type == 'resize' ) {
+ p.width += event_xy_delta.x;
+ p.height += event_xy_delta.y;
+ var min_dim = this.options.cell - this.options.margin - 1;
+ p.width = Math.max( p.width, min_dim );
+ p.height = Math.max( p.height, min_dim );
+ this._frameResize( this.event.target, p );
+ p.width = this._toGridCoord( 'width', p.width ) + 1;
+ p.height = this._toGridCoord( 'height', p.height ) + 1;
+ p.width = this._toPixelCoord( 'width', p.width );
+ p.height = this._toPixelCoord( 'height', p.height );
+ this._frameResize( this.frame_shadow, p );
+ this._frameInsert( this.frame_shadow, {
+ top : this._toGridCoord( 'top', p.top ),
+ left : this._toGridCoord( 'left', p.left )
+ });
+ } else if ( this.event.type == 'drag' ) {
+ p.left += event_xy_delta.x;
+ p.top += event_xy_delta.y;
+ this._frameOffset( this.event.target, p );
+ var l = {
+ top : this._toGridCoord( 'top', p.top ),
+ left : this._toGridCoord( 'left', p.left )
+ };
+ l.left !== 0 && l.left++;
+ this._frameInsert( this.frame_shadow, l );
+ }
}
},
- // show/hide panel
- _eventHide: function (e) {
- // check
- if (this.event.type !== null) {
- return;
+ /** Stop drag/resize events */
+ _eventFrameMouseUp: function ( e ) {
+ if ( this.event.type ) {
+ this._frameDragStop( this.event.target );
+ this.event.type = null;
}
-
- // hide panel
- this.hide();
},
- /**
- * Fired when scrolling occurs on panel.
- */
- _eventPanelScroll: function(e) {
- // check
- if (this.event.type !== null || !this.visible) {
- return;
+ /** Destroy a frame */
+ _eventFrameClose: function ( e ) {
+ if ( !this.event.type ) {
+ e.preventDefault();
+ this.del( this._frameIdentify( e.target ).id );
}
-
- // Stop propagation if scrolling is happening inside a frame.
- // TODO: could propagate scrolling if at top/bottom of frame.
- var frames = $(e.srcElement).parents('.frame')
- if (frames.length !== 0) {
- e.stopPropagation();
- return;
- }
-
- // prevent
- e.preventDefault();
-
- // get wheel delta
- var delta = e.originalEvent.detail ? e.originalEvent.detail : e.originalEvent.wheelDelta / -3;
-
- // refresh panel
- this._panelScroll(delta);
},
- // scroll up
- _eventPanelScroll_up: function(e) {
- // check
- if (this.event.type !== null)
- return;
-
- // prevent
- e.preventDefault();
-
- // scroll up
- this._panelScroll(-this.options.scroll);
+ /** Lock/Unlock the frame location */
+ _eventFrameLock: function ( e ) {
+ if ( !this.event.type ) {
+ e.preventDefault();
+ var frame = this._frameIdentify( e.target );
+ var locked = frame.grid_lock = !frame.grid_lock;
+ var $el = $( frame.id );
+ $el.find( '.f-pin' ) [ locked && 'addClass' || 'removeClass' ]( 'toggle' );
+ $el.find( '.f-header' ) [ locked && 'removeClass' || 'addClass' ]( 'f-not-allowed' );
+ $el.find( '.f-title' ) [ locked && 'removeClass' || 'addClass' ]( 'f-not-allowed' );
+ $el.find( '.f-resize' ) [ locked && 'hide' || 'show' ]();
+ $el.find( '.f-close' ) [ locked && 'hide' || 'show' ]();
+ }
},
- // scroll down
+ /** Hide all frames */
+ _eventHide: function ( e ) {
+ !this.event.type && this.hide();
+ },
+
+ /** Fired when scrolling occurs on panel */
+ _eventPanelScroll: function( e ) {
+ if ( !this.event.type && this.visible ) {
+ // Stop propagation if scrolling is happening inside a frame.
+ // TODO: could propagate scrolling if at top/bottom of frame.
+ var frames = $( e.srcElement ).parents( '.frame' );
+ if ( frames.length !== 0 ) {
+ e.stopPropagation();
+ } else {
+ e.preventDefault();
+ this._panelScroll( e.originalEvent.detail ? e.originalEvent.detail : e.originalEvent.wheelDelta / -3 );
+ }
+ }
+ },
+
+ /** Handle scroll up event */
+ _eventPanelScroll_up: function( e ) {
+ if ( !this.event.type ) {
+ e.preventDefault();
+ this._panelScroll( -this.options.scroll );
+ }
+ },
+
+ /** Handle scroll down */
_eventPanelScroll_down: function(e) {
- // check
- if (this.event.type !== null)
- return;
-
- // prevent
- e.preventDefault();
-
- // scroll down
- this._panelScroll(this.options.scroll);
+ if ( !this.event.type ) {
+ e.preventDefault();
+ this._panelScroll( this.options.scroll );
+ }
},
/*
FRAME EVENTS SUPPORT
*/
- // identify
- _frameIdentify: function(target) {
- return this.frame_list['#' + $(target).closest('.frame').attr('id')];
+ /** Identify the target frame */
+ _frameIdentify: function( target ) {
+ return this.frame_list[ '#' + $( target ).closest( '.frame' ).attr( 'id' ) ];
},
- // drag start
- _frameDragStart : function (frame) {
- // set focus
- this._frameFocus(frame, true);
-
- // get current dimensions
- var p = this._frameScreen (frame);
-
- // initialize shadow
- this._frameResize(this.frame_shadow, p);
- this._frameGrid(this.frame_shadow, frame.grid_location);
-
- // reset location
+ /** Provides drag support */
+ _frameDragStart : function ( frame ) {
+ this._frameFocus( frame, true );
+ var p = this._frameScreen( frame );
+ this._frameResize( this.frame_shadow, p );
+ this._frameGrid( this.frame_shadow, frame.grid_location );
frame.grid_location = null;
-
- // show shadow
- $(this.frame_shadow.id).show();
-
- // load frame cover
- $('.f-cover').show();
+ $( this.frame_shadow.id ).show();
+ $( '.f-cover' ).show();
},
- // drag stop
- _frameDragStop : function (frame) {
- // remove focus
- this._frameFocus(frame, false);
-
- // get new dimensions
- var p = this._frameScreen(this.frame_shadow);
-
- // update frame
- this._frameResize(frame, p);
- this._frameGrid(frame, this.frame_shadow.grid_location, true);
-
- // reset location of shadow
+ /** Removes drag support */
+ _frameDragStop : function ( frame ) {
+ this._frameFocus( frame, false );
+ var p = this._frameScreen( this.frame_shadow );
+ this._frameResize( frame, p );
+ this._frameGrid( frame, this.frame_shadow.grid_location, true );
this.frame_shadow.grid_location = null;
-
- // hide shadow
- $(this.frame_shadow.id).hide();
-
- // hide frame cover
- $('.f-cover').hide();
-
- // refresh scroll state once all animations completed
+ $( this.frame_shadow.id ).hide();
+ $( '.f-cover' ).hide();
this._panelAnimationComplete();
},
@@ -652,38 +358,38 @@ var View = Backbone.View.extend({
GRID/PIXEL CONVERTER
*/
- // converts a pixel coordinate to grids
- _toGridCoord: function (type, px) {
- var sign = (type == 'width' || type == 'height') ? 1 : -1;
- if (type == 'top') px -= this.top;
- return parseInt((px + sign * this.options.margin) / this.options.cell, 10);
+ /** Converts a pixel to a grid dimension */
+ _toGridCoord: function ( type, px ) {
+ var sign = ( type == 'width' || type == 'height' ) ? 1 : -1;
+ type == 'top' && ( px -= this.top );
+ return parseInt( ( px + sign * this.options.margin ) / this.options.cell, 10 );
},
- // converts a grid coordinate to pixels
- _toPixelCoord: function (type, g) {
- var sign = (type == 'width' || type == 'height') ? 1 : -1;
- var px = (g * this.options.cell) - sign * this.options.margin;
- if (type == 'top') px += this.top;
+ /** Converts a grid to a pixels dimension */
+ _toPixelCoord: function ( type, g ) {
+ var sign = ( type == 'width' || type == 'height' ) ? 1 : -1;
+ var px = ( g * this.options.cell ) - sign * this.options.margin;
+ type == 'top' && ( px += this.top );
return px;
},
- // get grid coordinates
- _toGrid: function (px) {
+ /** Converts a pixel to a grid coordinate set */
+ _toGrid: function ( px ) {
return {
- top : this._toGridCoord('top', px.top),
- left : this._toGridCoord('left', px.left),
- width : this._toGridCoord('width', px.width),
- height : this._toGridCoord('height', px.height)
+ top : this._toGridCoord( 'top', px.top ),
+ left : this._toGridCoord( 'left', px.left ),
+ width : this._toGridCoord( 'width', px.width ),
+ height : this._toGridCoord( 'height', px.height )
};
},
- // get pixel coordinates
- _toPixel: function(g) {
+ /** Converts a pixel to a grid coordinate set */
+ _toPixel: function( g ) {
return {
- top : this._toPixelCoord('top', g.top),
- left : this._toPixelCoord('left', g.left),
- width : this._toPixelCoord('width', g.width),
- height : this._toPixelCoord('height', g.height)
+ top : this._toPixelCoord( 'top', g.top ),
+ left : this._toPixelCoord( 'left', g.left ),
+ width : this._toPixelCoord( 'width', g.width ),
+ height : this._toPixelCoord( 'height', g.height )
};
},
@@ -691,347 +397,181 @@ var View = Backbone.View.extend({
COLLISION DETECTION
*/
- // check collision
- _isCollision: function(g) {
- // is collision pair
- function is_collision_pair (a, b) {
- return !(a.left > b.left + b.width - 1 || a.left + a.width - 1 < b.left ||
- a.top > b.top + b.height - 1 || a.top + a.height - 1 < b.top);
+ /** Check collisions for a grid coordinate set */
+ _isCollision: function( g ) {
+ function is_collision_pair ( a, b ) {
+ return !( a.left > b.left + b.width - 1 || a.left + a.width - 1 < b.left ||
+ a.top > b.top + b.height - 1 || a.top + a.height - 1 < b.top );
}
-
- // search
- for (var i in this.frame_list) {
- // get frame
- var frame = this.frame_list[i];
-
- // skip
- if (frame.grid_location === null)
- continue;
-
- // check if g collides with frame
- if (is_collision_pair (g, frame.grid_location))
+ for ( var i in this.frame_list ) {
+ var frame = this.frame_list[ i ];
+ if ( frame.grid_location !== null && is_collision_pair ( g, frame.grid_location ) ) {
return true;
+ }
}
-
- // return
return false;
},
- // location/grid rank
- _locationRank: function(loc) {
- return (loc.top * this.cols) + loc.left;
- },
-
- /*
- ONSCREEN MENU
- */
-
- // update frame counter
- _menuRefresh: function() {
- // scroll up possible?
- if (this.visible) {
- if (this.top == this.options.top_min)
- $(".frame-scroll-up").hide();
- else
- $(".frame-scroll-up").show();
-
- // scroll down possible?
- if (this.top == this.top_max)
- $(".frame-scroll-down").hide();
- else
- $(".frame-scroll-down").show();
- }
-
- // trigger onchange
- if (this.options.onchange) {
- this.options.onchange();
- }
+ /** Return location/grid rank */
+ _locationRank: function( loc ) {
+ return ( loc.top * this.cols ) + loc.left;
},
/*
PANEL/WINDOW FUNCTIONS
*/
- // panel on animation complete / frames not moving
+ /** Refresh panel */
+ _panelRefresh: function( animate ) {
+ this.cols = parseInt( $( window ).width() / this.options.cell, 10 ) + 1;
+ this._frameInsert( null, null, animate );
+ },
+
+ /** Complete panel animation / frames not moving */
_panelAnimationComplete: function() {
var self = this;
- $(".frame").promise().done(function() {self._panelScroll(0, true)});
+ $( '.frame' ).promise().done( function() { self._panelScroll( 0, true ) } );
},
- // refresh panel
- _panelRefresh: function(animate) {
- // get current size
- this.cols = parseInt($(window).width() / this.options.cell, 10) + 1;
-
- // recalculate frame positions
- this._frameInsert(null, null, animate);
- },
-
- // update scroll
- _panelScroll: function(delta, animate) {
- // new top value
+ /** Scroll panel */
+ _panelScroll: function( delta, animate ) {
var top_new = this.top - this.options.scroll * delta;
-
- // update top
- top_new = Math.max(top_new, this.top_max);
- top_new = Math.min(top_new, this.options.top_min);
-
- // update screen if necessary
- if (this.top != top_new) {
- // update screen
- for (var i in this.frame_list) {
- // get frame
- var frame = this.frame_list[i];
-
- // skip
- if (frame.grid_location !== null) {
+ top_new = Math.max( top_new, this.top_max );
+ top_new = Math.min( top_new, this.options.top_min );
+ if ( this.top != top_new ) {
+ for ( var i in this.frame_list ) {
+ var frame = this.frame_list[ i ];
+ if ( frame.grid_location !== null ) {
var screen_location = {
- top : frame.screen_location.top - (this.top - top_new),
+ top : frame.screen_location.top - ( this.top - top_new ),
left : frame.screen_location.left
}
- this._frameOffset(frame, screen_location, animate);
+ this._frameOffset( frame, screen_location, animate );
}
}
-
- // update top value
this.top = top_new;
}
-
- // refresh
- this._menuRefresh();
+ this.render();
},
/*
FRAME FUNCTIONS
*/
- // frame insert at given location
- _frameInsert: function(frame, new_loc, animate) {
- // define
+ /** Insert frame at given location */
+ _frameInsert: function( frame, new_loc, animate ) {
+ var self = this;
var place_list = [];
-
- // frame to place
- if (frame) {
- // reset grid location
+ if ( frame ) {
frame.grid_location = null;
-
- // set first one to be placed
- place_list.push([frame, this._locationRank(new_loc)]);
+ place_list.push( [ frame, this._locationRank( new_loc ) ] );
}
-
- // search
- var i = null;
- for (i in this.frame_list) {
- // get frame
- var f = this.frame_list[i];
-
- // check
- if (f.grid_location !== null && !f.grid_lock) {
- // reset grid location
+ _.each( this.frame_list, function( f ) {
+ if ( f.grid_location !== null && !f.grid_lock ) {
f.grid_location = null;
-
- // set up for placement
- place_list.push([f, f.grid_rank]);
+ place_list.push( [ f, f.grid_rank ] );
}
- }
-
- // sort place list by rank
- place_list.sort(function(a, b) {
- var i = a[1];
- var j = b[1];
- return i < j ? -1 : (i > j ? 1 : 0);
});
-
- // place
- for (i = 0; i < place_list.length; i++) {
- this._framePlace(place_list[i][0], animate);
- }
-
- // identify maximum viewport size
+ place_list.sort( function( a, b ) {
+ return a[ 1 ] < b[ 1 ] ? -1 : ( a[ 1 ] > b[ 1 ] ? 1 : 0 );
+ });
+ _.each( place_list, function( place ) {
+ self._framePlace( place[ 0 ], animate );
+ });
this.top_max = 0;
- for (var i in this.frame_list) {
- // get frame
- var frame = this.frame_list[i];
-
- // skip
- if (frame.grid_location !== null)
- this.top_max = Math.max(this.top_max, frame.grid_location.top + frame.grid_location.height);
- }
-
- // mesh maximum top with window size and margin
- this.top_max = $(window).height() - this.top_max * this.options.cell - 2 * this.options.margin;
-
- // fix value
- this.top_max = Math.min(this.top_max, this.options.top_min);
-
- // panel menu
- this._menuRefresh();
+ _.each( this.frame_list, function( f ) {
+ if ( f.grid_location !== null ) {
+ self.top_max = Math.max( self.top_max, f.grid_location.top + f.grid_location.height );
+ }
+ });
+ this.top_max = $( window ).height() - this.top_max * this.options.cell - 2 * this.options.margin;
+ this.top_max = Math.min( this.top_max, this.options.top_min );
+ this.render();
},
- // naive frame place
- _framePlace: function(frame, animate) {
- // reset grid location
+ /** Naive frame placement */
+ _framePlace: function( frame, animate ) {
frame.grid_location = null;
-
- // grid coordinates of new frame
- var g = this._toGrid(this._frameScreen(frame));
-
- // try grid coordinates
+ var g = this._toGrid( this._frameScreen( frame ) );
var done = false;
- for (var i = 0; i < this.options.rows; i++) {
- // ensure that the first grid column is checked despite limited window space
- for (var j = 0; j < Math.max(1, this.cols - g.width); j++) {
- // coordinates
+ for ( var i = 0; i < this.options.rows; i++ ) {
+ for ( var j = 0; j < Math.max(1, this.cols - g.width ); j++ ) {
g.top = i;
g.left = j;
-
- // no collision
- if (!this._isCollision(g)) {
+ if ( !this._isCollision( g ) ) {
done = true;
break;
}
}
-
- // break
- if (done) {
+ if ( done ) {
break;
}
}
-
- // check if valid spot was found
- if (done) {
- this._frameGrid(frame, g, animate);
+ if ( done ) {
+ this._frameGrid( frame, g, animate );
} else {
- console.log("Grid dimensions exceeded.");
+ console.log( 'Grid dimensions exceeded.' );
}
},
- // focus
- _frameFocus: function(frame, has_focus) {
- // get new z-value
- var z = this.frame_z + (has_focus ? 1 : 0);
-
- // update
- $(frame.id).css('z-index', z);
+ /** Handle frame focussing */
+ _frameFocus: function( frame, has_focus ) {
+ $( frame.id ).css( 'z-index', this.frame_z + ( has_focus ? 1 : 0 ) );
},
- // new left/top position frame
- _frameOffset: function(frame, p, animate) {
- // update screen location
+ /** New left/top position frame */
+ _frameOffset: function( frame, p, animate ) {
frame.screen_location.left = p.left;
frame.screen_location.top = p.top;
-
- // animate
- if (animate) {
- // set focus on animated
- this._frameFocus(frame, true);
-
- // prepare for callback
+ if ( animate ) {
+ this._frameFocus( frame, true );
var self = this;
-
- // animate and remove focus
- $(frame.id).animate({top: p.top, left: p.left}, 'fast', function() {
- self._frameFocus(frame, false);
+ $( frame.id ).animate({ top: p.top, left: p.left }, 'fast', function() {
+ self._frameFocus( frame, false );
});
} else {
- $(frame.id).css({top: p.top, left: p.left});
+ $( frame.id ).css( { top: p.top, left: p.left } );
}
},
- // resize frame
- _frameResize: function(frame, p) {
- // update css
- $(frame.id).css({width: p.width, height: p.height});
-
- // update descriptor
+ /** Resize frame */
+ _frameResize: function( frame, p ) {
+ $( frame.id ).css( { width: p.width, height: p.height } );
frame.screen_location.width = p.width;
frame.screen_location.height = p.height;
},
- // new grid location
- _frameGrid: function (frame, l, animate) {
- // update grid location
+ /** Push frame to new grid location */
+ _frameGrid: function ( frame, l, animate ) {
frame.grid_location = l;
-
- // place frame
- this._frameOffset(frame, this._toPixel(l), animate);
-
- // update grid rank
- frame.grid_rank = this._locationRank(l);
+ this._frameOffset( frame, this._toPixel( l ), animate );
+ frame.grid_rank = this._locationRank( l );
},
- // get frame dimensions
- _frameScreen: function(frame) {
+ /** Get frame dimensions */
+ _frameScreen: function( frame ) {
var p = frame.screen_location;
- return {top: p.top, left: p.left, width: p.width, height: p.height};
+ return { top: p.top, left: p.left, width: p.width, height: p.height };
},
- /*
- HTML TEMPLATES
- */
-
- // main element
- _template: function() {
- return '
';
- },
-
- // fill regular frame template
- _templateFrame: function(id, title) {
- // check title
- if (!title)
- title = '';
-
- // load template
+ /** Regular frame template */
+ _frameTemplate: function( id, title ) {
return '
' +
'' +
'
' +
- '
' +
+ '
' +
'
';
- },
-
- // fill regular frame template
- _templateFrameUrl: function(id, title, url) {
- // url
- if (url.indexOf('?') == -1)
- url += '?';
- else
- url += '&';
- url += 'widget=True';
-
- // element
- var $el = $(this._templateFrame(id, title));
- $el.find('.f-content').append('
');
-
- // load template
- return $el;
- },
-
- // fill shadow template
- _templateShadow: function(id) {
- return '
';
- },
-
- // fill background template in order to cover underlying iframes
- _templateBackground: function() {
- return '
';
- },
-
- // fill menu button template
- _templateMenu: function() {
- return '' +
- '';
}
});
-// return
return {
View: View
-};
+}
});
diff --git a/client/galaxy/scripts/onload.js b/client/galaxy/scripts/onload.js
index 59518c56add..b3dd1533678 100644
--- a/client/galaxy/scripts/onload.js
+++ b/client/galaxy/scripts/onload.js
@@ -127,25 +127,6 @@ function init_refresh_on_change () {
window.init_refresh_on_change = init_refresh_on_change;
$(document).ready( function() {
-
- // Masthead dropdown menus
- var $dropdowns = $("#masthead ul.nav > li.dropdown > .dropdown-menu");
- $("body").on( "click.nav_popups", function( e ) {
- $dropdowns.hide();
- $("#dd-helper").hide();
- // If the target is in the menu, treat normally
- if ( $(e.target).closest( "#masthead ul.nav > li.dropdown > .dropdown-menu" ).length ) {
- return;
- }
- // Otherwise, was the click in a tab
- var $clicked = $(e.target).closest( "#masthead ul.nav > li.dropdown" );
- if ( $clicked.length ) {
- $("#dd-helper").show();
- $clicked.children( ".dropdown-menu" ).show();
- e.preventDefault();
- }
- });
-
// Refresh events for form fields.
init_refresh_on_change();
diff --git a/client/galaxy/style/less/base.less b/client/galaxy/style/less/base.less
index 23c58b5dcec..f802604d303 100644
--- a/client/galaxy/style/less/base.less
+++ b/client/galaxy/style/less/base.less
@@ -31,7 +31,6 @@
@import "toastr.less";
@import "jstree.less";
-
// Mixins
.unselectable {
.user-select(none);
@@ -69,7 +68,6 @@ body {
width: 100%;
height: 100%;
}
-
}
// ==== Panel layout styles ====
@@ -103,6 +101,7 @@ body {
overflow: hidden;
border-bottom: solid #999 1px;
font-size: 90%;
+ display: none;
}
#inactivebox {
@@ -114,6 +113,7 @@ body {
overflow: hidden;
border-bottom: solid #999 1px;
font-size: 90%;
+ display: none;
}
// Panels
@@ -337,6 +337,7 @@ div.unified-panel-body-background {
left: 0;
width: 100%;
height: 100%;
+ display: none;
}
// Messages for message box, slightly different style
@@ -372,20 +373,17 @@ div.unified-panel-body-background {
}
// Masthead
-
#masthead {
-
position:absolute;
top:0;
left:0;
width:100%;
min-width:990px;
padding: 0;
-
+ margin-bottom: 0px;
.nav {
z-index: 15001;
}
-
.nav > li > a {
cursor: pointer;
text-decoration: none;
@@ -393,22 +391,10 @@ div.unified-panel-body-background {
color: gold;
}
}
-
- //.dropdown-menu {
- // z-index: 15002;
- //}
-
- li.dropdown > a:hover .caret {
- border-top-color: gold;
- border-bottom-color: gold;
- }
-
.navbar-brand {
-
position: absolute;
left: 0;
top: 0;
-
font-family: verdana;
font-weight: bold;
font-size: 20px;
@@ -418,53 +404,47 @@ div.unified-panel-body-background {
padding: 5px 20px 12px;
margin-left: -15px;
z-index: 2000;
-
img {
display: inline;
width: 26px;
vertical-align: top;
+ margin-left: 0.35em;
+ border: none;
}
a {
color: white;
text-decoration: none;
}
}
-
- .iconbar
- {
- position : absolute;
- top : 7px;
- right : 110px;
- cursor : pointer;
- color : @gray-light;
- overflow : hidden;
-
- .symbol
- {
- float : left;
- margin : 0px 10px;
- font-size : 11px;
+ .navbar-header {
+ position: relative;
+ right: -50%;
+ float: left;
+ .navbar-tabs {
+ display: block;
+ position: relative;
+ right: 50%;
}
-
- .symbol .number
- {
+ }
+ .navbar-tabs {
+ .toggle {
+ color : gold;
+ }
+ .dropdown-note {
font-weight : bold;
font-size : 10px;
- font-family : @font-family-sans-serif;
- position : relative;
- left : 23px;
- top : -12px;
- }
-
- .toggle
- {
+ position : absolute;
+ left : 35px;
+ top : 20px;
color : gold;
}
}
+ li.dropdown > a:hover .caret {
+ border-top-color: gold;
+ border-bottom-color: gold;
+ }
}
-
-
.quota-meter-container {
position: absolute;
top: 0;
diff --git a/client/galaxy/style/less/frame.less b/client/galaxy/style/less/frame.less
index 3568e3092a4..7cdb15dde8a 100644
--- a/client/galaxy/style/less/frame.less
+++ b/client/galaxy/style/less/frame.less
@@ -11,7 +11,6 @@
.frame-background {
z-index : @zindex-navbar;
position : absolute;
- display : none;
top : 0px;
left : 0px;
height : 100%;
diff --git a/client/galaxy/style/less/masthead.less b/client/galaxy/style/less/masthead.less
deleted file mode 100644
index de1a571177c..00000000000
--- a/client/galaxy/style/less/masthead.less
+++ /dev/null
@@ -1,65 +0,0 @@
-@import "galaxy_bootstrap/variables.less";
-@import "galaxy_variables.less";
-
-body
-{
- background: @navbar-inverse-bg;
- color: @navbar-inverse-color;
- padding: 0;
- border: 0;
- margin: 3px;
- margin-right: 5px;
- margin-left: 5px;
- overflow: hidden;
-}
-
-div.pageTitle
-{
- font-size: 175%;
- font-weight: bold;
-}
-
-div.pageTitle a:link, div.pageTitle a:visited, div.pageTitle a:active, div.pageTitle a:hover
-{
- text-decoration: none;
-}
-
-a:link, a:visited, a:active
-{
- color: $masthead_link;
-}
-
-#tab-bar-bottom
-{
- z-index: -1;
- position:absolute;
- top:27px; left: 0;
- width: 100%;
- height: 100%;
- background: @navbar-inverse-link-active-bg;
-}
-
-span.link-group
-{
- margin: 0;
- padding: 0;
- display: inline;
- padding-bottom: 10px;
- margin-bottom: -10px;
-}
-
-span.link-group span
-{
- margin: 0;
- padding: 0;
- display: inline;
-}
-
-span.link-group span.active-link
-{
- background: @navbar-inverse-link-active-bg;
- padding-left: 3px; padding-right: 3px;
- margin-left: -3px; margin-right: -3px;
- padding-bottom: 10px;
- margin-bottom: -10px;
-}
diff --git a/client/galaxy/style/less/ui.less b/client/galaxy/style/less/ui.less
index e2c8327ccd6..f4626ac62b1 100644
--- a/client/galaxy/style/less/ui.less
+++ b/client/galaxy/style/less/ui.less
@@ -68,6 +68,7 @@
}
.ui-modal {
+ display: none;
.modal-header.no-separator {
border: none !important;
padding-bottom: 0px !important;
diff --git a/config/plugins/visualizations/charts/templates/charts.mako b/config/plugins/visualizations/charts/templates/charts.mako
index 94c0de4a9a7..34d6286b0e1 100644
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -51,9 +51,14 @@
root : '${root}',
app_root : '${app_root}'
};
-
+
// link galaxy
- var Galaxy = Galaxy || parent.Galaxy;
+ var Galaxy = Galaxy || parent.Galaxy || {
+ root : '${root}',
+ emit : {
+ debug: function() {}
+ }
+ };
// console protection
window.console = window.console || {
diff --git a/static/maps/layout/masthead.js.map b/static/maps/layout/masthead.js.map
index 4986bfb11f3..2c8cd9410b8 100644
--- a/static/maps/layout/masthead.js.map
+++ b/static/maps/layout/masthead.js.map
@@ -1 +1 @@
-{"version":3,"file":"masthead.js","sources":["../../src/layout/masthead.js"],"names":["define","Utils","Menu","Scratchbook","QuotaMeter","GalaxyMasthead","Backbone","View","extend","el_masthead","options","$background","list","initialize","this","$","off","setElement","_template","replaceWith","$el","el","find","self","window","on","e","$download_link","target","closest","length","append","attr","preventDefault","text","key","onbeforeunload","q","menu","Galaxy","GalaxyMenu","masthead","config","frame","GalaxyFrame","quotaMeter","UserQuotaMeter","model","user","render","events","click","mousedown","item","_add","prepend","highlight","id","current","addClass","$loc","location","$current","push","_click","$all","hide","hasClass","show","brand_text","brand","logo_url","root"],"mappings":"AAAAA,QACI,cACA,cACA,qBACA,4BACD,SAASC,EAAOC,EAAMC,EAAaC,GAGtC,GAAIC,GAAiBC,SAASC,KAAKC,QAE/BC,YAAa,cAGbC,QAAU,KAGVC,YAAa,KAGbC,QAGAC,WAAa,SAASH,GAElBI,KAAKJ,QAAUA,EAGfK,EAAE,QAAQC,MAGVF,KAAKG,WAAWF,EAAED,KAAKI,UAAUR,KAEjCK,EAAG,aAAcI,YAAaL,KAAKM,KAGnCN,KAAKH,YAAcI,EAAED,KAAKO,IAAIC,KAAK,uBAGnC,IAAIC,GAAOT,IACXC,GAAES,QAAQC,GAAG,QAAS,SAAUC,GAC5B,GAAIC,GAAiBZ,EAAGW,EAAEE,QAASC,QAAS,cACd,IAAzBF,EAAeG,SAC0B,IAAtCf,EAAG,uBAAwBe,QAC3Bf,EAAG,QAASgB,OAAQhB,EAAG,oDAE3BA,EAAG,uBAAwBiB,KAAM,MAAOL,EAAeK,KAAM,SAC7DN,EAAEO,oBAEPR,GAAG,eAAgB,WAClB,GAAIS,GAAO,EACX,KAAK,GAAIC,KAAOZ,GAAKX,KACjB,GAAIW,EAAKX,KAAKuB,GAAKzB,QAAQ0B,eAAgB,CACvC,GAAIC,GAAId,EAAKX,KAAKuB,GAAKzB,QAAQ0B,gBAC3BC,KAAGH,GAAQG,EAAI,KAG3B,MAAa,KAATH,EACOA,EADX,SAMJpB,KAAKwB,KAAOC,OAAOD,KAAO,GAAIpC,GAAKsC,YAC/BC,SAAc3B,KACd4B,OAAc5B,KAAKJ,UAIvBI,KAAK6B,MAAQJ,OAAOI,MAAQ,GAAIxC,GAAYyC,aACxCH,SAAc3B,OAKlBA,KAAK+B,WAAaN,OAAOM,WAAa,GAAIzC,GAAW0C,gBACjDC,MAAcR,OAAOS,KACrB3B,GAAcP,KAAKC,EAAG,4BACvBkC,UAIPC,QACIC,MAAc,SACdC,UAAc,SAAS1B,GAAKA,EAAEO,mBAIlCF,OAAS,SAASsB,GACd,MAAOvC,MAAKwC,KAAKD,GAAM,IAI3BE,QAAU,SAASF,GACf,MAAOvC,MAAKwC,KAAKD,GAAM,IAI3BG,UAAW,SAASC,GAChB,GAAIC,GAAU3C,EAAED,KAAKO,IAAIC,KAAK,IAAMmC,EAAK,OACrCC,IACAA,EAAQC,SAAS,WAKzBL,KAAO,SAASD,EAAMtB,GAClB,GAAI6B,GAAO7C,EAAED,KAAKO,IAAIC,KAAK,IAAM+B,EAAKQ,SACtC,IAAID,EAAK,CAEL,GAAIE,GAAW/C,EAAEsC,EAAKhC,GAGtByC,GAASH,SAAS,iBAGd5B,EACA6B,EAAK7B,OAAO+B,GAEZF,EAAKL,QAAQO,GAIjBhD,KAAKF,KAAKmD,KAAKV,GAInB,MAAO,OAIXW,OAAQ,SAAStC,GAEb,GAAIuC,GAAOlD,EAAED,KAAKO,IAAIC,KAAK,SACvB2C,IACAA,EAAKC,MAIT,IAAIJ,GAAW/C,EAAEW,EAAEE,QAAQC,QAAQ,kBAAkBP,KAAK,SACtDP,GAAEW,EAAEE,QAAQuC,SAAS,SACrBL,EAASM,OACTtD,KAAKH,YAAYyD,QAEjBtD,KAAKH,YAAYuD,QASzBhD,UAAW,SAASR,GAChB,GAAI2D,GAAa3D,EAAQ4D,MAAS,KAAO5D,EAAQ4D,MAAS,EAC1D,OAAQ,6PAKsB5D,EAAQ6D,SAAW,uDAC0BhC,OAAOiC,KAAO,iEACvCH,EAAa,sPAYvE,QACIhE,eAAgBA"}
\ No newline at end of file
+{"version":3,"file":"masthead.js","sources":["../../src/layout/masthead.js"],"names":["define","Utils","Menu","Scratchbook","QuotaMeter","View","Backbone","extend","initialize","options","self","this","setElement","_template","$navbarBrandLink","$","$navbarBrandImage","$navbarBrandTitle","$navbarTabs","$quoteMeter","collection","Collection","on","model","append","Tab","render","$el","empty","callback","each","m","fetch","Galaxy","frame","quotaMeter","UserQuotaMeter","user","el","window","e","$download_link","target","closest","length","attr","hide","preventDefault","text","q","get","html","brand","logo_url","root"],"mappings":"AAAAA,QACI,cACA,cACA,qBACA,4BACD,SAAUC,EAAOC,EAAMC,EAAaC,GAGvC,GAAIC,GAAOC,SAASD,KAAKE,QACrBC,WAAa,SAAUC,GACnB,GAAIC,GAAOC,IACXA,MAAKF,QAAUA,EACfE,KAAKC,WAAYD,KAAKE,aACtBF,KAAKG,iBAAqBH,KAAKI,EAAG,sBAClCJ,KAAKK,kBAAqBL,KAAKI,EAAG,uBAClCJ,KAAKM,kBAAqBN,KAAKI,EAAG,uBAClCJ,KAAKO,YAAqBP,KAAKI,EAAG,gBAClCJ,KAAKQ,YAAqBR,KAAKI,EAAG,0BAGlCJ,KAAKS,WAAa,GAAIlB,GAAKmB,WAC3BV,KAAKS,WAAWE,GAAI,MAAO,SAAUC,GACjCb,EAAKQ,YAAYM,OAAQ,GAAItB,GAAKuB,KAAOF,MAAQA,IAAUG,SAASC,OACrEL,GAAI,QAAS,WACZZ,EAAKQ,YAAYU,UAClBN,GAAI,WAAY,SAAUO,GACzBnB,EAAKU,WAAWU,KAAM,SAAWC,GAAMF,EAAUE,OAClDC,MAAOrB,KAAKF,SAGfwB,OAAOC,MAAQvB,KAAKuB,MAAQ,GAAI/B,IAAeiB,WAAYT,KAAKS,aAChEL,EAAG,QAASS,OAAQb,KAAKuB,MAAMP,KAI/BM,OAAOE,WAAaxB,KAAKwB,WAAa,GAAI/B,GAAWgC,gBACjDb,MAAUU,OAAOI,KACjBC,GAAU3B,KAAKQ,cAInBJ,EAAGwB,QAASjB,GAAI,QAAS,SAAUkB,GAC/B,GAAIC,GAAiB1B,EAAGyB,EAAEE,QAASC,QAAS,cACd,IAAzBF,EAAeG,SAC0B,IAAtC7B,EAAG,uBAAwB6B,QAC3B7B,EAAG,QAASS,OAAQT,EAAG,aAAc8B,KAAM,KAAM,YAAaC,QAElE/B,EAAG,uBAAwB8B,KAAM,MAAOJ,EAAeI,KAAM,SAC7DL,EAAEO,oBAEPzB,GAAI,eAAgB,WACnB,GAAI0B,GAAO,EAKX,OAJAtC,GAAKU,WAAWU,KAAM,SAAUP,GAC5B,GAAI0B,GAAI1B,EAAM2B,IAAK,mBAAsB3B,EAAM2B,IAAK,mBACpDD,KAAOD,GAAQC,EAAI,OAET,KAATD,EACMA,EADX,UAMRtB,OAAQ,WAKJ,MAJAf,MAAKM,kBAAkBkC,KAAM,WAAcxC,KAAKF,QAAQ2C,OAAS,KAAOzC,KAAKF,QAAQ2C,OAAS,KAC9FzC,KAAKG,iBAAiB+B,KAAM,OAAQlC,KAAKF,QAAQ4C,UACjD1C,KAAKK,kBAAkB6B,KAAM,MAAOZ,OAAOqB,KAAO,uCAClD3C,KAAKwB,WAAWT,SACTf,MAIXE,UAAW,WACP,MAAQ,2UAgBhB,QACIR,KAAMA"}
\ No newline at end of file
diff --git a/static/maps/layout/menu.js.map b/static/maps/layout/menu.js.map
index a05ec8f10b3..7f1ea24fb12 100644
--- a/static/maps/layout/menu.js.map
+++ b/static/maps/layout/menu.js.map
@@ -1 +1 @@
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diff --git a/static/maps/layout/page.js.map b/static/maps/layout/page.js.map
index 1da6fbc6ed7..e31ad05e187 100644
--- a/static/maps/layout/page.js.map
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diff --git a/static/maps/layout/scratchbook.js.map b/static/maps/layout/scratchbook.js.map
index 145bd0252f4..a376e4ae552 100644
--- a/static/maps/layout/scratchbook.js.map
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diff --git a/static/maps/mvc/dataset/dataset-li-edit.js.map b/static/maps/mvc/dataset/dataset-li-edit.js.map
index aec80e56d5e..c68338f78cf 100644
--- a/static/maps/mvc/dataset/dataset-li-edit.js.map
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diff --git a/static/maps/mvc/dataset/dataset-li.js.map b/static/maps/mvc/dataset/dataset-li.js.map
index 423b1e888a2..62fe708321c 100644
--- a/static/maps/mvc/dataset/dataset-li.js.map
+++ b/static/maps/mvc/dataset/dataset-li.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/ui/ui-frames.js.map b/static/maps/mvc/ui/ui-frames.js.map
index 7acda5bbaf1..8e5a5c375a9 100644
--- a/static/maps/mvc/ui/ui-frames.js.map
+++ b/static/maps/mvc/ui/ui-frames.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/static/maps/onload.js.map b/static/maps/onload.js.map
index 9324bd3ad2c..a45f56fb8ca 100644
--- a/static/maps/onload.js.map
+++ b/static/maps/onload.js.map
@@ -1 +1 @@
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diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index 0f236c91233..f599687a8ab 100644
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0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(15),i(6),i(5)],s=function(t,e,i){var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(46),i(96),i(45),i(6),i(5)],
+this.model.on("change",function(t,e){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},remove:function(t,e){var i=this;t=t||this.fxSpeed,this.$el.fadeOut(t,function(){a.View.prototype.remove.call(i),e&&e.call(i)})},render:function(t){return d.prototype.render.call(this,t)},_swapNewRender:function(t){return d.prototype._swapNewRender.call(this,t),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var t=this.model.get("state");if(t===e.NOT_VIEWABLE||t===e.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(t===e.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(t===e.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),t.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===e.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var t=d.prototype._renderDetails.call(this);return t.find(".actions .left").empty().append(this._renderSecondaryActions()),t.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),t.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(t),t},_renderSummary:function(){var t=this.model.toJSON(),e=this.templates.summaries[t.state];return(e=e||this.templates.summaries.unknown)(t,this)},_renderDetailMessages:function(){var t=this,e=r(''),i=t.model.toJSON();return l.each(t.templates.detailMessages,function(n){e.append(r(n(i,t)))}),e},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case e.NOT_VIEWABLE:return[];case e.OK:case e.FAILED_METADATA:case e.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:l.isEmpty(this.model.get("meta_files"))?r(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return r(['"].join("\n"))},events:l.extend(l.clone(d.prototype.events),{"click .display-btn":function(t){this.trigger("display",this,t)},"click .params-btn":function(t){this.trigger("params",this,t)},"click .download-btn":function(t){this.trigger("download",this,t)}}),toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetListItemView("+t+")"}});return h.prototype.templates=function(){var t=l.extend({},d.prototype.templates.warnings,{failed_metadata:n.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','',s("An error occurred setting the metadata for this dataset")," ","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'',s("There was an error getting the data for this dataset"),": <%- model.error %>"," ","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'',s("This dataset has been deleted and removed from disk")," ","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'',s("This dataset has been deleted")," ","<% } %>"])}),i=n.wrapTemplate(['',' ',' ","<% if( !dataset.deleted && !dataset.purged ){ %>",' ',' ',' ',"<% if( dataset.peek ){ %>",' <%= dataset.peek %> ',"<% } %>","<% } %>"," ',' ',s("You do not have permission to view this dataset")," "," ','<%- dataset.misc_blurb %>'," ","<% } %>","<% if( dataset.file_ext ){ %>",'','",'<%- dataset.file_ext %>'," ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'','",'',"<%- dataset.metadata_dbkey %>",""," ","<% } %>","<% if( dataset.misc_info ){ %>",'','<%- dataset.misc_info %>'," ","<% } %>"],"dataset"),a[e.NEW]=n.wrapTemplate(["",s("This is a new dataset and not all of its data are available yet")," "],"dataset"),a[e.NOT_VIEWABLE]=n.wrapTemplate(["",s("You do not have permission to view this dataset")," "],"dataset"),a[e.DISCARDED]=n.wrapTemplate(["",s("The job creating this dataset was cancelled before completion")," "],"dataset"),a[e.QUEUED]=n.wrapTemplate(["",s("This job is waiting to run")," "],"dataset"),a[e.RUNNING]=n.wrapTemplate(["",s("This job is currently running")," "],"dataset"),a[e.UPLOAD]=n.wrapTemplate(["",s("This dataset is currently uploading")," "],"dataset"),a[e.SETTING_METADATA]=n.wrapTemplate(["",s("Metadata is being auto-detected")," "],"dataset"),a[e.PAUSED]=n.wrapTemplate(["",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')," "],"dataset"),a[e.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","<%- dataset.misc_blurb %> ","<% } %>",'',s("An error occurred with this dataset"),":",'<%- dataset.misc_info %> '],"dataset"),a[e.EMPTY]=n.wrapTemplate(["",s("No data"),": <%- dataset.misc_blurb %> "],"dataset"),a.unknown=n.wrapTemplate(['Error: unknown dataset state: "<%- dataset.state %>" '],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'',s("The job creating this dataset has been resubmitted")," ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'',' <%- app.label %> ',' ',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>",""," This is a batch mode input field. A separate job will be triggered for each dataset. '}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(11),i(7),i(42),i(38)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement(""),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(35),i(46),i(5)],s=function(t,e,i){function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(15),i(6),i(5)],s=function(t,e,i){var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(46),i(96),i(45),i(6),i(5)],
s=function(t,e,i,n,s){var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a(''),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['"]),i={},n=t.wrapTemplate(['',' ',' ','<%- element.name %>'," ",' '," '," "],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(60),i(7),i(44),i(23),i(21),i(33)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("").append(s.help(t));if(t.citations){var i=o(""),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(20),i(14),i(22),i(64),i(65),i(63),i(66)],s=function(t,e,i,n,s,r,l,c){var d={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},h=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new h(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),u=o.Collection.extend({model:h}),p=h.extend({}),f=h.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),g=f.extend({set_value:function(t){this.set("value",parseFloat(t))}}),m=h.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});h.subModelTypes={integer:f,"float":g,data:p,select:m};var v=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new u(t.map(e.inputs,function(t){var e=h.subModelTypes[t.type]||h;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new v(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(v.prototype,d);var _=(o.View.extend({}),o.Collection.extend({model:v})),y=o.Model.extend(d),w=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof y?(i=t,i.hide()):t instanceof v&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(w.prototype,d);var b=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length");if(t.append(r(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),this}}),$=C.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),S=C.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){C.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(l(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof v){var i=new E({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof y){var n=new $({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),k=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(c(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),T=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new k({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof w){var i=new S({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof v){var n=new E({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof y){var s=new $({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),D=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(s(this.model.toJSON()))}});o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new T({collection:this.collection}),this.tool_form_view=new D},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}});return{ToolParameter:h,IntegerToolParameter:f,SelectToolParameter:m,Tool:v,ToolCollection:_,ToolSearch:b,ToolPanel:x,ToolPanelView:T,ToolFormView:D}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i,o,a,r){n=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.size()||(this.$button=o("")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return o(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var n=t.options[e];n.func&&o(this).children("a.popupmenu-option").click(function(e){n.func.call(t,e,n),e.preventDefault()})})}return this},template:function(t,e){return['"].join("")},_templateOptions:function(t){return t.length?a.map(t,function(t){if(t.divider)return'';if(t.header)return['',t.html,""].join("");var e=t.href||"javascript:void(0);",i=t.target?' target="'+t.target+'"':"",n=t.checked?'':"";return['"].join("")}).join(""):"(no options)"},_getShownPosition:function(t){var e=this.$el.width(),i=t.pageX-e/2;return i=Math.min(i,o(document).scrollLeft()+o(window).width()-e-5),i=Math.max(i,o(document).scrollLeft()+5),{top:t.pageY,left:i}},_setUpCloseBehavior:function(){function t(t){if(o(document).off("click.close_popup"),window.parent!==window)try{o(window.parent.document).off("click.close_popup")}catch(i){}else try{o("iframe#galaxy_main").contents().off("click.close_popup")}catch(i){}e.remove()}var e=this;if(o("html").one("click.close_popup",t),window.parent!==window)try{o(window.parent.document).find("html").one("click.close_popup",t)}catch(i){}else try{o("iframe#galaxy_main").contents().one("click.close_popup",t)}catch(i){}},addItem:function(t,e){return e=e>=0?e:this.options.length,this.options.splice(e,0,t),this},removeItem:function(t){return t>=0&&this.options.splice(t,1),this},findIndexByHtml:function(t){for(var e=0;e'},_templateContent:function(){return''},_templateBox:function(t){return''},_template:function(){return''}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,n){var s,o;(function(a){s=[n(4),n(25)],o=function(t,e){var n=e.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.display,e.BaseIcons.prototype.initialize.call(this,t),this.initial=!0},value:function(t){var i=e.BaseIcons.prototype.value.call(this,t);if(this.initial&&null!==i&&this.header_index){this.initial=!1;var n=i;a.isArray(n)||(n=[n]);for(var s in n){var o=this.header_index[n[s]];for(var r in o)this._setState(o[r],!0)}}return i},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.fadeIn("fast"),i.removeClass("fa-plus-square"),i.addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square"),i.addClass("fa-plus-square"))},_templateOptions:function(e){function n(t,e){var i=t.find(".button-"+e);i.on("click",function(){o._setState(e,!i.data("is_expanded"))})}function s(e,r,l){l=l||[];for(i in r){var c=r[i],d=c.options.length>0,h=l.slice(0);o.header_index[c.value]=h.slice(0);var u=a(" ");if(d){var p=t.uid(),f=a(' '),g=a(' ');h.push(p);var m=a(" ");m.append(f),m.append(o._templateOption({label:c.name,
value:c.value})),u.append(m),s(g,c.options,h),u.append(g),n(u,p)}else u.append(o._templateOption({label:c.name,value:c.value}));e.append(u)}}var o=this;this.header_index={};var r=a(" ");return s(r,e),r},_template:function(t){return' '}});return{View:n}}.apply(e,s),!(void 0!==o&&(t.exports=o))}).call(e,n(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(16)],s=function(t,e){var i=o.View.extend({optionsDefault:{id:t.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(i){var n=this;this.options=t.merge(i,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown"),this.$icon_dropdown.on("click",function(){n.$select.select2&&n.$select.select2("open")});var s=null;this.$(".icon-resize").on("mousedown",function(t){var e=t.pageY,i=n.$select.height();s=s||i,a("#dd-helper").show().on("mousemove",function(t){n.$select.height(Math.max(i+(t.pageY-e),s))}).on("mouseup mouseleave",function(){a("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new e.ButtonCheck({onclick:function(){var t=[];0!==n.all_button.value()&&(t=n._availableOptions()),n.value(t),n.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){n.trigger("change")}),this.on("change",function(){n.options.onchange&&n.options.onchange(this.value())})},value:function(t){void 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u=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(t){},initialize:function(t){},progress:function(t,e){},success:function(t,e){},error:function(t,e){alert(e)},complete:function(){}},t),p={},f=0,g=0,m=!1,v=!1,_=i(this).uploadinput({multiple:!0,onchange:function(t){n(t)},ondragover:t.ondragover,ondragleave:t.ondragleave});return{select:a,add:n,remove:s,start:l,stop:c,reset:r,configure:d,compatible:h}}}(t)}).call(e,i(1),i(3))},function(t,e,i){var n=i(13).RightPanel,s=i(7),o=i(131);CurrentHistoryView=i(128).CurrentHistoryView,_l=i(5);var a=n.extend({title:_l("History"),initialize:function(t){n.prototype.initialize.call(this,t);var e=this;this.refreshButton=new s.ButtonLink({id:"history-refresh-button",title:_l("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){e.historyView.loadCurrentHistory()}}),this.optionsButton=new s.ButtonLink({id:"history-options-button",title:_l("History options"),cls:"panel-header-button",icon:"fa 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s=i(13).LeftPanel,o=i(50),a=i(137),r=i(5),l=s.extend({title:r("Tools"),initialize:function(t){s.prototype.initialize.call(this,t),this.log(this+".initialize:",t),this.stored_workflow_menu_entries=t.stored_workflow_menu_entries||[];var e=new o.ToolSearch({spinner_url:t.spinner_url,search_url:t.search_url,hidden:!1}),i=new o.ToolCollection(t.toolbox);this.tool_panel=new o.ToolPanel({tool_search:e,tools:i,layout:t.toolbox_in_panel}),this.tool_panel_view=new o.ToolPanelView({model:this.tool_panel}),this.uploadButton=new a({nginx_upload_path:t.nginx_upload_path,ftp_upload_site:t.ftp_upload_site,default_genome:t.default_genome,default_extension:t.default_extension})},render:function(){var t=this;s.prototype.render.call(t),t.$(".panel-header-buttons").append(t.uploadButton.$el),t.tool_panel.get("layout").size()>0&&(t.tool_panel_view.render(),t.$(".toolMenu").show()),t.$(".toolMenuContainer").prepend(t.tool_panel_view.$el),t._renderWorkflowMenu(),t.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint(e(t).attr("minsizehint"))})},_renderWorkflowMenu:function(){var t=this;t.$("#internal-workflows").append(t._templateTool({title:r("All workflows"),href:"workflow/list_for_run"})),n.each(t.stored_workflow_menu_entries,function(e){t.$("#internal-workflows").append(t._templateTool({title:e.stored_workflow.name,href:"workflow/run?id="+e.encoded_stored_workflow_id}))})},_templateTool:function(t){return[' "].join("")},_templateBody:function(){return[' ','"," "].join("")},toString:function(){return"ToolPanel"}});t.exports=l}).call(e,i(1),i(3))},,,,,,,,,,function(t,e,i){var n,s;(function(o,a){n=[i(34),i(93),i(6),i(5)],s=function(t,e,i,n){var s=t.DCListItemView,r=s.extend({initialize:function(t){s.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCListItemEdit("+t+")"}}),l=t.DCEListItemView,c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCEListItemEdit("+t+")"}}),d=e.DatasetListItemEdit.extend({initialize:function(t){e.DatasetListItemEdit.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},_renderDeleteButton:function(){return null},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemEdit("+t+")"}});d.prototype.templates=function(){return a.extend({},e.DatasetListItemEdit.prototype.templates,{titleBar:t.DatasetDCEListItemView.prototype.templates.titleBar})}();var h=t.NestedDCDCEListItemView.extend({toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemEdit("+t+")"}});return{DCListItemEdit:r,DCEListItemEdit:c,DatasetDCEListItemEdit:d,NestedDCDCEListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(3))},function(t,e,i){var n,s;n=[i(92),i(35),i(121),i(6),i(5),i(19)],s=function(t,e,i,n,s){var o=t.CollectionView,a=o.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,NestedDCDCEViewClass:i.NestedDCDCEListItemEdit,initialize:function(t){o.prototype.initialize.call(this,t)},_setUpBehaviors:function(t){if(t=t||this.$el,o.prototype._setUpBehaviors.call(this,t),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){var e=this,i="> .controls .name";t.find(i).attr("title",s("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(t){var n=e.model.get("name");t&&t!==n?(e.$el.find(i).text(t),e.model.save({name:t}).fail(function(){e.$el.find(i).text(e.model.previous("name"))})):e.$el.find(i).text(n)}})}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),r=a.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),l=r.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),c=l.extend({_setUpBehaviors:function(t){o.prototype._setUpBehaviors.call(this,t)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),d=a.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemEdit.extend({foldoutPanelClass:c}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{CollectionViewEdit:a,ListCollectionViewEdit:r,PairCollectionViewEdit:l,ListOfPairsCollectionViewEdit:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(144),i(108),i(36),i(6),i(5),i(105)],s=function(t,e,i,n,s){function c(t){function e(){return i.length||(i=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),i}t=t||{},t.createPair=t.createPair||function(t){t=t||{};var e=t.listA.splice(t.indexA,1)[0],i=t.listB.splice(t.indexB,1)[0],n=t.listB.indexOf(e),s=t.listA.indexOf(i);return-1!==n&&t.listB.splice(n,1),-1!==s&&t.listA.splice(s,1),this._pair(e,i,{silent:!0})};var i=[];return t.preprocessMatch=t.preprocessMatch||function(t){var i=e.call(this);return a.extend(t,{matchTo:t.matchTo.name.replace(i[0],""),possible:t.possible.name.replace(i[1],"")})},function(e){this.debug("autopair _strategy ---------------------------"),e=e||{};var i,n=e.listA,s=e.listB,o=0,a={score:0,index:null},r=[];for(this.debug("starting list lens:",n.length,s.length),this.debug("bestMatch (starting):",JSON.stringify(a,null," "));o =d?r.push(t.createPair.call(this,{listA:n,indexA:o,listB:s,indexB:a.index})):o+=1,!n.length||!s.length)return r}return this.debug("paired:",JSON.stringify(r,null," ")),this.debug("autopair _strategy ---------------------------"),r}}function d(t){var e=t.toJSON();return f(e,{historyId:t.historyId})}var h="collections",u=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"dataset paired",initialize:function(t){this.pair=t.pair||{}},template:a.template(['<%- pair.forward.name %>','','<%- pair.name %>',"",'<%- pair.reverse.name %>'].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(t){t.currentTarget.style.opacity="0.4",t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(t){t.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"PairView("+this.pair.name+")"}}),p=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(t){this.metric("PairedCollectionCreator.initialize",t),t=a.defaults(t,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=t.datasets,this.historyId=t.historyId,this.filters=this.commonFilters[t.filters]||this.commonFilters[this.DEFAULT_FILTERS],a.isArray(t.filters)&&(this.filters=t.filters),this.automaticallyPair=t.automaticallyPair,this.strategy=this.strategies[t.strategy]||this.strategies[this.DEFAULT_STRATEGY],a.isFunction(t.strategy)&&(this.strategy=t.strategy),this.matchPercentage=t.matchPercentage,this.twoPassAutopairing=t.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=t.oncancel,this.oncreate=t.oncreate,this.autoscrollDist=t.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(t){return t.sort(function(t,i){return e(t.name,i.name)}),t},_ensureIds:function(){return this.initialList.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.initialList},_splitByFilters:function(){function t(t,e){return e.test(t.name)}var e=this.filters.map(function(t){return new RegExp(t)}),i=[[],[]];return this.unpaired.forEach(function(n){e.forEach(function(e,s){t(n,e)&&i[s].push(n)})}),i},_addToUnpaired:function(t){var i=function(n,s){if(n===s)return n;var o=Math.floor((s-n)/2)+n,a=e(t.name,this.unpaired[o].name);if(0>a)return i(n,o);if(a>0)return i(o+1,s);for(;this.unpaired[o]&&this.unpaired[o].name===t.name;)o++;return o}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,t)},autoPair:function(t){var e=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:e[0],listB:e[1]}),e=this._splitByFilters()),t=t||this.strategy,e=this._splitByFilters(),i=i.concat(this[t].call(this,{listA:e[0],listB:e[1]}))},autopairSimple:c({scoreThreshold:function(){return 1},match:function(t){return t=t||{},t.matchTo===t.possible?{index:t.index,score:1}:t.bestMatch}}),autopairLevenshtein:c({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var i=t(e.matchTo,e.possible),n=1-i/Math.max(e.matchTo.length,e.possible.length);return n>e.bestMatch.score?{index:e.index,score:n}:e.bestMatch}}),autopairLCS:c({scoreThreshold:function(){return this.matchPercentage},match:function(t){t=t||{};var e=this._naiveStartingAndEndingLCS(t.matchTo,t.possible).length,i=e/Math.max(t.matchTo.length,t.possible.length);return i>t.bestMatch.score?{index:t.index,score:i}:t.bestMatch}}),_naiveStartingAndEndingLCS:function(t,e){for(var i="",n="",s=0,o=0;s=0&&o>=0&&t[s]===e[o];)n=[t[s],n].join(""),s-=1,o-=1;return i+n},_pair:function(t,e,i){i=i||{},this.debug("_pair:",t,e);var n=this._createPair(t,e,i.name);return this.paired.push(n),this.unpaired=a.without(this.unpaired,t,e),i.silent||this.trigger("pair:new",n),n},_createPair:function(t,e,i){if(!t||!e||t===e)throw new Error("Bad pairing: "+[JSON.stringify(t),JSON.stringify(e)]);return i=i||this._guessNameForPair(t,e),{forward:t,name:i,reverse:e}},_guessNameForPair:function(t,e,i){i=void 0!==i?i:this.removeExtensions;var n=t.name,s=e.name,o=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var a=o.lastIndexOf(".");if(a>0){var r=o.slice(a,o.length);o=o.replace(r,""),n=n.replace(r,""),s=s.replace(r,"")}}return o||n+" & "+s},_unpair:function(t,e){if(e=e||{},!t)throw new Error("Bad pair: "+JSON.stringify(t));return this.paired=a.without(this.paired,t),this._addToUnpaired(t.forward),this._addToUnpaired(t.reverse),e.silent||this.trigger("pair:unpair",[t]),t},unpairAll:function(){for(var t=[];this.paired.length;)t.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",t)},_pairToJSON:function(t,e){return e=e||"hda",{collection_type:"paired",src:"new_collection",name:t.name,element_identifiers:[{name:"forward",id:t.forward.id,src:e},{name:"reverse",id:t.reverse.id,src:e}]}},createList:function(t){var e=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",n={type:"dataset_collection",collection_type:"list:paired",name:a.escape(t||e.$(".collection-name").val()),element_identifiers:e.paired.map(function(t){return e._pairToJSON(t)})};return e.blocking=!0,r.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(n)}).always(function(){e.blocking=!1}).fail(function(t,i,n){e._ajaxErrHandler(t,i,n)}).done(function(t,i,n){e.trigger("collection:created",t,i,n),e.metric("collection:created",t),"function"==typeof e.oncreate&&e.oncreate.call(this,t,i,n)})},_ajaxErrHandler:function(t,e,i){this.error(t,e,i);var n=s("An error occurred while creating this collection");t&&(n+=0===t.readyState&&0===t.status?": "+s("Galaxy could not be reached and may be updating.")+s(" Try again in a few minutes."):t.responseJSON?"
"+JSON.stringify(t.responseJSON)+" ":": "+i),creator._showAlert(n,"alert-danger")},render:function(t,e){return this.$el.empty().html(p.templates.main()),this._renderHeader(t),this._renderMiddle(t),this._renderFooter(t),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(t,e){var i=this.$(".header").empty().html(p.templates.header()).find(".help-content").prepend(l(p.templates.helpContent()));return this._renderFilters(),i},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(t,e){var i=this.$(".middle").empty().html(p.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),i},_renderUnpaired:function(t,e){var i,n,o=this,a=[],r=this._splitByFilters();return this.$(".forward-column .title").text([r[0].length,s("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-r[0].length)),this.$(".reverse-column .title").text([r[1].length,s("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-r[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(n=r[1].map(function(t,e){return void 0!==r[0][e]&&r[0][e]!==t&&a.push(o._renderPairButton()),o._renderUnpairedDataset(t)}),i=r[0].map(function(t){return o._renderUnpairedDataset(t)}),i.length||n.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(i).add(this.$(".unpaired-columns .paired-column .column-datasets").append(a)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(t){return["(",t," ",s("filtered out"),")"].join("")},_renderUnpairedDataset:function(t){return l("").attr("id","dataset-"+t.id).addClass("dataset unpaired").attr("draggable",!0).addClass(t.selected?"selected":"").append(l("").addClass("dataset-name").text(t.name)).data("dataset",t)},_renderPairButton:function(){return l("").addClass("dataset unpaired").append(l("").addClass("dataset-name").text(s("Pair these datasets")))},_renderUnpairedEmpty:function(){var t=l('').text("("+s("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(t),t},_renderUnpairedNotShown:function(){var t=l('').text("("+s("no datasets were found matching the current filters")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(t),t},_adjUnpairedOnScrollbar:function(){var t=this.$(".unpaired-columns").last(),e=this.$(".unpaired-columns .reverse-column .dataset").first();if(e.size()){var i=t.offset().left+t.outerWidth(),n=e.offset().left+e.outerWidth(),s=Math.floor(i)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",s>0?s:0)}},_renderPaired:function(t,e){if(this.$(".paired-column-title .title").text([this.paired.length,s("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(t,e){var n=new u({pair:t});i.$(".paired-columns .column-datasets").append(n.render().$el).append(['"].join(""))})},_renderPairedEmpty:function(){var t=l('').text("("+s("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(t),t},_renderFooter:function(t,e){var i=this.$(".footer").empty().html(p.templates.footer());
return this.$(".remove-extensions").prop("checked",this.removeExtensions),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),i},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(t){function e(t,e){return['"].join("")}var i=l(a.template(['',' ',s("Choose from the following filters to change which unpaired reads are shown in the display"),": ",a.values(this.commonFilters).map(function(t){return e(t[0],t[1])}).join("")," | | 
' +
- '![](\"')
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