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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f938aac3397b/
Changeset: f938aac3397b
User: jgoecks
Date: 2013-10-13 22:28:13
Summary: Trackster: fold content_visible flag into config.
Affected #: 1 file
diff -r 5c10579e88db53ed05013c4314573d3919d72e17 -r f938aac3397bfd12da241b3f60daecf90574d0ec static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -207,6 +207,11 @@
this.name = obj_dict.name;
this.view = view;
this.container = container;
+ this.drag_handle_class = obj_dict.drag_handle_class;
+ this.is_overview = false;
+ this.action_icons = {};
+
+ // Set up drawable configuration.
this.config = new Config({
params: this.config_params,
onchange: this.config_onchange,
@@ -216,12 +221,6 @@
this.config.on('change:values', this.config_onchange, this);
}
this.prefs = this.config.get('values');
- this.drag_handle_class = obj_dict.drag_handle_class;
- this.is_overview = false;
- this.action_icons = {};
-
- // FIXME: this should be a saved setting
- this.content_visible = true;
// Build Drawable HTML and behaviors.
this.container_div = this.build_container_div();
@@ -258,13 +257,14 @@
title: "Hide/show content",
css_class: "toggle",
on_click_fn: function(drawable) {
- if ( drawable.content_visible ) {
+ if ( drawable.prefs.content_visible ) {
drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");
drawable.hide_contents();
- drawable.content_visible = false;
- } else {
+ drawable.prefs.content_visible = false;
+ }
+ else {
drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");
- drawable.content_visible = true;
+ drawable.prefs.content_visible = true;
drawable.show_contents();
}
}
@@ -296,7 +296,8 @@
extend(Drawable.prototype, {
config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name }
+ { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'content_visible', type: 'bool', default_value: true, hidden: true }
],
config_onchange: function() {
@@ -310,7 +311,7 @@
},
can_draw: function() {
- if (this.enabled && this.content_visible) {
+ if (this.enabled && this.prefs.content_visible) {
return true;
}
@@ -2541,7 +2542,7 @@
var drag_control = $( "<div class='track-resize'>" );
// Control shows on hover over track, stays while dragging
$(track.container_div).hover( function() {
- if ( track.content_visible ) {
+ if ( track.prefs.content_visible ) {
in_handle = true;
drag_control.show();
}
@@ -2831,6 +2832,9 @@
// Add tiles_div, overlay_div to content_div.
this.tiles_div = $("<div/>").addClass("tiles").appendTo(this.content_div);
+ if (!this.prefs.content_visible) {
+ this.tiles_div.hide();
+ }
this.overlay_div = $("<div/>").addClass("overlay").appendTo(this.content_div);
if (obj_dict.mode) {
@@ -3808,14 +3812,13 @@
extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
display_modes: CONTINUOUS_DATA_MODES,
- config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ config_params: _.union( Drawable.prototype.config_params, [
{ key: 'color', label: 'Color', type: 'color', default_value: util.get_random_color() },
{ key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined },
{ key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 30, hidden: true }
- ],
+ ] ),
config_onchange: function() {
this.set_name(this.prefs.name);
@@ -3863,15 +3866,14 @@
extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
display_modes: ["Heatmap"],
- config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ config_params: _.union( Drawable.prototype.config_params, [
{ key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
{ key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
{ key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 },
{ key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 500, hidden: true }
- ],
+ ] ),
config_onchange: function() {
this.set_name(this.prefs.name);
@@ -3908,8 +3910,7 @@
extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
- config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ config_params: _.union( Drawable.prototype.config_params, [
{ key: 'block_color', label: 'Block color', type: 'color', default_value: util.get_random_color() },
{ key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
@@ -3921,7 +3922,7 @@
options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 0, hidden: true}
- ],
+ ] ),
config_onchange: function() {
this.set_name(this.prefs.name);
@@ -4207,14 +4208,13 @@
extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
- config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ config_params: _.union( Drawable.prototype.config_params, [
{ key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() },
{ key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true },
{ key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true },
{ key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true }
- ],
+ ] ),
config_onchange: function() {
this.set_name(this.prefs.name);
@@ -4352,8 +4352,7 @@
};
extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
- config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ config_params: _.union( Drawable.prototype.config_params, [
{ key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: util.get_random_color() },
{ key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
@@ -4364,7 +4363,7 @@
{ key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
{ key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
{ key: 'height', type: 'int', default_value: 0, hidden: true}
- ],
+ ] ),
config_onchange: function() {
this.set_name(this.prefs.name);
https://bitbucket.org/galaxy/galaxy-central/commits/ae23a7b44e3e/
Changeset: ae23a7b44e3e
User: jgoecks
Date: 2013-10-13 23:00:27
Summary: Trackster: fold name attribute into object preferences.
Affected #: 2 files
diff -r f938aac3397bfd12da241b3f60daecf90574d0ec -r ae23a7b44e3eb1679cd4befd5f26a0c514649554 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1082,7 +1082,6 @@
return {
"dataset_id": trans.security.decode_id( dataset_dict['id'] ),
"hda_ldda": dataset_dict.get('hda_ldda', 'hda'),
- "name": track_dict['name'],
"track_type": track_dict['track_type'],
"prefs": track_dict['prefs'],
"mode": track_dict['mode'],
@@ -1101,7 +1100,6 @@
drawable = unpack_collection( drawable_json )
unpacked_drawables.append( drawable )
return {
- "name": collection_json.get( 'name', '' ),
"obj_type": collection_json[ 'obj_type' ],
"drawables": unpacked_drawables,
"prefs": collection_json.get( 'prefs' , [] ),
@@ -1192,7 +1190,6 @@
return {
"track_type": dataset.datatype.track_type,
"dataset": trans.security.encode_dict_ids( dataset.to_dict() ),
- "name": track_dict['name'],
"prefs": prefs,
"mode": track_dict.get( 'mode', 'Auto' ),
"filters": track_dict.get( 'filters', { 'filters' : track_data_provider.get_filters() } ),
@@ -1208,7 +1205,6 @@
else:
drawables.append( pack_collection( drawable_dict ) )
return {
- 'name': collection_dict.get( 'name', 'dummy' ),
'obj_type': collection_dict[ 'obj_type' ],
'drawables': drawables,
'prefs': collection_dict.get( 'prefs', [] ),
diff -r f938aac3397bfd12da241b3f60daecf90574d0ec -r ae23a7b44e3eb1679cd4befd5f26a0c514649554 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -204,23 +204,28 @@
var Drawable = function(view, container, obj_dict) {
if (!Drawable.id_counter) { Drawable.id_counter = 0; }
this.id = Drawable.id_counter++;
- this.name = obj_dict.name;
this.view = view;
this.container = container;
this.drag_handle_class = obj_dict.drag_handle_class;
this.is_overview = false;
this.action_icons = {};
- // Set up drawable configuration.
+ // -- Set up drawable configuration. --
+
this.config = new Config({
params: this.config_params,
onchange: this.config_onchange,
saved_values: obj_dict.prefs
});
+ this.prefs = this.config.get('values');
+
+ // If there's no saved name, use object name.
+ if (!this.prefs.name) {
+ this.prefs.name = obj_dict.name;
+ }
if (this.config_onchange) {
this.config.on('change:values', this.config_onchange, this);
}
- this.prefs = this.config.get('values');
// Build Drawable HTML and behaviors.
this.container_div = this.build_container_div();
@@ -296,7 +301,7 @@
extend(Drawable.prototype, {
config_params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'name', label: 'Name', type: 'text', default_value: '' },
{ key: 'content_visible', type: 'bool', default_value: true, hidden: true }
],
@@ -332,9 +337,9 @@
* Set drawable name.
*/
set_name: function(new_name) {
- this.old_name = this.name;
- this.name = new_name;
- this.name_div.text(this.name);
+ this.old_name = this.prefs.name;
+ this.prefs.name = new_name;
+ this.name_div.text(this.prefs.name);
},
/**
@@ -342,8 +347,8 @@
*/
revert_name: function() {
if (this.old_name) {
- this.name = this.old_name;
- this.name_div.text(this.name);
+ this.prefs.name = this.old_name;
+ this.name_div.text(this.prefs.name);
}
},
@@ -473,7 +478,6 @@
dictified_drawables.push(this.drawables[i].to_dict());
}
return {
- name: this.name,
prefs: this.prefs,
obj_type: this.obj_type,
drawables: dictified_drawables
@@ -669,7 +673,7 @@
build_header_div: function() {
var header_div = $("<div/>").addClass("track-header");
header_div.append($("<div/>").addClass(this.drag_handle_class));
- this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div);
+ this.name_div = $("<div/>").addClass("track-name").text(this.prefs.name).appendTo(header_div);
return header_div;
},
@@ -830,7 +834,7 @@
*/
show_composite_track: function() {
var composite_track = new CompositeTrack(this.view, this.view, {
- name: this.name,
+ name: this.prefs.name,
drawables: this.drawables
});
var index = this.container.replace_drawable(this, composite_track, true);
@@ -1792,7 +1796,7 @@
// already in group, add track to group.
if (current_track.container === view) {
// Create new group.
- var group = new DrawableGroup(view, view, { name: this.name });
+ var group = new DrawableGroup(view, view, { name: this.prefs.name });
// Replace track with group.
var index = current_track.container.replace_drawable(current_track, group, false);
@@ -2512,8 +2516,8 @@
build_header_div: function() {
var header_div = $("<div class='track-header'/>");
if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); }
- this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.name)
- .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
+ this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.prefs.name)
+ .attr( "id", this.prefs.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
return header_div;
},
@@ -2889,7 +2893,6 @@
to_dict: function() {
return {
track_type: this.get_type(),
- name: this.name,
dataset: {
id: this.dataset.id,
hda_ldda: this.dataset.get('hda_ldda')
@@ -3643,7 +3646,7 @@
show_group: function() {
// Create group with individual tracks.
var group = new DrawableGroup(this.view, this.container, {
- name: this.name
+ name: this.prefs.name
}),
track;
for (var i = 0; i < this.drawables.length; i++) {
https://bitbucket.org/galaxy/galaxy-central/commits/7781a13a9ba0/
Changeset: 7781a13a9ba0
User: jgoecks
Date: 2013-10-13 23:09:39
Summary: Trackster: prevent inadvertent keyboard navigation when configuring track.
Affected #: 1 file
diff -r ae23a7b44e3eb1679cd4befd5f26a0c514649554 -r 7781a13a9ba0adf43cba0b1949fa84fd074c5323 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1986,7 +1986,11 @@
//
var track_config = this.model;
- var container = $("<div />");
+
+ // Prevent propagation of keydown events to viz to avoid inadvertent navigation.
+ var container = $("<div/>").keydown(function(e) {
+ e.stopPropagation();
+ });
var param;
// Function to process parameters recursively
function handle_params( params, container ) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5b1e3adfafb4/
Changeset: 5b1e3adfafb4
User: jgoecks
Date: 2013-10-12 03:59:34
Summary: Trackster: clean up link attributes.
Affected #: 1 file
diff -r 34ff4b571205e3d28adcf2d553e6aa0c15364d94 -r 5b1e3adfafb419eb8b3ec61af04a00604b02712c static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -367,7 +367,7 @@
*/
add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) {
var drawable = this;
- this.action_icons[name] = $("<a/>").attr("href", "").attr("title", title)
+ this.action_icons[name] = $("<a/>").attr("title", title)
.addClass("icon-button").addClass(css_class).tooltip()
.click( function() { on_click_fn(drawable); } )
.appendTo(this.icons_div);
@@ -942,7 +942,10 @@
// Overview (scrollbar and overview plot) at bottom
this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container);
this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview);
- this.overview_close = $("<a/>").attr("href", "").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);
+ this.overview_close = $("<a/>").attr("title", "Close overview")
+ .addClass("icon-button overview-close tooltip")
+ .hide()
+ .appendTo(this.overview_viewport);
this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);
this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);
this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport);
https://bitbucket.org/galaxy/galaxy-central/commits/a7837763dbaf/
Changeset: a7837763dbaf
User: jgoecks
Date: 2013-10-13 21:39:08
Summary: Trackster: simplify constructor and config logic using object attributes.
Affected #: 1 file
diff -r 5b1e3adfafb419eb8b3ec61af04a00604b02712c -r a7837763dbaf2ec540a39c6d0c24bfae5645a1f4 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -208,15 +208,13 @@
this.view = view;
this.container = container;
this.config = new Config({
- track: this,
- params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name }
- ],
- saved_values: obj_dict.prefs,
- onchange: function() {
- this.track.set_name(this.track.config.get('values').name);
- }
+ params: this.config_params,
+ onchange: this.config_onchange,
+ saved_values: obj_dict.prefs
});
+ if (this.config_onchange) {
+ this.config.on('change:values', this.config_onchange, this);
+ }
this.prefs = this.config.get('values');
this.drag_handle_class = obj_dict.drag_handle_class;
this.is_overview = false;
@@ -297,10 +295,20 @@
];
extend(Drawable.prototype, {
+ config_params: [
+ { key: 'name', label: 'Name', type: 'text', default_value: this.name }
+ ],
+
+ config_onchange: function() {
+ this.track.set_name(this.track.config.get('values').name);
+ },
+
init: function() {},
+
changed: function() {
this.view.changed();
},
+
can_draw: function() {
if (this.enabled && this.content_visible) {
return true;
@@ -308,6 +316,7 @@
return false;
},
+
request_draw: function() {},
_draw: function(options) {},
@@ -1909,13 +1918,6 @@
}
this.set('values', values);
-
- // HACK: to make onchange work as written, attach track at the
- // top level of model and call onchange on custom event.
- if (options.onchange) {
- this.track = options.track;
- this.on('change:values', options.onchange, this);
- }
},
/**
@@ -2161,7 +2163,7 @@
canvas = this.html_elt.children()[0],
message_div = $("<div/>").addClass("tile-message")
// -1 to account for border.
- .css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt);
+ .css({'height': ERROR_PADDING, 'width': canvas.width}).prependTo(this.html_elt);
// Handle message; only message currently is that only the first N elements are displayed.
var tile_region = new visualization.GenomeRegion({
@@ -2170,10 +2172,10 @@
end: this.high
}),
num_features = data.length,
- more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down")
+ more_down_icon = $("<a/>").addClass("icon more-down")
.attr("title", "For speed, only the first " + num_features + " features in this region were obtained from server. Click to get more data including depth")
.tooltip().appendTo(message_div),
- more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across")
+ more_across_icon = $("<a/>").addClass("icon more-across")
.attr("title", "For speed, only the first " + num_features + " features in this region were obtained from server. Click to get more data excluding depth")
.tooltip().appendTo(message_div);
@@ -2356,7 +2358,7 @@
// Height attributes: min height, max height, and visible height.
this.min_height_px = 16;
this.max_height_px = 800;
- this.visible_height_px = 0;
+ this.visible_height_px = this.prefs.height;
//
// Create content div, which is where track is displayed, and add to container if available.
@@ -3529,7 +3531,6 @@
* bigwig data for now.
*/
var CompositeTrack = function(view, container, obj_dict) {
- this.display_modes = CONTINUOUS_DATA_MODES;
TiledTrack.call(this, view, container, obj_dict);
// Init drawables; each drawable is a copy so that config/preferences
@@ -3564,6 +3565,8 @@
};
extend(CompositeTrack.prototype, TiledTrack.prototype, {
+ display_modes: CONTINUOUS_DATA_MODES,
+
action_icons_def:
[
// Create composite track from group's tracks.
@@ -3728,7 +3731,6 @@
var ReferenceTrack = function (view) {
TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false });
- this.visible_height_px = 13;
// Use offset to ensure that bases at tile edges are drawn.
this.left_offset = view.canvas_manager.char_width_px;
this.container_div.addClass("reference-track");
@@ -3741,6 +3743,10 @@
this.hide_contents();
};
extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ config_params: [
+ { name: 'height', default: 13 }
+ ],
+
build_header_div: function() {},
init: function() {
@@ -3796,33 +3802,25 @@
* Track displays continuous/numerical data. Track expects position data in 1-based format, i.e. wiggle format.
*/
var LineTrack = function (view, container, obj_dict) {
- var track = this;
- this.display_modes = CONTINUOUS_DATA_MODES;
this.mode = "Histogram";
TiledTrack.call(this, view, container, obj_dict);
-
- // Define track configuration
- this.config = new Config( {
- track: this,
- params: [
+};
+extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ display_modes: CONTINUOUS_DATA_MODES,
+
+ config_params: [
{ key: 'name', label: 'Name', type: 'text', default_value: this.name },
{ key: 'color', label: 'Color', type: 'color', default_value: util.get_random_color() },
{ key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined },
{ key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'height', type: 'int', default_value: 30, hidden: true }
- ],
- saved_values: obj_dict.prefs,
- onchange: function() {
- track.set_name(track.prefs.name);
- track.request_redraw({ clear_tile_cache: true });
- }
- });
-
- this.prefs = this.config.get('values');
- this.visible_height_px = this.prefs.height;
-};
-extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ ],
+
+ config_onchange: function() {
+ this.set_name(this.prefs.name);
+ this.request_draw({ clear_tile_cache: true });
+ },
/**
* Actions to be taken before drawing.
@@ -3854,35 +3852,32 @@
}
});
+/**
+ * Diagonal heatmap for showing interactions data.
+ */
var DiagonalHeatmapTrack = function (view, container, obj_dict) {
- var track = this;
- this.display_modes = ["Heatmap"];
this.mode = "Heatmap";
TiledTrack.call(this, view, container, obj_dict);
-
- // Define track configuration
- this.config = new Config( {
- track: this,
- params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
- { key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
- { key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
- { key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 },
- { key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 },
- { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
- { key: 'height', type: 'int', default_value: 500, hidden: true }
- ],
- saved_values: obj_dict.prefs,
- onchange: function() {
- track.set_name(track.prefs.name);
- this.request_redraw({ clear_tile_cache: true });
- }
- });
-
- this.prefs = this.config.get('values');
- this.visible_height_px = this.prefs.height;
};
+
extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ display_modes: ["Heatmap"],
+
+ config_params: [
+ { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
+ { key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
+ { key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 },
+ { key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 },
+ { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
+ { key: 'height', type: 'int', default_value: 500, hidden: true }
+ ],
+
+ config_onchange: function() {
+ this.set_name(this.prefs.name);
+ this.request_draw({ clear_tile_cache: true });
+ },
+
/**
* Draw tile.
*/
@@ -3900,51 +3895,8 @@
* A track that displays features/regions. Track expects position data in BED format, i.e. 0-based, half-open.
*/
var FeatureTrack = function(view, container, obj_dict) {
- //
- // Preinitialization: do things that need to be done before calling Track and TiledTrack
- // initialization code.
- //
- var track = this;
- this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
-
- //
- // Initialization.
- //
TiledTrack.call(this, view, container, obj_dict);
-
- // Define and restore track configuration.
- var
- block_color = util.get_random_color(),
- reverse_strand_color = util.get_random_color( [ block_color, "#FFFFFF" ] );
- this.config = new Config( {
- track: this,
- params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
- { key: 'block_color', label: 'Block color', type: 'color', default_value: block_color },
- { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color },
- { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
- { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true,
- help: 'Show the number of items in each bin when drawing summary histogram' },
- { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
- { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
- { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones',
- options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
- { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
- { key: 'height', type: 'int', default_value: this.visible_height_px, hidden: true}
- ],
- saved_values: obj_dict.prefs,
- onchange: function() {
- track.set_name(track.prefs.name);
- track.set_painter_from_config();
- track.request_draw({ clear_tile_cache: true });
- }
- });
- this.prefs = this.config.get('values');
- this.visible_height_px = this.prefs.height;
-
this.container_div.addClass( "feature-track" );
- this.show_labels_scale = 0.001;
- this.showing_details = false;
this.summary_draw_height = 30;
this.slotters = {};
this.start_end_dct = {};
@@ -3954,6 +3906,28 @@
this.set_painter_from_config();
};
extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
+
+ config_params: [
+ { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'block_color', label: 'Block color', type: 'color', default_value: util.get_random_color() },
+ { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
+ { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
+ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true,
+ help: 'Show the number of items in each bin when drawing summary histogram' },
+ { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+ { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+ { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones',
+ options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
+ { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
+ { key: 'height', type: 'int', default_value: 0, hidden: true}
+ ],
+
+ config_onchange: function() {
+ this.set_name(this.prefs.name);
+ this.set_painter_from_config();
+ this.request_draw({ clear_tile_cache: true });
+ },
set_painter_from_config: function() {
if ( this.config.get('values').connector_style === 'arcs' ) {
@@ -4221,27 +4195,7 @@
* Displays variant data.
*/
var VariantTrack = function(view, container, obj_dict) {
- this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
TiledTrack.call(this, view, container, obj_dict);
-
- this.config = new Config( {
- track: this,
- params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
- { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() },
- { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true },
- { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true },
- { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 },
- { key: 'mode', type: 'string', default_value: this.mode, hidden: true }
- ],
- saved_values: obj_dict.prefs,
- onchange: function() {
- this.track.set_name(this.track.prefs.name);
- this.track.request_draw({ clear_tile_cache: true });
- }
- });
- this.prefs = this.config.get('values');
-
this.painter = painters.VariantPainter;
this.summary_draw_height = 30;
@@ -4251,6 +4205,22 @@
};
extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
+
+ config_params: [
+ { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() },
+ { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true },
+ { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true },
+ { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 },
+ { key: 'mode', type: 'string', default_value: this.mode, hidden: true }
+ ],
+
+ config_onchange: function() {
+ this.set_name(this.prefs.name);
+ this.request_draw({ clear_tile_cache: true });
+ },
+
/**
* Draw tile.
*/
@@ -4375,39 +4345,32 @@
* Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format.
*/
var ReadTrack = function (view, container, obj_dict) {
- FeatureTrack.call(this, view, container, obj_dict);
-
- var
- block_color = util.get_random_color(),
- reverse_strand_color = util.get_random_color( [ block_color, "#ffffff" ] );
- this.config = new Config( {
- track: this,
- params: [
- { key: 'name', label: 'Name', type: 'text', default_value: this.name },
- { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: block_color },
- { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color },
- { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
- { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
- { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
- { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
- { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
- { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
- { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' }
- ],
- saved_values: obj_dict.prefs,
- onchange: function() {
- this.track.set_name(this.track.prefs.name);
- this.track.request_draw({ clear_tile_cache: true });
- }
- });
- this.prefs = this.config.get('values');
-
+ FeatureTrack.call(this, view, container, obj_dict);
// Choose painter based on whether there is reference data.
this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter);
-
this.update_icons();
};
-extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
+
+extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
+ config_params: [
+ { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: util.get_random_color() },
+ { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
+ { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
+ { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
+ { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
+ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
+ { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
+ { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+ { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+ { key: 'height', type: 'int', default_value: 0, hidden: true}
+ ],
+
+ config_onchange: function() {
+ this.set_name(this.prefs.name);
+ this.request_draw({ clear_tile_cache: true });
+ }
+});
/**
* Objects that can be added to a view.
https://bitbucket.org/galaxy/galaxy-central/commits/5c10579e88db/
Changeset: 5c10579e88db
User: jgoecks
Date: 2013-10-13 21:46:27
Summary: Automated merge.
Affected #: 1 file
diff -r a7837763dbaf2ec540a39c6d0c24bfae5645a1f4 -r 5c10579e88db53ed05013c4314573d3919d72e17 static/scripts/utils/galaxy.uploadbox.js
--- a/static/scripts/utils/galaxy.uploadbox.js
+++ b/static/scripts/utils/galaxy.uploadbox.js
@@ -46,6 +46,9 @@
// element
var el = null;
+ // xml request element
+ var xhr = null;
+
// attach to element
$.fn.uploadbox = function(options)
{
@@ -237,7 +240,7 @@
formData.append(opts.paramname, file, file.name);
// prepare request
- var xhr = new XMLHttpRequest();
+ xhr = new XMLHttpRequest();
// captures state changes
xhr.onreadystatechange = function()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1
0
12 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7eeb3d1065bf/
Changeset: 7eeb3d1065bf
User: guerler
Date: 2013-10-12 19:07:00
Summary: Fix upload box plugin
Affected #: 1 file
diff -r 34ff4b571205e3d28adcf2d553e6aa0c15364d94 -r 7eeb3d1065bf27497a2effeee135cd288edb8218 static/scripts/utils/galaxy.uploadbox.js
--- a/static/scripts/utils/galaxy.uploadbox.js
+++ b/static/scripts/utils/galaxy.uploadbox.js
@@ -46,6 +46,9 @@
// element
var el = null;
+ // xml request element
+ var xhr = null;
+
// attach to element
$.fn.uploadbox = function(options)
{
@@ -237,7 +240,7 @@
formData.append(opts.paramname, file, file.name);
// prepare request
- var xhr = new XMLHttpRequest();
+ xhr = new XMLHttpRequest();
// captures state changes
xhr.onreadystatechange = function()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: JSHint-driven Trackster code cleanup.
by commits-noreply＠bitbucket.org 11 Oct '13
by commits-noreply＠bitbucket.org 11 Oct '13
11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/34ff4b571205/
Changeset: 34ff4b571205
User: jgoecks
Date: 2013-10-11 23:27:18
Summary: JSHint-driven Trackster code cleanup.
Affected #: 1 file
diff -r 1eb4d4077a91914f0f3df70d9ce39d1087744f26 -r 34ff4b571205e3d28adcf2d553e6aa0c15364d94 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -59,10 +59,10 @@
if (container.length !== 0) {
top = container.position().top;
bottom = top + container.outerHeight();
+ var cur_container = html_elt_js_obj_dict[container.attr("id")];
if (d.offsetY < top) {
// Moving above container.
$(this).insertBefore(container);
- var cur_container = html_elt_js_obj_dict[container.attr("id")];
cur_container.remove_drawable(this_obj);
cur_container.container.add_drawable_before(this_obj, cur_container);
return;
@@ -70,7 +70,6 @@
else if (d.offsetY > bottom) {
// Moving below container.
$(this).insertAfter(container);
- var cur_container = html_elt_js_obj_dict[container.attr("id")];
cur_container.remove_drawable(this_obj);
cur_container.container.add_drawable(this_obj);
return;
@@ -368,7 +367,7 @@
*/
add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) {
var drawable = this;
- this.action_icons[name] = $("<a/>").attr("href", "javascript:void(0);").attr("title", title)
+ this.action_icons[name] = $("<a/>").attr("href", "").attr("title", title)
.addClass("icon-button").addClass(css_class).tooltip()
.click( function() { on_click_fn(drawable); } )
.appendTo(this.icons_div);
@@ -943,7 +942,7 @@
// Overview (scrollbar and overview plot) at bottom
this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container);
this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview);
- this.overview_close = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);
+ this.overview_close = $("<a/>").attr("href", "").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);
this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);
this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);
this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport);
@@ -1129,7 +1128,7 @@
},
get_base_color: function(base) {
- return this.config.get('values')[ base.toLowerCase() + '_color' ] || this.config.get('values')[ 'n_color' ];
+ return this.config.get('values')[ base.toLowerCase() + '_color' ] || this.config.get('values').n_color;
}
});
@@ -2246,8 +2245,7 @@
var popup = popups[feature_uid];
if (!popup) {
// Create feature's popup element.
- var feature_uid = feature_data[0],
- feature_dict = {
+ var feature_dict = {
name: feature_data[3],
start: feature_data[1],
end: feature_data[2],
@@ -2263,8 +2261,8 @@
}
// Build popup.
- var popup = $("<div/>").attr("id", feature_uid).addClass("feature-popup"),
- table = $("<table/>"),
+ popup = $("<div/>").attr("id", feature_uid).addClass("feature-popup");
+ var table = $("<table/>"),
key, value, row;
for (key in feature_dict) {
value = feature_dict[key];
@@ -2572,8 +2570,8 @@
// Set modes, init mode.
this.display_modes = new_modes;
this.mode = (init_mode ? init_mode :
- (this.config && this.config.get('values')['mode'] ?
- this.config.get('values')['mode'] : this.display_modes[0])
+ (this.config && this.config.get('values').mode ?
+ this.config.get('values').mode : this.display_modes[0])
);
this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")");
@@ -2927,7 +2925,7 @@
var track = this;
// TODO: is it necessary to store the mode in two places (.mode and track_config)?
track.mode = new_mode;
- track.config.get('values')['mode'] = new_mode;
+ track.config.get('values').mode = new_mode;
// FIXME: find a better way to get Auto data w/o clearing cache; using mode in the
// data manager would work if Auto data were checked for compatibility when a specific
// mode is chosen.
@@ -3045,7 +3043,7 @@
// Draw tiles.
while ( ( tile_index * TILE_SIZE * resolution ) < high ) {
// Get tile region.
- tile_low = Math.floor(tile_index * TILE_SIZE * resolution)
+ tile_low = Math.floor(tile_index * TILE_SIZE * resolution);
tile_region = new visualization.GenomeRegion({
chrom: this.view.chrom,
start: tile_low,
@@ -3089,12 +3087,13 @@
css_class = (type === 'max' ? 'top' : 'bottom'),
text = (type === 'max' ? 'max' : 'min'),
pref_name = (type === 'max' ? 'max_value' : 'min_value'),
- // Default action for on_change is to redraw track.
- on_change = on_change || function() {
- track.request_draw({ clear_tile_cache: true });
- },
label = this.container_div.find(".yaxislabel." + css_class);
+ // Default action for on_change is to redraw track.
+ on_change = on_change || function() {
+ track.request_draw({ clear_tile_cache: true });
+ };
+
if (label.length !== 0) {
// Label already exists, so update value.
label.text(track.prefs[pref_name]);
@@ -3198,8 +3197,6 @@
if (!options) { options = {}; }
var force = options.force,
- // Fetch data as long as data_fetch option is not set to false.
- data_fetch = !( options.data_fetch === false ),
mode = options.mode || this.mode,
resolution = 1 / w_scale,
@@ -3219,7 +3216,7 @@
}
// If not fetching data, nothing more to do because data is needed to draw tile.
- if (!data_fetch) { return null; }
+ if (options.data_fetch === false) { return null; }
// Function that returns data/Deferreds needed to draw tile.
var get_tile_data = function() {
@@ -3696,15 +3693,15 @@
TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
// All tiles must be the same height in order to draw LineTracks, so redraw tiles as needed.
- var max_height = -1;
- for (var i = 0; i < tiles.length; i++) {
+ var max_height = -1, i;
+ for (i = 0; i < tiles.length; i++) {
var height = tiles[i].html_elt.find("canvas").height();
if (height > max_height) {
max_height = height;
}
}
- for (var i = 0; i < tiles.length; i++) {
+ for (i = 0; i < tiles.length; i++) {
var tile = tiles[i];
if (tile.html_elt.find("canvas").height() !== max_height) {
this.draw_helper(tile.region, w_scale, { force: true, height: max_height } );
@@ -3722,6 +3719,9 @@
}
});
+/**
+ * Displays reference genome data.
+ */
var ReferenceTrack = function (view) {
TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false });
@@ -3953,7 +3953,7 @@
extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
set_painter_from_config: function() {
- if ( this.config.get('values')['connector_style'] === 'arcs' ) {
+ if ( this.config.get('values').connector_style === 'arcs' ) {
this.painter = painters.ArcLinkedFeaturePainter;
} else {
this.painter = painters.LinkedFeaturePainter;
@@ -3999,8 +3999,9 @@
// Update filtering UI.
if (track.filters_manager) {
- var filters = track.filters_manager.filters;
- for (var f = 0; f < filters.length; f++) {
+ var filters = track.filters_manager.filters,
+ f;
+ for (f = 0; f < filters.length; f++) {
filters[f].update_ui_elt();
}
@@ -4012,7 +4013,7 @@
for (i = 0; i < tiles.length; i++) {
if (tiles[i].data.length) {
example_feature = tiles[i].data[0];
- for (var f = 0; f < filters.length; f++) {
+ for (f = 0; f < filters.length; f++) {
filter = filters[f];
if ( filter.applies_to(example_feature) &&
filter.min !== filter.max ) {
@@ -4214,7 +4215,7 @@
});
/**
- * Track for displaying variant data.
+ * Displays variant data.
*/
var VariantTrack = function(view, container, obj_dict) {
this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
@@ -4453,5 +4454,4 @@
object_from_template: object_from_template
};
-// End trackster_module encapsulation
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1eb4d4077a91/
Changeset: 1eb4d4077a91
User: jgoecks
Date: 2013-10-11 22:34:28
Summary: More trackster cleanup.
Affected #: 3 files
diff -r 1c714b4bea0794266dfaa10491ff8d80163aee19 -r 1eb4d4077a91914f0f3df70d9ce39d1087744f26 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -145,19 +145,12 @@
* Init constants & functions used throughout trackster.
*/
var
- // Minimum height of a track's contents; this must correspond to the .track-content's minimum height.
- MIN_TRACK_HEIGHT = 16,
- // FIXME: font size may not be static
- CHAR_HEIGHT_PX = 9,
// Padding at the top of tracks for error messages
ERROR_PADDING = 20,
// Maximum number of rows un a slotted track
MAX_FEATURE_DEPTH = 100,
// Minimum width for window for squish to be used.
MIN_SQUISH_VIEW_WIDTH = 12000,
-
- // Other constants.
-
// Number of pixels per tile, not including left offset.
TILE_SIZE = 400,
DEFAULT_DATA_QUERY_WAIT = 5000,
@@ -3732,7 +3725,7 @@
var ReferenceTrack = function (view) {
TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false });
- this.visible_height_px = 12;
+ this.visible_height_px = 13;
// Use offset to ensure that bases at tile edges are drawn.
this.left_offset = view.canvas_manager.char_width_px;
this.container_div.addClass("reference-track");
@@ -4139,7 +4132,7 @@
// HACK: use dummy painter to get required height. Painter should be extended so that get_required_height
// works as a static function.
var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode);
- return Math.max(MIN_TRACK_HEIGHT, dummy_painter.get_required_height(rows_required, canvas_width) );
+ return Math.max(this.min_height_px, dummy_painter.get_required_height(rows_required, canvas_width) );
}
},
diff -r 1c714b4bea0794266dfaa10491ff8d80163aee19 -r 1eb4d4077a91914f0f3df70d9ce39d1087744f26 static/style/blue/trackster.css
--- a/static/style/blue/trackster.css
+++ b/static/style/blue/trackster.css
@@ -42,7 +42,7 @@
.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden}
.label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block}
.label-track .track-content{border:none}
-.reference-track{border:none;margin:0;padding:0}
+.reference-track{border:none;margin:0;padding:0;line-height:1}
.right-float{float:right;margin-left:5px}
.top-labeltrack{position:relative;border-bottom:solid #999 1px}
.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px}
diff -r 1c714b4bea0794266dfaa10491ff8d80163aee19 -r 1eb4d4077a91914f0f3df70d9ce39d1087744f26 static/style/src/less/trackster.less
--- a/static/style/src/less/trackster.less
+++ b/static/style/src/less/trackster.less
@@ -283,6 +283,8 @@
border: none;
margin: 0;
padding: 0;
+ // Override Galaxy defaults.
+ line-height: 1;
}
.right-float {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Fix for removed galaxy.css
by commits-noreply＠bitbucket.org 11 Oct '13
by commits-noreply＠bitbucket.org 11 Oct '13
11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1c714b4bea07/
Changeset: 1c714b4bea07
User: guerler
Date: 2013-10-11 22:09:16
Summary: Fix for removed galaxy.css
Affected #: 6 files
diff -r a221a2734261849a49a0f42af6473d4fed06075d -r 1c714b4bea0794266dfaa10491ff8d80163aee19 static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -82,20 +82,13 @@
},
- // events
- events :
- {
- 'mouseover' : 'event_mouseover',
- 'mouseleave' : 'event_mouseleave'
- },
-
// mouse over
- event_mouseover : function (e)
+ event_dragover : function (e)
{
},
// mouse left
- event_mouseleave : function (e)
+ event_dragleave : function (e)
{
},
@@ -420,8 +413,8 @@
var self = this;
this.uploadbox = this.$el.uploadbox(
{
- dragover : self.event_mouseover,
- dragleave : self.event_mouseleave,
+ dragover : function() { self.event_dragover() },
+ dragleave : function() { self.event_dragleave() },
announce : function(index, file, message) { self.event_announce(index, file, message) },
initialize : function(index, file, message) { return self.event_initialize(index, file, message) },
success : function(index, file, message) { self.event_success(index, file, message) },
diff -r a221a2734261849a49a0f42af6473d4fed06075d -r 1c714b4bea0794266dfaa10491ff8d80163aee19 static/scripts/packed/galaxy.upload.js
--- a/static/scripts/packed/galaxy.upload.js
+++ b/static/scripts/packed/galaxy.upload.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{auto:"Auto-detect"},state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){var f=g[key];e.select_extension[f]=f}})},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(f){},event_mouseleave:function(f){},event_announce:function(f,g,i){var j="#upload-"+f;$(this.el).find("tbody:last").append(this.template_row(j,this.select_extension));var h=this.get_upload_item(f);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var e=this;h.find("#symbol").on("click",function(){e.event_remove(f)});this.event_progress(f,g,0);this.counter.announce++;this.update_screen()},event_initialize:function(g,h,k){this.button_show.number(this.counter.announce);var i=this.get_upload_item(g);var l=i.find("#symbol");l.addClass(this.state.running);var e=Galaxy.currHistoryPanel.model.get("id");var f=i.find("#extension").val();var j=i.find("#space_to_tabs").is(":checked");this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey="?";tool_input.file_type=f;tool_input["files_0|NAME"]=h.name;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=j;data={};data.history_id=e;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refresh()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.upload()},event_pause:function(){if(this.counter.running==0){return}this.uploadbox.pause();$("#upload-info").html("Queueing will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Upload:function(){f.event_upload()},Pause:function(){f.event_pause()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()}},height:"350"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:f.event_mouseover,dragleave:f.event_mouseleave,announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select")}else{this.modal.disableButton("Select")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(g,f){var e='<tr id="'+g.substr(1)+'" class="upload-item"><td><div id="title" class="title"></div></td><td><div id="size" class="size"></div></td><td><select id="extension" class="extension">';for(key in f){e+='<option value="'+key+'">'+f[key]+"</option>"}e+='</select></td><td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
+define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{auto:"Auto-detect"},state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){var f=g[key];e.select_extension[f]=f}})},event_dragover:function(f){},event_dragleave:function(f){},event_announce:function(f,g,i){var j="#upload-"+f;$(this.el).find("tbody:last").append(this.template_row(j,this.select_extension));var h=this.get_upload_item(f);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var e=this;h.find("#symbol").on("click",function(){e.event_remove(f)});this.event_progress(f,g,0);this.counter.announce++;this.update_screen()},event_initialize:function(g,h,k){this.button_show.number(this.counter.announce);var i=this.get_upload_item(g);var l=i.find("#symbol");l.addClass(this.state.running);var e=Galaxy.currHistoryPanel.model.get("id");var f=i.find("#extension").val();var j=i.find("#space_to_tabs").is(":checked");this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey="?";tool_input.file_type=f;tool_input["files_0|NAME"]=h.name;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=j;data={};data.history_id=e;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refresh()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.upload()},event_pause:function(){if(this.counter.running==0){return}this.uploadbox.pause();$("#upload-info").html("Queueing will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Upload:function(){f.event_upload()},Pause:function(){f.event_pause()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()}},height:"350"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select")}else{this.modal.disableButton("Select")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(g,f){var e='<tr id="'+g.substr(1)+'" class="upload-item"><td><div id="title" class="title"></div></td><td><div id="size" class="size"></div></td><td><select id="extension" class="extension">';for(key in f){e+='<option value="'+key+'">'+f[key]+"</option>"}e+='</select></td><td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
diff -r a221a2734261849a49a0f42af6473d4fed06075d -r 1c714b4bea0794266dfaa10491ff8d80163aee19 static/scripts/packed/utils/galaxy.uploadbox.js
--- a/static/scripts/packed/utils/galaxy.uploadbox.js
+++ b/static/scripts/packed/utils/galaxy.uploadbox.js
@@ -1,1 +1,1 @@
-(function(d){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:250,maxfilenumber:20,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(j,k,l){alert(l)},complete:function(){},error_filesize:"File exceeds 250MB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"The server is unavailable.",error_toomany:"You can only queue <20 files per upload session."};var b={};var f={};var g=0;var i=0;var e=false;var a=false;var c=null;d.fn.uploadbox=function(z){b=d.extend({},h,z);c=this;c.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');c.on("drop",m);c.on("dragover",n);c.on("dragleave",u);d("#uploadbox_input").change(function(A){w(A.target.files);d(this).val("")});function m(A){if(!A.dataTransfer){return}w(A.dataTransfer.files);A.preventDefault();return false}function n(A){A.preventDefault();b.dragover.call(A)}function u(A){A.stopPropagation();b.dragleave.call(A)}function j(A){if(A.lengthComputable){b.progress(this.index,this.file,Math.round((A.loaded*100)/A.total))}}function w(C){if(e){return}for(var B=0;B<C.length;B++){if(i>=b.maxfilenumber){break}var A=String(g++);f[A]=C[B];b.announce(A,f[A],"");i++}}function p(A){if(f[A]){delete f[A];i--}}function k(){if(i==0||a){a=false;e=false;b.complete();return}else{e=true}var D=-1;for(var F in f){D=F;break}var E=f[D];p(D);var H=b.initialize(D,E);try{var B=new FileReader();var C=E.size;var A=1048576*b.maxfilesize;B.index=D;if(C<A){B.onload=function(I){o(D,E,H)};B.onerror=function(I){s(D,E,b.error_default)};B.onabort=function(I){s(D,E,b.error_default)};B.readAsDataURL(E)}else{s(D,E,b.error_filesize)}}catch(G){s(D,E,G)}}function o(A,C,D){var E=new FormData();for(var B in D){E.append(B,D[B])}E.append(b.paramname,C,C.name);var F=new XMLHttpRequest();F.onreadystatechange=function(){if(F.readyState!=F.DONE){return}var G=null;if(F.responseText){try{G=jQuery.parseJSON(F.responseText)}catch(H){G=F.responseText}}if(F.status<200||F.status>299){var I=F.statusText;if(!F.statusText){if(F.status==0){I=b.error_server}else{I=b.error_default}}s(A,C,I+" ("+F.status+")")}else{v(A,C,G)}};F.upload.index=A;F.upload.file=C;F.upload.addEventListener("progress",j,false);F.open("POST",b.url,true);F.setRequestHeader("Accept","application/json");F.setRequestHeader("Cache-Control","no-cache");F.setRequestHeader("X-Requested-With","XMLHttpRequest");F.send(E)}function v(A,B,C){b.success(A,B,C);k()}function s(A,B,C){b.error(A,B,C);k()}function t(){d("#uploadbox_input").trigger("click")}function r(A){for(A in f){p(A)}}function y(){if(!e){e=true;k()}}function x(){a=true}function l(A){b=d.extend({},b,A);return b}function q(){return window.File&&window.FileReader&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:t,remove:p,upload:y,pause:x,reset:r,configure:l,compatible:q}}})(jQuery);
\ No newline at end of file
+(function(d){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:2048,maxfilenumber:20,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(j,k,l){alert(l)},complete:function(){},error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"The server is unavailable.",error_toomany:"You can only queue <20 files per upload session."};var b={};var f={};var g=0;var i=0;var e=false;var a=false;var c=null;d.fn.uploadbox=function(z){b=d.extend({},h,z);c=this;c.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');c.on("drop",m);c.on("dragover",n);c.on("dragleave",u);d("#uploadbox_input").change(function(A){w(A.target.files);d(this).val("")});function m(A){if(!A.dataTransfer){return}w(A.dataTransfer.files);A.preventDefault();return false}function n(A){A.preventDefault();b.dragover.call(A)}function u(A){A.stopPropagation();b.dragleave.call(A)}function j(A){if(A.lengthComputable){b.progress(this.index,this.file,Math.round((A.loaded*100)/A.total))}}function w(C){if(e){return}for(var B=0;B<C.length;B++){if(i>=b.maxfilenumber){break}var A=String(g++);f[A]=C[B];b.announce(A,f[A],"");i++}}function p(A){if(f[A]){delete f[A];i--}}function k(){if(i==0||a){a=false;e=false;b.complete();return}else{e=true}var D=-1;for(var F in f){D=F;break}var E=f[D];p(D);var H=b.initialize(D,E);try{var B=new FileReader();var C=E.size;var A=1048576*b.maxfilesize;B.index=D;if(C<A){B.onload=function(I){o(D,E,H)};B.onerror=function(I){s(D,E,b.error_default)};B.onabort=function(I){s(D,E,b.error_default)};B.readAsDataURL(E)}else{s(D,E,b.error_filesize)}}catch(G){s(D,E,G)}}function o(A,C,D){var E=new FormData();for(var B in D){E.append(B,D[B])}E.append(b.paramname,C,C.name);var F=new XMLHttpRequest();F.onreadystatechange=function(){if(F.readyState!=F.DONE){return}var G=null;if(F.responseText){try{G=jQuery.parseJSON(F.responseText)}catch(H){G=F.responseText}}if(F.status<200||F.status>299){var I=F.statusText;if(!F.statusText){if(F.status==0){I=b.error_server}else{I=b.error_default}}s(A,C,I+" ("+F.status+")")}else{v(A,C,G)}};F.upload.index=A;F.upload.file=C;F.upload.addEventListener("progress",j,false);F.open("POST",b.url,true);F.setRequestHeader("Accept","application/json");F.setRequestHeader("Cache-Control","no-cache");F.setRequestHeader("X-Requested-With","XMLHttpRequest");F.send(E)}function v(A,B,C){b.success(A,B,C);k()}function s(A,B,C){b.error(A,B,C);k()}function t(){d("#uploadbox_input").trigger("click")}function r(A){for(A in f){p(A)}}function y(){if(!e){e=true;k()}}function x(){a=true}function l(A){b=d.extend({},b,A);return b}function q(){return window.File&&window.FileReader&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:t,remove:p,upload:y,pause:x,reset:r,configure:l,compatible:q}}})(jQuery);
\ No newline at end of file
diff -r a221a2734261849a49a0f42af6473d4fed06075d -r 1c714b4bea0794266dfaa10491ff8d80163aee19 static/scripts/packed/viz/trackster.js
--- a/static/scripts/packed/viz/trackster.js
+++ b/static/scripts/packed/viz/trackster.js
@@ -1,1 +1,1 @@
-var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("static/style/jquery.rating.css");a.load_file("static/style/autocomplete_tagging.css");a.load_file("static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("static/style/library.css");a.load_file("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}});
\ No newline at end of file
+var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}});
\ No newline at end of file
diff -r a221a2734261849a49a0f42af6473d4fed06075d -r 1c714b4bea0794266dfaa10491ff8d80163aee19 static/scripts/utils/galaxy.uploadbox.js
--- a/static/scripts/utils/galaxy.uploadbox.js
+++ b/static/scripts/utils/galaxy.uploadbox.js
@@ -11,7 +11,7 @@
{
url : '',
paramname : 'content',
- maxfilesize : 250,
+ maxfilesize : 2048,
maxfilenumber : 20,
dragover : function() {},
dragleave : function() {},
@@ -21,7 +21,7 @@
success : function() {},
error : function(index, file, message) { alert(message); },
complete : function() {},
- error_filesize : "File exceeds 250MB. Please use an FTP client.",
+ error_filesize : "File exceeds 2GB. Please use an FTP client.",
error_default : "Please make sure the file is available.",
error_server : "The server is unavailable.",
error_toomany : "You can only queue <20 files per upload session."
diff -r a221a2734261849a49a0f42af6473d4fed06075d -r 1c714b4bea0794266dfaa10491ff8d80163aee19 static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -7,7 +7,7 @@
require(
[
// load js libraries
- 'utils/galaxy.css',
+ 'utils/galaxy.utils',
'libs/jquery/jstorage',
'libs/jquery/jquery.event.drag',
'libs/jquery/jquery.event.hover',
@@ -18,14 +18,14 @@
'libs/jquery/jquery.form',
'libs/jquery/jquery.rating',
'mvc/ui'
-], function(css)
+], function(mod_utils)
{
// load css
- css.load_file("static/style/jquery.rating.css");
- css.load_file("static/style/autocomplete_tagging.css");
- css.load_file("static/style/jquery-ui/smoothness/jquery-ui.css");
- css.load_file("static/style/library.css");
- css.load_file("static/style/trackster.css");
+ mod_utils.cssLoadFile("static/style/jquery.rating.css");
+ mod_utils.cssLoadFile("static/style/autocomplete_tagging.css");
+ mod_utils.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");
+ mod_utils.cssLoadFile("static/style/library.css");
+ mod_utils.cssLoadFile("static/style/trackster.css");
});
// trackster viewer
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Better handling of creating peek for tabular files when metadata is missing.
by commits-noreply＠bitbucket.org 11 Oct '13
by commits-noreply＠bitbucket.org 11 Oct '13
11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a221a2734261/
Changeset: a221a2734261
User: dan
Date: 2013-10-11 21:03:13
Summary: Better handling of creating peek for tabular files when metadata is missing.
Affected #: 1 file
diff -r 4eb6fc99fda92e240a1efaaf169c26effa70d429 -r a221a2734261849a49a0f42af6473d4fed06075d lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -33,8 +33,6 @@
MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] )
MetadataElement( name="column_names", default=[], desc="Column names", readonly=True, visible=False, optional=True, no_value=[] )
- def init_meta( self, dataset, copy_from=None ):
- data.Text.init_meta( self, dataset, copy_from=copy_from )
def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 100000, max_guess_type_data_lines = None, **kwd ):
"""
Tries to determine the number of columns as well as those columns that
@@ -199,10 +197,13 @@
if not column_names and dataset.metadata.column_names:
column_names = dataset.metadata.column_names
- column_headers = [None] * dataset.metadata.columns
+ columns = dataset.metadata.columns
+ if columns is None:
+ columns = dataset.metadata.spec.columns.no_value
+ column_headers = [None] * columns
# fill in empty headers with data from column_names
- for i in range( min( dataset.metadata.columns, len( column_names ) ) ):
+ for i in range( min( columns, len( column_names ) ) ):
if column_headers[i] is None and column_names[i] is not None:
column_headers[i] = column_names[i]
@@ -213,7 +214,7 @@
i = int( getattr( dataset.metadata, name ) ) - 1
except:
i = -1
- if 0 <= i < dataset.metadata.columns and column_headers[i] is None:
+ if 0 <= i < columns and column_headers[i] is None:
column_headers[i] = column_parameter_alias.get(name, name)
out.append( '<tr>' )
@@ -236,13 +237,16 @@
try:
if not dataset.peek:
dataset.set_peek()
+ columns = dataset.metadata.columns
+ if columns is None:
+ columns = dataset.metadata.spec.columns.no_value
for line in dataset.peek.splitlines():
if line.startswith( tuple( skipchars ) ):
out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) )
elif line:
elems = line.split( '\t' )
# we may have an invalid comment line or invalid data
- if len( elems ) != dataset.metadata.columns:
+ if len( elems ) != columns:
out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) )
else:
out.append( '<tr>' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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0
11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4eb6fc99fda9/
Changeset: 4eb6fc99fda9
User: guerler
Date: 2013-10-11 20:58:57
Summary: Deactivate upload icon
Affected #: 1 file
diff -r b694170a3ad6017079a552c91bb2fd89ca1493ad -r 4eb6fc99fda92e240a1efaaf169c26effa70d429 templates/base/base_panels.mako
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -107,7 +107,7 @@
Galaxy.master = new master.GalaxyMaster();
Galaxy.frame_manager = new frame.GalaxyFrameManager();
Galaxy.modal = new modal.GalaxyModal();
- Galaxy.upload = new upload.GalaxyUpload();
+ ##Galaxy.upload = new upload.GalaxyUpload();
});
</script></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Adjustments for IE10, upload front end
by commits-noreply＠bitbucket.org 11 Oct '13
by commits-noreply＠bitbucket.org 11 Oct '13
11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b694170a3ad6/
Changeset: b694170a3ad6
User: guerler
Date: 2013-10-11 20:57:45
Summary: Adjustments for IE10, upload front end
Affected #: 5 files
diff -r 2157b57ca8e49985cc9c0139a9cf771115e12934 -r b694170a3ad6017079a552c91bb2fd89ca1493ad static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -529,7 +529,7 @@
'<th>Size</th>' +
'<th>Type</th>' +
'<th>Space→Tab</th>' +
- '<th>Progress</th>' +
+ '<th>Status</th>' +
'<th></th>' +
'</tr>' +
'</thead>' +
@@ -546,7 +546,7 @@
'<td><div id="title" class="title"></div></td>' +
'<td><div id="size" class="size"></div></td>' +
'<td>' +
- '<select id="extension">';
+ '<select id="extension" class="extension">';
// add file types to selection
for (key in select_extension)
diff -r 2157b57ca8e49985cc9c0139a9cf771115e12934 -r b694170a3ad6017079a552c91bb2fd89ca1493ad static/scripts/packed/galaxy.upload.js
--- a/static/scripts/packed/galaxy.upload.js
+++ b/static/scripts/packed/galaxy.upload.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{auto:"Auto-detect"},state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){var f=g[key];e.select_extension[f]=f}})},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(f){},event_mouseleave:function(f){},event_announce:function(f,g,i){var j="#upload-"+f;$(this.el).find("tbody:last").append(this.template_row(j,this.select_extension));var h=this.get_upload_item(f);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var e=this;h.find("#symbol").on("click",function(){e.event_remove(f)});this.event_progress(f,g,0);this.counter.announce++;this.update_screen()},event_initialize:function(g,h,k){this.button_show.number(this.counter.announce);var i=this.get_upload_item(g);var l=i.find("#symbol");l.addClass(this.state.running);var e=Galaxy.currHistoryPanel.model.get("id");var f=i.find("#extension").val();var j=i.find("#space_to_tabs").is(":checked");this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey="?";tool_input.file_type=f;tool_input["files_0|NAME"]=h.name;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=j;data={};data.history_id=e;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refresh()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.upload()},event_pause:function(){if(this.counter.running==0){return}this.uploadbox.pause();$("#upload-info").html("Queueing will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Upload:function(){f.event_upload()},Pause:function(){f.event_pause()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()}},height:"350"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:f.event_mouseover,dragleave:f.event_mouseleave,announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select")}else{this.modal.disableButton("Select")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Space→Tab</th><th>Progress</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(g,f){var e='<tr id="'+g.substr(1)+'" class="upload-item"><td><div id="title" class="title"></div></td><td><div id="size" class="size"></div></td><td><select id="extension">';for(key in f){e+='<option value="'+key+'">'+f[key]+"</option>"}e+='</select></td><td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
+define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{auto:"Auto-detect"},state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){var f=g[key];e.select_extension[f]=f}})},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(f){},event_mouseleave:function(f){},event_announce:function(f,g,i){var j="#upload-"+f;$(this.el).find("tbody:last").append(this.template_row(j,this.select_extension));var h=this.get_upload_item(f);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var e=this;h.find("#symbol").on("click",function(){e.event_remove(f)});this.event_progress(f,g,0);this.counter.announce++;this.update_screen()},event_initialize:function(g,h,k){this.button_show.number(this.counter.announce);var i=this.get_upload_item(g);var l=i.find("#symbol");l.addClass(this.state.running);var e=Galaxy.currHistoryPanel.model.get("id");var f=i.find("#extension").val();var j=i.find("#space_to_tabs").is(":checked");this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey="?";tool_input.file_type=f;tool_input["files_0|NAME"]=h.name;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=j;data={};data.history_id=e;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refresh()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.upload()},event_pause:function(){if(this.counter.running==0){return}this.uploadbox.pause();$("#upload-info").html("Queueing will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Upload:function(){f.event_upload()},Pause:function(){f.event_pause()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()}},height:"350"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:f.event_mouseover,dragleave:f.event_mouseleave,announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select")}else{this.modal.disableButton("Select")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(g,f){var e='<tr id="'+g.substr(1)+'" class="upload-item"><td><div id="title" class="title"></div></td><td><div id="size" class="size"></div></td><td><select id="extension" class="extension">';for(key in f){e+='<option value="'+key+'">'+f[key]+"</option>"}e+='</select></td><td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
diff -r 2157b57ca8e49985cc9c0139a9cf771115e12934 -r b694170a3ad6017079a552c91bb2fd89ca1493ad static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1125,11 +1125,12 @@
.galaxy-frame .frame .f-pin{left:6px;top:1px}
.galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px}
.upload-info{font-weight:normal;text-align:center}
-.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px}.upload-box .table{width:100%}
+.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%}
.upload-box .table th{text-align:center;white-space:nowrap}
.upload-box .table td{margin:0px;paddign:0px}
-.upload-box .title{width:120px;word-wrap:break-word;font-size:11px}
-.upload-box .size{white-space:nowrap}
+.upload-box .title{width:130px;word-wrap:break-word;font-size:11px}
+.upload-box .extension{width:100px;font-size:11px}
+.upload-box .size{width:60px;white-space:nowrap}
.upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit}
.upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff}
.upload-box .symbol{cursor:pointer}
diff -r 2157b57ca8e49985cc9c0139a9cf771115e12934 -r b694170a3ad6017079a552c91bb2fd89ca1493ad static/style/src/less/upload.less
--- a/static/style/src/less/upload.less
+++ b/static/style/src/less/upload.less
@@ -16,6 +16,8 @@
border-radius : @border-radius-large;
border : 1px dashed @btn-default-border;
padding : 10px;
+ overflow-x : hidden;
+ -ms-overflow-style: none;
.table {
width : 100%;
@@ -32,12 +34,18 @@
}
.title {
- width: 120px;
+ width: 130px;
word-wrap: break-word;
font-size : @font-size-small;
}
+ .extension {
+ width: 100px;
+ font-size : @font-size-small;
+ }
+
.size {
+ width: 60px;
white-space: nowrap;
}
diff -r 2157b57ca8e49985cc9c0139a9cf771115e12934 -r b694170a3ad6017079a552c91bb2fd89ca1493ad templates/base/base_panels.mako
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -107,7 +107,7 @@
Galaxy.master = new master.GalaxyMaster();
Galaxy.frame_manager = new frame.GalaxyFrameManager();
Galaxy.modal = new modal.GalaxyModal();
- ##Galaxy.upload = new upload.GalaxyUpload();
+ Galaxy.upload = new upload.GalaxyUpload();
});
</script></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Add datatypes to api and connect with file type selector of the upload front end
by commits-noreply＠bitbucket.org 11 Oct '13
by commits-noreply＠bitbucket.org 11 Oct '13
11 Oct '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2157b57ca8e4/
Changeset: 2157b57ca8e4
User: guerler
Date: 2013-10-11 20:29:38
Summary: Add datatypes to api and connect with file type selector of the upload front end
Affected #: 14 files
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 lib/galaxy/webapps/galaxy/api/datatypes.py
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -0,0 +1,25 @@
+"""
+API operations allowing clients to determine datatype supported by Galaxy.
+"""
+
+from galaxy import web
+from galaxy.web.base.controller import BaseAPIController
+from galaxy.datatypes.registry import Registry
+
+import logging
+log = logging.getLogger( __name__ )
+
+class DatatypesController( BaseAPIController ):
+ @web.expose_api
+ def index( self, trans, **kwd ):
+ """
+ GET /api/datatypes
+ Return an object containing datatypes.
+ """
+ try:
+ return trans.app.datatypes_registry.upload_file_formats
+
+ except Exception, exception:
+ log.error( 'could not get datatypes: %s', str( exception ), exc_info=True )
+ trans.response.status = 500
+ return { 'error': str( exception ) }
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -162,6 +162,7 @@
webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' )
+ webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api' )
#webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) )
webapp.mapper.resource( 'search', 'search', path_prefix='/api' )
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -3,7 +3,7 @@
*/
// dependencies
-define(["galaxy.modal", "galaxy.master", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_master) {
+define(["galaxy.modal", "galaxy.master", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_master, mod_util) {
// galaxy upload
var GalaxyUpload = Backbone.View.extend(
@@ -69,6 +69,17 @@
// add to master
Galaxy.master.prepend(this.button_show);
+
+ // load extension
+ var self = this;
+ mod_util.jsonFromUrl(galaxy_config.root + "api/datatypes",
+ function(datatypes) {
+ for (key in datatypes) {
+ var filetype = datatypes[key];
+ self.select_extension[filetype] = filetype;
+ }
+ });
+
},
// events
@@ -294,9 +305,20 @@
if (this.counter.running == 0)
return;
- // initiate upload procedure in plugin
+ // request pause
this.uploadbox.pause();
-
+
+ // set html content
+ $('#upload-info').html('Queueing will pause after completing the current file...');
+ },
+
+ // queue is done
+ event_complete: function()
+ {
+ // update running
+ this.counter.running = 0;
+ this.update_screen();
+
// switch icons for new uploads
var items = $(this.el).find('.upload-item');
var self = this;
@@ -314,17 +336,6 @@
$(this).find('#space_to_tabs').attr('disabled', false);
}
});
-
- // set html content
- $('#upload-info').html('Queueing will pause after completing the current file.');
- },
-
- // queue is done
- event_complete: function()
- {
- // update running
- this.counter.running = 0;
- this.update_screen();
},
// remove all
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/packed/galaxy.upload.js
--- a/static/scripts/packed/galaxy.upload.js
+++ b/static/scripts/packed/galaxy.upload.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{auto:"Auto-detect"},state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){var i="#upload-"+e;$(this.el).find("tbody:last").append(this.template_row(i,this.select_extension));var g=this.get_upload_item(e);g.fadeIn();g.find("#title").html(f.name);g.find("#size").html(this.size_to_string(f.size));var d=this;g.find("#symbol").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.counter.announce++;this.update_screen()},event_initialize:function(f,g,j){this.button_show.number(this.counter.announce);var h=this.get_upload_item(f);var k=h.find("#symbol");k.addClass(this.state.running);var d=Galaxy.currHistoryPanel.model.get("id");var e=h.find("#extension").val();var i=h.find("#space_to_tabs").is(":checked");this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey="?";tool_input.file_type=e;tool_input["files_0|NAME"]=g.name;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=i;data={};data.history_id=d;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});if(d!=100){g.find("#percentage").html(d+"%")}else{g.find("#percentage").html("Adding to history...")}},event_success:function(d,e,g){Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var f=this.get_upload_item(d);f.addClass("success");f.find("#percentage").html("100%");var h=f.find("#symbol");h.removeClass(this.state.running);h.removeClass(this.state.queued);h.addClass(this.state.success)},event_error:function(d,e,g){this.event_progress(d,e,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var f=this.get_upload_item(d);f.addClass("danger");f.find(".progress").remove();f.find("#info").html("<strong>Failed: </strong>"+g).show();var h=f.find("#symbol");h.removeClass(this.state.running);h.removeClass(this.state.queued);h.addClass(this.state.error)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var e=$(this.el).find(".upload-item");var d=this;e.each(function(){var f=$(this).find("#symbol");if(f.hasClass(d.state.init)){f.removeClass(d.state.init);f.addClass(d.state.queued);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.upload()},event_pause:function(){if(this.counter.running==0){return}this.uploadbox.pause();var e=$(this.el).find(".upload-item");var d=this;e.each(function(){var f=$(this).find("#symbol");if(f.hasClass(d.state.queued)&&!f.hasClass(d.state.running)){f.removeClass(d.state.queued);f.addClass(d.state.init);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_complete:function(){this.counter.running=0;this.update_screen()},event_reset:function(){if(this.counter.running==0){var d=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){d.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(d){var e=this.get_upload_item(d);var f=e.find("#symbol");if(f.hasClass(this.state.init)||f.hasClass(this.state.success)||f.hasClass(this.state.error)){if(e.hasClass("success")){this.counter.success--}else{if(e.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(d);e.remove()}},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Pause:function(){d.event_pause()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}},height:"350"});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},complete:function(){d.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select")}else{this.modal.disableButton("Select")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(e,d){return'<div id="'+e+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Space→Tab</th><th>Progress</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+d+'" class="upload-info"></h6>'},template_row:function(f,e){var d='<tr id="'+f.substr(1)+'" class="upload-item"><td><div id="title" class="title"></div></td><td><div id="size" class="size"></div></td><td><select id="extension">';for(key in e){d+='<option value="'+key+'">'+e[key]+"</option>"}d+='</select></td><td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return d}});return{GalaxyUpload:a}});
\ No newline at end of file
+define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{auto:"Auto-detect"},state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){var f=g[key];e.select_extension[f]=f}})},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(f){},event_mouseleave:function(f){},event_announce:function(f,g,i){var j="#upload-"+f;$(this.el).find("tbody:last").append(this.template_row(j,this.select_extension));var h=this.get_upload_item(f);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var e=this;h.find("#symbol").on("click",function(){e.event_remove(f)});this.event_progress(f,g,0);this.counter.announce++;this.update_screen()},event_initialize:function(g,h,k){this.button_show.number(this.counter.announce);var i=this.get_upload_item(g);var l=i.find("#symbol");l.addClass(this.state.running);var e=Galaxy.currHistoryPanel.model.get("id");var f=i.find("#extension").val();var j=i.find("#space_to_tabs").is(":checked");this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey="?";tool_input.file_type=f;tool_input["files_0|NAME"]=h.name;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=j;data={};data.history_id=e;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refresh()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.upload()},event_pause:function(){if(this.counter.running==0){return}this.uploadbox.pause();$("#upload-info").html("Queueing will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Upload:function(){f.event_upload()},Pause:function(){f.event_pause()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()}},height:"350"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:f.event_mouseover,dragleave:f.event_mouseleave,announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select")}else{this.modal.disableButton("Select")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Space→Tab</th><th>Progress</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(g,f){var e='<tr id="'+g.substr(1)+'" class="upload-item"><td><div id="title" class="title"></div></td><td><div id="size" class="size"></div></td><td><select id="extension">';for(key in f){e+='<option value="'+key+'">'+f[key]+"</option>"}e+='</select></td><td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/packed/utils/galaxy.css.js
--- a/static/scripts/packed/utils/galaxy.css.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["libs/underscore"],function(a){function b(g,d){var e=$('<div class="'+g+'"></div>');e.appendTo(":eq(0)");var f=e.css(d);e.remove();return f}function c(d){if(!$('link[href^="'+d+'"]').length){$('<link href="'+galaxy_config.root+d+'" rel="stylesheet">').appendTo("head")}}return{load_file:c,get_attribute:b}});
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/packed/utils/galaxy.uploadbox.js
--- a/static/scripts/packed/utils/galaxy.uploadbox.js
+++ b/static/scripts/packed/utils/galaxy.uploadbox.js
@@ -1,1 +1,1 @@
-(function(g){jQuery.event.props.push("dataTransfer");var c={url:"",paramname:"content",maxfilesize:250,maxfilenumber:20,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(i,j,k){alert(k)},complete:function(){},error_filesize:"File exceeds 250MB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_toomany:"You can only queue <20 files per upload session."};var f={};var a={};var b=0;var d=0;var h=false;var e=null;g.fn.uploadbox=function(y){f=g.extend({},c,y);e=this;e.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');e.on("drop",l);e.on("dragover",m);e.on("dragleave",t);g("#uploadbox_input").change(function(z){v(z.target.files);g(this).val("")});function l(z){if(!z.dataTransfer){return}v(z.dataTransfer.files);z.preventDefault();return false}function m(z){z.preventDefault();f.dragover.call(z)}function t(z){z.stopPropagation();f.dragleave.call(z)}function i(z){if(z.lengthComputable){f.progress(this.index,this.file,Math.round((z.loaded*100)/z.total))}}function v(B){if(h){return}for(var A=0;A<B.length;A++){if(d>=f.maxfilenumber){break}var z=String(b++);a[z]=B[A];f.announce(z,a[z],"");d++}}function o(z){if(a[z]){delete a[z];d--}}function j(){if(d==0||!h){h=false;f.complete();return}else{h=true}var C=-1;for(var E in a){C=E;break}var D=a[C];o(C);var G=f.initialize(C,D);try{var A=new FileReader();var B=D.size;var z=1048576*f.maxfilesize;A.index=C;if(B<z){A.onload=function(H){n(C,D,G)};A.onerror=function(H){r(C,D,f.error_default)};A.readAsDataURL(D)}else{r(C,D,f.error_filesize)}}catch(F){r(C,D,F)}}function n(z,B,C){var D=new FormData();for(var A in C){D.append(A,C[A])}D.append(f.paramname,B,B.name);var E=new XMLHttpRequest();E.onloadend=function(){var F=null;if(E.responseText){try{F=jQuery.parseJSON(E.responseText)}catch(G){F=E.responseText}}if(E.status<200||E.status>299){var H=E.statusText;if(!E.statusText){H=f.error_default}r(z,B,H+" (Server Code "+E.status+")")}else{u(z,B,F)}};E.upload.index=z;E.upload.file=B;E.upload.addEventListener("progress",i,false);E.open("POST",f.url,true);E.setRequestHeader("Accept","application/json");E.setRequestHeader("Cache-Control","no-cache");E.setRequestHeader("X-Requested-With","XMLHttpRequest");E.send(D)}function u(z,A,B){f.success(z,A,B);j()}function r(z,A,B){f.error(z,A,B);j()}function s(){g("#uploadbox_input").trigger("click")}function q(z){for(z in a){o(z)}}function x(){if(!h){h=true;j()}}function w(){h=false}function k(z){f=g.extend({},f,z);return f}function p(){return window.File&&window.FileReader&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:s,remove:o,upload:x,pause:w,reset:q,configure:k,compatible:p}}})(jQuery);
\ No newline at end of file
+(function(d){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:250,maxfilenumber:20,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(j,k,l){alert(l)},complete:function(){},error_filesize:"File exceeds 250MB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"The server is unavailable.",error_toomany:"You can only queue <20 files per upload session."};var b={};var f={};var g=0;var i=0;var e=false;var a=false;var c=null;d.fn.uploadbox=function(z){b=d.extend({},h,z);c=this;c.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');c.on("drop",m);c.on("dragover",n);c.on("dragleave",u);d("#uploadbox_input").change(function(A){w(A.target.files);d(this).val("")});function m(A){if(!A.dataTransfer){return}w(A.dataTransfer.files);A.preventDefault();return false}function n(A){A.preventDefault();b.dragover.call(A)}function u(A){A.stopPropagation();b.dragleave.call(A)}function j(A){if(A.lengthComputable){b.progress(this.index,this.file,Math.round((A.loaded*100)/A.total))}}function w(C){if(e){return}for(var B=0;B<C.length;B++){if(i>=b.maxfilenumber){break}var A=String(g++);f[A]=C[B];b.announce(A,f[A],"");i++}}function p(A){if(f[A]){delete f[A];i--}}function k(){if(i==0||a){a=false;e=false;b.complete();return}else{e=true}var D=-1;for(var F in f){D=F;break}var E=f[D];p(D);var H=b.initialize(D,E);try{var B=new FileReader();var C=E.size;var A=1048576*b.maxfilesize;B.index=D;if(C<A){B.onload=function(I){o(D,E,H)};B.onerror=function(I){s(D,E,b.error_default)};B.onabort=function(I){s(D,E,b.error_default)};B.readAsDataURL(E)}else{s(D,E,b.error_filesize)}}catch(G){s(D,E,G)}}function o(A,C,D){var E=new FormData();for(var B in D){E.append(B,D[B])}E.append(b.paramname,C,C.name);var F=new XMLHttpRequest();F.onreadystatechange=function(){if(F.readyState!=F.DONE){return}var G=null;if(F.responseText){try{G=jQuery.parseJSON(F.responseText)}catch(H){G=F.responseText}}if(F.status<200||F.status>299){var I=F.statusText;if(!F.statusText){if(F.status==0){I=b.error_server}else{I=b.error_default}}s(A,C,I+" ("+F.status+")")}else{v(A,C,G)}};F.upload.index=A;F.upload.file=C;F.upload.addEventListener("progress",j,false);F.open("POST",b.url,true);F.setRequestHeader("Accept","application/json");F.setRequestHeader("Cache-Control","no-cache");F.setRequestHeader("X-Requested-With","XMLHttpRequest");F.send(E)}function v(A,B,C){b.success(A,B,C);k()}function s(A,B,C){b.error(A,B,C);k()}function t(){d("#uploadbox_input").trigger("click")}function r(A){for(A in f){p(A)}}function y(){if(!e){e=true;k()}}function x(){a=true}function l(A){b=d.extend({},b,A);return b}function q(){return window.File&&window.FileReader&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:t,remove:p,upload:y,pause:x,reset:r,configure:l,compatible:q}}})(jQuery);
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/packed/utils/galaxy.utils.js
--- /dev/null
+++ b/static/scripts/packed/utils/galaxy.utils.js
@@ -0,0 +1,1 @@
+define(["libs/underscore"],function(c){function d(g,f,e){var h=new XMLHttpRequest();h.open("GET",g,true);h.setRequestHeader("Accept","application/json");h.setRequestHeader("Cache-Control","no-cache");h.setRequestHeader("X-Requested-With","XMLHttpRequest");h.onloadend=function(){var i=h.status;if(i==200){try{response=jQuery.parseJSON(h.responseText)}catch(j){response=h.responseText}f&&f(response)}else{e&&e(i)}};h.send()}function b(h,e){var f=$('<div class="'+h+'"></div>');f.appendTo(":eq(0)");var g=f.css(e);f.remove();return g}function a(e){if(!$('link[href^="'+e+'"]').length){$('<link href="'+galaxy_config.root+e+'" rel="stylesheet">').appendTo("head")}}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:d}});
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ad,y,l,u,M,i,Y,S){var q=ad.extend;var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};var ab=16,H=9,F=20,B=100,J=12000,T=400,L=5000,x=100,o="Cannot display dataset due to an error. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",V="Ready for display",R=10,I=20,C=["Histogram","Line","Filled","Intensity"];function W(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.get("values").name)}});this.prefs=this.config.get("values");this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ae=new a({model:af.config});ae.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ae){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(ae){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw(ae)}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ah){var ae=this.drawables.slice(0),af=[],ag;while(ae.length!==0){ag=ae.shift();if(ag instanceof ah){af.push(ag)}else{if(ag.drawables){ae=ae.concat(ag.drawables)}}}return af}});var Q=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(Q.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw({clear_tile_cache:true})}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof d){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var af=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ae=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ae){A.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){A.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae){ad.each(this.drawables,function(af){af.request_draw(ae)})}});var Z=Backbone.View.extend({initialize:function(ae){q(ae,{obj_type:"View"});A.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ae.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ae.dbkey},function(ai){ad.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_tracks(d),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ae){return this.config.get("values")[ae.toLowerCase()+"_color"]||this.config.get("values")["n_color"]}});q(Z.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=x;var ae=this,af=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){var aj=new D(ae);ae.add_label_track(aj);ae.reference_track=aj}ae.chrom_data=ai.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ah=ae.chrom_data.length;al<ah;al++){var ak=ae.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(ai.prev_chroms){am+='<option value="previous">Previous '+x+"</option>"}if(ai.next_chroms){am+='<option value="next">Next '+x+"</option>"}ae.chrom_select.html(am);ae.chrom_start_index=ai.start_index;af.resolve(ai.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-x});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+x});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af&&al){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/,/g,"");ai=ai.replace(/:|\-/g," ");var af=ai.split(/\s+/),ah=af[0],ag=(af[1]?parseInt(af[1],10):null),ae=(af[2]?parseInt(af[2],10):null);if(!ae){ag=ag-15;ae=ag+15}this.change_chrom(ah,ag,ae)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ae.request_redraw()},200);var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){A.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){A.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(af,ag){var ae=this,ah=(ag?[ag]:ae.drawables);ad.each(ah,function(ai){var aj=ad.find(ae.tracks_to_be_redrawn,function(ak){return ak[0]===ai});if(aj){aj[1]=af}else{ae.tracks_to_be_redrawn.push([ai,af])}});if(!this.requested_redraw){requestAnimationFrame(function(){ae._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ae=this.low,ai=this.high;if(ae<this.max_low){ae=this.max_low}if(ai>this.max_high){ai=this.max_high}var af=this.high-this.low;if(this.high!==0&&af<this.min_separation){ai=ae+this.min_separation}this.low=Math.floor(ae);this.high=Math.ceil(ai);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aj=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=13;this.overview_box.css({left:ah,width:Math.max(ag,aj)}).show();if(aj<ag){this.overview_box.css("left",ah-(ag-aj)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:aj})}ad.each(this.tracks_to_be_redrawn,function(am){var ak=am[0],al=am[1];if(ak){ak._draw(al)}});this.tracks_to_be_redrawn=[];ad.each(this.label_tracks,function(ak){ak._draw()})},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ag.dataset.id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=S.Tool.extend({defaults:{track:null},initialize:function(ae){if(ae.tool_state!==undefined){this.set("hidden",ae.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ae){return ad.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ag=this.$el.addClass("param-row"),ah=this.model;var ae=$("<div>").addClass("param-label").text(ah.get("label")).appendTo(ag);var af=$("<div/>").addClass("param-input").html(ah.get("html")).appendTo(ag);af.find(":input").val(ah.get("value"));$("<div style='clear: both;'/>").appendTo(ag)},update_value:function(ae){this.model.set_value($(ae.target).val())}});var ac=Backbone.View.extend({initialize:function(ae){this.model.on("change:hidden",this.set_visible,this)},render:function(){var af=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).keydown(function(aj){aj.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ak){var aj=new v({model:ak});aj.render();parent_div.append(aj.$el)});parent_div.find("input").click(function(){$(this).select()});var ah=$("<div>").addClass("param-row").appendTo(parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ah);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ah);ae.click(function(){af.run_on_region()});ai.click(function(){af.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},run_on_dataset:function(){var ae=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ae.id},null,function(af){Galaxy.modal.show({title:ae.get("name")+" is Running",body:ae.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var af=this.model.get("track"),ai=this.model,ak=new y.GenomeRegion({chrom:af.view.chrom,start:af.view.low,end:af.view.high}),al={target_dataset_id:af.dataset.id,action:"rerun",tool_id:ai.id,regions:[ak.toJSON()]},aj=af,an=al.tool_id+aj.tool_region_and_parameters_str(ak),ae;if(aj.container===view){var am=new Q(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,am,false);am.container_div.insertBefore(aj.view.content_div.children()[ah]);am.add_drawable(aj);aj.container_div.appendTo(am.content_div);ae=am}else{ae=aj.container}var ag=new aj.constructor(view,ae,{name:an,hda_ldda:"hda"});ag.init_for_tool_data();ag.change_mode(aj.mode);ag.set_filters_manager(aj.filters_manager.copy(ag));ag.update_icons();ae.add_drawable(ag);ag.tiles_div.text("Starting job.");this.run(al,ag,function(ao){ag.set_dataset(new Y.Dataset(ao));ag.tiles_div.text("Running job.");ag.init()})},run:function(ae,ag,ah){ae.inputs=this.model.get_inputs_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(K)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(z+ai.message)}else{ah(ai)}}})}});var E=function(ae,af){M.Scaler.call(this,af);this.filter=ae};E.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(af){var ae={};ad.each(af.params,function(ag){ae[ag.key]=ag.default_value});if(af.saved_values){ad.each(this.get("params"),function(ag){if(ag.key in af.saved_values){ae[ag.key]=af.saved_values[ag.key]}})}this.set("values",ae);if(af.onchange){this.track=af.track;this.on("change:values",af.onchange,this)}},set_param_default_value:function(af,ae){var ag=ad.find(this.get("params"),function(ah){return ah.key===af});if(ag){ag.default_value=ae}},set_param_value:function(ae,af){var ag=ad.find(this.get("params"),function(ah){return ah.key===ae});if(ag){if(typeof af==="string"||af instanceof String){if(af.trim()===""){af=ag.default_value}else{if(ag.type==="float"){af=parseFloat(af)}else{if(ag.type==="int"){af=parseInt(af,10)}}}}}if(this.get("values")[ae]!==af){this.get("values")[ae]=af;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var al=this.model;var ae=$("<div />");var ak;function aj(aq,am){for(var av=0;av<aq.length;av++){ak=aq[av];if(ak.hidden){continue}var ao="param_"+av;var az=al.get("values")[ak.key];var aB=$("<div class='form-row' />").appendTo(am);aB.append($("<label />").attr("for",ao).text(ak.label+":"));if(ak.type==="bool"){aB.append($('<input type="checkbox" />').attr("id",ao).attr("name",ao).attr("checked",az))}else{if(ak.type==="text"){aB.append($('<input type="text"/>').attr("id",ao).val(az).click(function(){$(this).select()}))}else{if(ak.type==="select"){var ax=$("<select />").attr("id",ao);for(var at=0;at<ak.options.length;at++){$("<option/>").text(ak.options[at].label).attr("value",ak.options[at].value).appendTo(ax)}ax.val(az);aB.append(ax)}else{if(ak.type==="color"){var aA=$("<div/>").appendTo(aB),aw=$("<input />").attr("id",ao).attr("name",ao).val(az).css("float","left").appendTo(aA).click(function(aD){$(".tooltip").removeClass("in");var aC=$(this).siblings(".tooltip").addClass("in");aC.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aC).height()/2)+($(this).height()/2)}).show();aC.click(function(aE){aE.stopPropagation()});$(document).bind("click.color-picker",function(){aC.hide();$(document).unbind("click.color-picker")});aD.stopPropagation()}),au=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aA).attr("title","Set new random color").tooltip(),ay=$("<div class='tooltip right' style='position: absolute;' />").appendTo(aA).hide(),ap=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ay),an=$("<div class='tooltip-arrow'></div>").appendTo(ay),ar=$.farbtastic(ap,{width:100,height:100,callback:aw,color:az});aA.append($("<div/>").css("clear","both"));(function(aC){au.click(function(){aC.setColor(l.get_random_color())})})(ar)}else{aB.append($("<input />").attr("id",ao).attr("name",ao).val(az))}}}}if(ak.help){aB.append($("<div class='help'/>").text(ak.help))}}}aj(al.get("params"),ae);var af=this,ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ag=function(){af.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ah=function(am){if((am.keyCode||am.which)===27){ai()}else{if((am.keyCode||am.which)===13){ag()}}};$(window).bind("keypress.check_enter_esc",ah);Galaxy.modal.show({title:"Configure",body:ae,buttons:{Cancel:ai,Ok:ag}})},update_from_form:function(ae){var af=this.model;var ag=false;ad.each(af.get("params"),function(aj,ah){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}ag=af.set_param_value(aj.key,ai)||ag}})}});var c=function(ae,ah,ai,af,ag){this.track=ae;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.w_scale=ai;this.canvas=af;this.html_elt=$("<div class='track-tile'/>").append(af);this.data=ag;this.stale=false};c.prototype.predisplay_actions=function(){};var N=function(ae,ah,ai,af,ag){c.call(this,ae,ah,ai,af,ag)};N.prototype.predisplay_actions=function(){};var P=function(ah,ao,aq,ag,aj,ak,ar,af,an){c.call(this,ah,ao,aq,ag,aj);this.mode=ak;this.all_slotted=af;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F-1,width:ag.width}).prependTo(this.html_elt);var am=new y.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ah.data_manager.get_more_data(am,ah.mode,1/al.w_scale,{},ah.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ah.request_draw()}).dblclick(function(at){at.stopPropagation()});ae.click(function(){al.stale=true;ah.data_manager.get_more_data(am,ah.mode,1/al.w_scale,{},ah.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ah.request_draw()}).dblclick(function(at){at.stopPropagation()})}};q(P.prototype,c.prototype);P.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?W(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=null;if(ag.dataset){this.dataset=(ag.dataset instanceof Backbone.Model?ag.dataset:Y.Dataset.findOrCreate(ag.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:L);this.data_manager=("data_manager" in ag?ag.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:af.dbkey,chroms_info:{chrom_info:af.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.tool.toggle();if(ae.tool.is_visible()){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ad.template(ah,{track:ae});var aj=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ad.map($(".bookmark"),function(ao){return new y.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ag,buttons:{No:aj,Yes:af}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},set_dataset:function(ae){this.dataset=ae;this.data_manager.set("dataset",ae)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.get("values").height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.get("values")["mode"]?this.config.get("values")["mode"]:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof aa){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ag){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.tiles_div.css("height","auto");af.tiles_div.text("").children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset.id){return}var ae=$.Deferred(),ah={hda_ldda:af.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:af.view.chrom,retry:ag};$.getJSON(this.dataset.url(),ah,function(ai){if(!ai||ai==="error"||ai.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ai.message){af.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ai.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));af.tiles_div.append($("<span/>").text(" "));af.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){af.init(true)}))}}else{if(ai==="no converter"){af.container_div.addClass("error");af.tiles_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(G)}else{if(ai==="pending"){af.container_div.addClass("pending");af.tiles_div.html(w);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ai==="data"||ai.status==="data"){if(ai.valid_chroms){af.valid_chroms=ai.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when.apply($,af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){var ae=this;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.dataset.get("hda_ldda")},function(af){ae.container_div.addClass("line-track");var ah=af.data;if(ah&&ah.min&&ah.max){var ag=ah.min,ai=ah.max;ag=Math.floor(Math.min(0,Math.max(ag,ah.mean-2*ah.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ah.mean+2*ah.sd)));ae.config.set_param_default_value("min_value",ag);ae.config.set_param_default_value("max_value",ai);ae.prefs.min_value=ag;ae.prefs.max_value=ai}})},get_drawables:function(){return this}});var O=function(ag,af,ai){g.call(this,ag,af,ai);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ai?ai.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ai.tool?new s(ad.extend(ai.tool,{track:this,tool_state:ai.tool_state})):null);this.tile_cache=new y.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ah=new ac({model:this.tool});ah.render();this.dynamic_tool_div=ah.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ai.mode){this.change_mode(ai.mode)}};q(O.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ae=this;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.dataset.get("hda_ldda")},function(af){var ah=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ah.min,ai=ah.max;ag=Math.floor(Math.min(0,Math.max(ag,ah.mean-2*ah.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ah.mean+2*ah.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ai}})},change_mode:function(af){var ae=this;ae.mode=af;ae.config.get("values")["mode"]=af;if(af==="Auto"){this.data_manager.clear()}ae.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ae){return af+"_"+ae},request_draw:function(ae){if(ae&&ae.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ae,this)},before_draw:function(){this.max_height_px=0},_draw:function(at){if(!this.can_draw()){return}var ap=at&&at.clear_after,an=this.view.low,ai=this.view.high,al=ai-an,af=this.view.container.width(),ar=this.view.resolution_px_b,ah=1/ar;if(this.is_overview){an=this.view.max_low;ai=this.view.max_high;ar=af/(view.max_high-view.max_low);ah=1/ar}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ah*T)),am,ao,aj,ak=[],aq=[];while((ae*T*ah)<ai){am=Math.floor(ae*T*ah);ao=new y.GenomeRegion({chrom:this.view.chrom,start:am,end:Math.min(am+Math.ceil(T*ah),this.view.max_high)});aj=this.draw_helper(ao,ar,at);ak.push(aj);$.when(aj).then(function(au){aq.push(au)});ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ag=this;$.when.apply($,ak).then(function(){ag.tiles_div.children(".remove").remove();aq=ad.filter(aq,function(au){return au!==null});if(aq.length!==0){ag.postdraw_actions(aq,af,ar,ap)}})},_add_yaxis_label:function(ah,aj){var af=this,ai=(ah==="max"?"top":"bottom"),ak=(ah==="max"?"max":"min"),ae=(ah==="max"?"max_value":"min_value"),aj=aj||function(){af.request_draw({clear_tile_cache:true})},ag=this.container_div.find(".yaxislabel."+ai);if(ag.length!==0){ag.text(af.prefs[ae])}else{ag=$("<div/>").text(af.prefs[ae]).make_text_editable({num_cols:12,on_finish:function(al){$(".tooltip").remove();af.config.set_param_value(ae,al);aj()},help_text:"Set "+ak+" value"}).addClass("yaxislabel "+ai).css("color",this.prefs.label_color);this.container_div.prepend(ag)}},postdraw_actions:function(ah,ai,ak,ae){var ag=ad.filter(ah,function(al){return(al instanceof N)});if(ag.length>0){this.max_height_px=0;var af=this;ad.each(ah,function(al){if(!(al instanceof N)){al.html_elt.remove();af.draw_helper(al.region,ak,{force:true,mode:"Coverage"})}});af._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var aj=ad.find(ah,function(al){return al.has_icons});if(aj){ad.each(ah,function(al){if(!al.has_icons){al.html_elt.css("padding-top",F)}})}}},get_mode:function(ae){return this.mode},update_auto_mode:function(ae){},_get_drawables:function(){return[this]},draw_helper:function(an,aq,ar){if(!ar){ar={}}var af=ar.force,ap=!(ar.data_fetch===false),ak=ar.mode||this.mode,ah=1/aq,ag=this,ai=this._get_drawables(),ao=this._gen_tile_cache_key(aq,an),aj=function(at){return(at&&"track" in at)};var al=(af?undefined:ag.tile_cache.get_elt(ao));if(al){if(aj(al)){ag.show_tile(al,aq)}return al}if(!ap){return null}var am=function(){var at=(ad.find(C,function(av){return av===ak})?"Coverage":ak);var au=ad.map(ai,function(av){return av.data_manager.get_data(an,at,ah,ag.data_url_extra_params)});if(view.reference_track){au.push(view.reference_track.data_manager.get_data(an,ak,ah,view.reference_track.data_url_extra_params))}return au};var ae=$.Deferred();ag.tile_cache.set_elt(ao,ae);$.when.apply($,am()).then(function(){var at=am(),ay=at,aE;if(view.reference_track){aE=view.reference_track.data_manager.subset_entry(at.pop(),an)}var az=[],aw=[];ad.each(ai,function(aJ,aG){var aI=aJ.mode,aH=ay[aG];if(aI==="Auto"){aI=aJ.get_mode(aH);aJ.update_auto_mode(aI)}az.push(aI);aw.push(aJ.get_canvas_height(aH,aI,aq,au))});var ax=ag.view.canvas_manager.new_canvas(),aA=an.get("start"),aF=an.get("end"),av=0,au=Math.ceil((aF-aA)*aq)+ag.left_offset,aC=ad.max(aw),aB;ax.width=au;ax.height=(ar.height||aC);var aD=ax.getContext("2d");aD.translate(ag.left_offset,0);if(ai.length>1){aD.globalAlpha=0.5;aD.globalCompositeOperation="source-over"}ad.each(ai,function(aH,aG){aB=aH.draw_tile(ay[aG],aD,az[aG],an,aq,aE)});if(aB!==undefined){ag.tile_cache.set_elt(ao,aB);ag.show_tile(aB,aq)}ae.resolve(aB)});return ae},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},_draw_line_track_tile:function(ae,ag,aj,ai,ak){var ah=ag.canvas,af=new M.LinePainter(ae.data,ai.get("start"),ai.get("end"),this.prefs,aj);af.draw(ag,ah.width,ah.height,ak);return new N(this,ai,ak,ah,ae.data)},draw_tile:function(ae,af,ai,ah,aj,ag){},show_tile:function(ag,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ai=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ai-=this.left_offset}ae.css({position:"absolute",top:0,left:ai});if(ae.hasClass("remove")){ae.removeClass("remove")}else{this.tiles_div.append(ae)}this.max_height_px=Math.max(this.max_height_px,$(ag.canvas).height());ae.parent().children().css("height",this.max_height_px+"px");var ah=this.max_height_px;if(this.visible_height_px!==0){ah=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ah+"px")},tool_region_and_parameters_str:function(ah){var ae=this,ag=(ah!==undefined?ah.toString():"all"),af=ad.values(ae.tool.get_inputs_dict()).join(", ");return" - region=["+ag+"], parameters=["+af+"]"},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="bigwig"}else{if(ae.dataset_type==="bigwig"||ae.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ae){if(ae.message||ae.extra_info==="no_detail"){return false}else{if(ae.dataset_type==="bigwig"){return(ae.data[1][0]-ae.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var X=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ai){var ag=this.view,ah=ag.high-ag.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/al)*al,aj=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var ak=(ae-ag.low)/ah*aj;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:ak-1}));ae+=al}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){this.display_modes=C;O.call(this,af,ae,ai);this.drawables=[];if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}ad.each(this.drawables,function(aj){if(aj instanceof d||aj instanceof U){aj.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,O.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".tooltip").remove();ae.show_group()}}].concat(O.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ae){O.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ah=new Q(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw({clear_tile_cache:true})},before_draw:function(){O.prototype.before_draw.call(this);var af=ad.min(ad.map(this.drawables,function(ag){return ag.prefs.min_value})),ae=ad.max(ad.map(this.drawables,function(ag){return ag.prefs.max_value}));this.prefs.min_value=af;this.prefs.max_value=ae;ad.each(this.drawables,function(ag){ag.prefs.min_value=af;ag.prefs.max_value=ae})},update_all_min_max:function(){var ae=this;ad.each(this.drawables,function(af){af.prefs.min_value=ae.prefs.min_value;af.prefs.max_value=ae.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ak,ae,an,aj){O.prototype.postdraw_actions.call(this,ak,ae,an,aj);var ai=-1;for(var ag=0;ag<ak.length;ag++){var al=ak[ag].html_elt.find("canvas").height();if(al>ai){ai=al}}for(var ag=0;ag<ak.length;ag++){var ah=ak[ag];if(ah.html_elt.find("canvas").height()!==ai){this.draw_helper(ah.region,an,{force:true,height:ai});ah.html_elt.remove()}}var af=this,am=function(){af.update_all_min_max()};this._add_yaxis_label("min",am);this._add_yaxis_label("max",am)}});var D=function(ae){O.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});this.visible_height_px=12;this.left_offset=ae.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,O.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(af,ag,ae){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return O.prototype.draw_helper.call(this,af,ag,ae)}else{this.tiles_div.hide();return null}},can_subset:function(ae){return true},draw_tile:function(ag,am,ah,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ae=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new c(this,aj,an,ae,af)}});var h=function(ag,af,ah){var ae=this;this.display_modes=C;this.mode="Histogram";O.call(this,ag,af,ah);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.visible_height_px=this.prefs.height};q(h.prototype,r.prototype,O.prototype,{before_draw:function(){},draw_tile:function(ae,af,ah,ag,ai){return this._draw_line_track_tile(ae,af,ah,ag,ai)},can_subset:function(ae){return(ae.data[1][0]-ae.data[0][0]===1)},postdraw_actions:function(af,ag,ah,ae){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";O.call(this,ag,af,ah);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.visible_height_px=this.prefs.height};q(t.prototype,r.prototype,O.prototype,{draw_tile:function(ae,ag,aj,ai,ak){var ah=ag.canvas,af=new M.DiagonalHeatmapPainter(ae.data,ai.get("start"),ai.get("end"),this.prefs,aj);af.draw(ag,ah.width,ah.height,ak);return new c(this,ai,ak,ah,ae.data)}});var d=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];O.call(this,ah,ag,aj);var ai=l.get_random_color(),ae=l.get_random_color([ai,"#FFFFFF"]);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.set_painter_from_config();af.request_draw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.visible_height_px=this.prefs.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,O.prototype,{set_painter_from_config:function(){if(this.config.get("values")["connector_style"]==="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(ao,ag,ap,an){O.prototype.postdraw_actions.call(this,ao,ag,ap,an);var ai=this,aj;if(ai.filters_manager){var ah=ai.filters_manager.filters;for(var al=0;al<ah.length;al++){ah[al].update_ui_elt()}var ak=false,am,af;for(aj=0;aj<ao.length;aj++){if(ao[aj].data.length){am=ao[aj].data[0];for(var al=0;al<ah.length;al++){af=ah[al];if(af.applies_to(am)&&af.min!==af.max){ak=true;break}}}}if(ai.filters_available!==ak){ai.filters_available=ak;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}if(ao[0] instanceof P){var ae=true;for(aj=0;aj<ao.length;aj++){if(!ao[aj].all_slotted){ae=false;break}}if(!ae){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,B,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>J){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="Coverage"||ae.dataset_type==="bigwig"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,ah,al,ag){var ar=this,af=at.canvas,az=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(ao.dataset_type==="bigwig"){return this._draw_line_track_tile(ao,at,aq,ah,al)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var au=0,aw=ao.data.length;au<aw;au++){var aj=ao.data[au];var av=false;var an;for(var ay=0,aD=am.length;ay<aD;ay++){an=am[ay];an.update_attrs(aj);if(!an.keep(aj)){av=true;break}}if(!av){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),aB=new (this.painter)(ak,az,ae,this.prefs,aq,aC,aA,ag,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ax=aB.draw(at,af.width,af.height,al,ap);ax.translation=-ai}return new P(ar,ah,al,af,ao.data,aq,ao.message,all_slotted,ax)}});var aa=function(af,ae,ag){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];O.call(this,af,ae,ag);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.painter=M.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(aa.prototype,r.prototype,O.prototype,{draw_tile:function(ae,ah,aj,ai,ak){if(ae.dataset_type==="bigwig"){return this._draw_line_track_tile(ae,ah,"Histogram",ai,ak)}else{var ag=this.view,af=new (this.painter)(ae.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return ag.get_base_color(al)});af.draw(ah,ah.canvas.width,ah.canvas.height,ak);return new c(this,ai,ak,ah.canvas,ae.data)}},get_canvas_height:function(ae,ai,aj,ag){if(ae.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(af===0&&ae.data.length!==0){af=ae.data[0][7].match(/,/g);if(af===null){af=1}else{af=af.length+1}}var ah=new (this.painter)(null,null,null,this.prefs,ai);return ah.get_required_height(af)}},predraw_init:function(){var ae=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ae.push(this.dataset.fetch())}return ae},postdraw_actions:function(ai,aj,al,af){O.prototype.postdraw_actions.call(this,ai,aj,al,af);var ah=ad.filter(ai,function(am){return(am instanceof N)});var ag=this.dataset.get_metadata("sample_names");if(ah.length===0&&this.prefs.show_labels&&ag){var ae;if(this.container_div.find(".yaxislabel.variant").length===0){ae=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ae+"px",top:(this.prefs.summary_height-ae)/2+"px"}));if(this.prefs.show_sample_data){var ak=ag.join("<br/>");this.tiles_div.prepend($("<div/>").html(ak).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ae=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ae,"line-height":ae});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var U=function(ag,af,ai){d.call(this,ag,af,ai);var ah=l.get_random_color(),ae=l.get_random_color([ah,"#ffffff"]);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.painter=(ag.reference_track?M.RefBasedReadPainter:M.ReadPainter);this.update_icons()};q(U.prototype,r.prototype,O.prototype,d.prototype);var e={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:U,VariantTrack:aa,VcfTrack:aa};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new e[ah](af,ae,ag)}};return{TracksterView:Z,DrawableGroup:Q,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:U,VariantTrack:aa,CompositeTrack:f,object_from_template:p}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ad,y,l,u,M,i,Y,S){var q=ad.extend;var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};var ab=16,H=9,F=20,B=100,J=12000,T=400,L=5000,x=100,o="Cannot display dataset due to an error. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",V="Ready for display",R=10,I=20,C=["Histogram","Line","Filled","Intensity"];function W(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.get("values").name)}});this.prefs=this.config.get("values");this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ae=new a({model:af.config});ae.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ae){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(ae){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw(ae)}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ah){var ae=this.drawables.slice(0),af=[],ag;while(ae.length!==0){ag=ae.shift();if(ag instanceof ah){af.push(ag)}else{if(ag.drawables){ae=ae.concat(ag.drawables)}}}return af}});var Q=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(Q.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw({clear_tile_cache:true})}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof d){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var af=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ae=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ae){A.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){A.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae){ad.each(this.drawables,function(af){af.request_draw(ae)})}});var Z=Backbone.View.extend({initialize:function(ae){q(ae,{obj_type:"View"});A.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ae.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ae.dbkey},function(ai){ad.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_tracks(d),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ae){return this.config.get("values")[ae.toLowerCase()+"_color"]||this.config.get("values")["n_color"]}});q(Z.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=x;var ae=this,af=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){var aj=new D(ae);ae.add_label_track(aj);ae.reference_track=aj}ae.chrom_data=ai.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ah=ae.chrom_data.length;al<ah;al++){var ak=ae.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(ai.prev_chroms){am+='<option value="previous">Previous '+x+"</option>"}if(ai.next_chroms){am+='<option value="next">Next '+x+"</option>"}ae.chrom_select.html(am);ae.chrom_start_index=ai.start_index;af.resolve(ai.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-x});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+x});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af&&al){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/,/g,"");ai=ai.replace(/:|\-/g," ");var af=ai.split(/\s+/),ah=af[0],ag=(af[1]?parseInt(af[1],10):null),ae=(af[2]?parseInt(af[2],10):null);if(!ae){ag=ag-15;ae=ag+15}this.change_chrom(ah,ag,ae)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ae.request_redraw()},200);var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){A.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){A.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(af,ag){var ae=this,ah=(ag?[ag]:ae.drawables);ad.each(ah,function(ai){var aj=ad.find(ae.tracks_to_be_redrawn,function(ak){return ak[0]===ai});if(aj){aj[1]=af}else{ae.tracks_to_be_redrawn.push([ai,af])}});if(!this.requested_redraw){requestAnimationFrame(function(){ae._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ae=this.low,ai=this.high;if(ae<this.max_low){ae=this.max_low}if(ai>this.max_high){ai=this.max_high}var af=this.high-this.low;if(this.high!==0&&af<this.min_separation){ai=ae+this.min_separation}this.low=Math.floor(ae);this.high=Math.ceil(ai);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aj=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=13;this.overview_box.css({left:ah,width:Math.max(ag,aj)}).show();if(aj<ag){this.overview_box.css("left",ah-(ag-aj)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:aj})}ad.each(this.tracks_to_be_redrawn,function(am){var ak=am[0],al=am[1];if(ak){ak._draw(al)}});this.tracks_to_be_redrawn=[];ad.each(this.label_tracks,function(ak){ak._draw()})},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ag.dataset.id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=S.Tool.extend({defaults:{track:null},initialize:function(ae){if(ae.tool_state!==undefined){this.set("hidden",ae.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ae){return ad.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ag=this.$el.addClass("param-row"),ah=this.model;var ae=$("<div>").addClass("param-label").text(ah.get("label")).appendTo(ag);var af=$("<div/>").addClass("param-input").html(ah.get("html")).appendTo(ag);af.find(":input").val(ah.get("value"));$("<div style='clear: both;'/>").appendTo(ag)},update_value:function(ae){this.model.set_value($(ae.target).val())}});var ac=Backbone.View.extend({initialize:function(ae){this.model.on("change:hidden",this.set_visible,this)},render:function(){var af=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).keydown(function(aj){aj.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ak){var aj=new v({model:ak});aj.render();parent_div.append(aj.$el)});parent_div.find("input").click(function(){$(this).select()});var ah=$("<div>").addClass("param-row").appendTo(parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ah);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ah);ae.click(function(){af.run_on_region()});ai.click(function(){af.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},run_on_dataset:function(){var ae=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ae.id},null,function(af){Galaxy.modal.show({title:ae.get("name")+" is Running",body:ae.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var af=this.model.get("track"),ai=this.model,ak=new y.GenomeRegion({chrom:af.view.chrom,start:af.view.low,end:af.view.high}),al={target_dataset_id:af.dataset.id,action:"rerun",tool_id:ai.id,regions:[ak.toJSON()]},aj=af,an=al.tool_id+aj.tool_region_and_parameters_str(ak),ae;if(aj.container===view){var am=new Q(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,am,false);am.container_div.insertBefore(aj.view.content_div.children()[ah]);am.add_drawable(aj);aj.container_div.appendTo(am.content_div);ae=am}else{ae=aj.container}var ag=new aj.constructor(view,ae,{name:an,hda_ldda:"hda"});ag.init_for_tool_data();ag.change_mode(aj.mode);ag.set_filters_manager(aj.filters_manager.copy(ag));ag.update_icons();ae.add_drawable(ag);ag.tiles_div.text("Starting job.");this.run(al,ag,function(ao){ag.set_dataset(new Y.Dataset(ao));ag.tiles_div.text("Running job.");ag.init()})},run:function(ae,ag,ah){ae.inputs=this.model.get_inputs_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(K)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(z+ai.message)}else{ah(ai)}}})}});var E=function(ae,af){M.Scaler.call(this,af);this.filter=ae};E.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(af){var ae={};ad.each(af.params,function(ag){ae[ag.key]=ag.default_value});if(af.saved_values){ad.each(this.get("params"),function(ag){if(ag.key in af.saved_values){ae[ag.key]=af.saved_values[ag.key]}})}this.set("values",ae);if(af.onchange){this.track=af.track;this.on("change:values",af.onchange,this)}},set_param_default_value:function(af,ae){var ag=ad.find(this.get("params"),function(ah){return ah.key===af});if(ag){ag.default_value=ae}},set_param_value:function(ae,af){var ag=ad.find(this.get("params"),function(ah){return ah.key===ae});if(ag){if(typeof af==="string"||af instanceof String){if(af.trim()===""){af=ag.default_value}else{if(ag.type==="float"){af=parseFloat(af)}else{if(ag.type==="int"){af=parseInt(af,10)}}}}}if(this.get("values")[ae]!==af){this.get("values")[ae]=af;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var al=this.model;var ae=$("<div />");var ak;function aj(aq,am){for(var av=0;av<aq.length;av++){ak=aq[av];if(ak.hidden){continue}var ao="param_"+av;var az=al.get("values")[ak.key];var aB=$("<div class='form-row' />").appendTo(am);aB.append($("<label />").attr("for",ao).text(ak.label+":"));if(ak.type==="bool"){aB.append($('<input type="checkbox" />').attr("id",ao).attr("name",ao).attr("checked",az))}else{if(ak.type==="text"){aB.append($('<input type="text"/>').attr("id",ao).val(az).click(function(){$(this).select()}))}else{if(ak.type==="select"){var ax=$("<select />").attr("id",ao);for(var at=0;at<ak.options.length;at++){$("<option/>").text(ak.options[at].label).attr("value",ak.options[at].value).appendTo(ax)}ax.val(az);aB.append(ax)}else{if(ak.type==="color"){var aA=$("<div/>").appendTo(aB),aw=$("<input />").attr("id",ao).attr("name",ao).val(az).css("float","left").appendTo(aA).click(function(aD){$(".tooltip").removeClass("in");var aC=$(this).siblings(".tooltip").addClass("in");aC.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aC).height()/2)+($(this).height()/2)}).show();aC.click(function(aE){aE.stopPropagation()});$(document).bind("click.color-picker",function(){aC.hide();$(document).unbind("click.color-picker")});aD.stopPropagation()}),au=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aA).attr("title","Set new random color").tooltip(),ay=$("<div class='tooltip right' style='position: absolute;' />").appendTo(aA).hide(),ap=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ay),an=$("<div class='tooltip-arrow'></div>").appendTo(ay),ar=$.farbtastic(ap,{width:100,height:100,callback:aw,color:az});aA.append($("<div/>").css("clear","both"));(function(aC){au.click(function(){aC.setColor(l.get_random_color())})})(ar)}else{aB.append($("<input />").attr("id",ao).attr("name",ao).val(az))}}}}if(ak.help){aB.append($("<div class='help'/>").text(ak.help))}}}aj(al.get("params"),ae);var af=this,ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ag=function(){af.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ah=function(am){if((am.keyCode||am.which)===27){ai()}else{if((am.keyCode||am.which)===13){ag()}}};$(window).bind("keypress.check_enter_esc",ah);Galaxy.modal.show({title:"Configure",body:ae,buttons:{Cancel:ai,Ok:ag}})},update_from_form:function(ae){var af=this.model;var ag=false;ad.each(af.get("params"),function(aj,ah){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}ag=af.set_param_value(aj.key,ai)||ag}})}});var c=function(ae,ah,ai,af,ag){this.track=ae;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.w_scale=ai;this.canvas=af;this.html_elt=$("<div class='track-tile'/>").append(af);this.data=ag;this.stale=false};c.prototype.predisplay_actions=function(){};var N=function(ae,ah,ai,af,ag){c.call(this,ae,ah,ai,af,ag)};N.prototype.predisplay_actions=function(){};var P=function(ah,ao,aq,ag,aj,ak,ar,af,an){c.call(this,ah,ao,aq,ag,aj);this.mode=ak;this.all_slotted=af;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F-1,width:ag.width}).prependTo(this.html_elt);var am=new y.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ah.data_manager.get_more_data(am,ah.mode,1/al.w_scale,{},ah.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ah.request_draw()}).dblclick(function(at){at.stopPropagation()});ae.click(function(){al.stale=true;ah.data_manager.get_more_data(am,ah.mode,1/al.w_scale,{},ah.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ah.request_draw()}).dblclick(function(at){at.stopPropagation()})}};q(P.prototype,c.prototype);P.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?W(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"),10)-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"),10)+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=null;if(ag.dataset){this.dataset=(ag.dataset instanceof Backbone.Model?ag.dataset:Y.Dataset.findOrCreate(ag.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:L);this.data_manager=("data_manager" in ag?ag.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:af.dbkey,chroms_info:{chrom_info:af.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.tool.toggle();if(ae.tool.is_visible()){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ad.template(ah,{track:ae});var aj=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ad.map($(".bookmark"),function(ao){return new y.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ag,buttons:{No:aj,Yes:af}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},set_dataset:function(ae){this.dataset=ae;this.data_manager.set("dataset",ae)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.get("values").height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.get("values")["mode"]?this.config.get("values")["mode"]:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof aa){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ag){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.tiles_div.css("height","auto");af.tiles_div.text("").children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset.id){return}var ae=$.Deferred(),ah={hda_ldda:af.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:af.view.chrom,retry:ag};$.getJSON(this.dataset.url(),ah,function(ai){if(!ai||ai==="error"||ai.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ai.message){af.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ai.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));af.tiles_div.append($("<span/>").text(" "));af.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){af.init(true)}))}}else{if(ai==="no converter"){af.container_div.addClass("error");af.tiles_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(G)}else{if(ai==="pending"){af.container_div.addClass("pending");af.tiles_div.html(w);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ai==="data"||ai.status==="data"){if(ai.valid_chroms){af.valid_chroms=ai.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when.apply($,af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){var ae=this;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.dataset.get("hda_ldda")},function(af){ae.container_div.addClass("line-track");var ah=af.data;if(ah&&ah.min&&ah.max){var ag=ah.min,ai=ah.max;ag=Math.floor(Math.min(0,Math.max(ag,ah.mean-2*ah.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ah.mean+2*ah.sd)));ae.config.set_param_default_value("min_value",ag);ae.config.set_param_default_value("max_value",ai);ae.prefs.min_value=ag;ae.prefs.max_value=ai}})},get_drawables:function(){return this}});var O=function(ag,af,ai){g.call(this,ag,af,ai);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ai?ai.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ai.tool?new s(ad.extend(ai.tool,{track:this,tool_state:ai.tool_state})):null);this.tile_cache=new y.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ah=new ac({model:this.tool});ah.render();this.dynamic_tool_div=ah.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ai.mode){this.change_mode(ai.mode)}};q(O.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ae=this;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.dataset.get("hda_ldda")},function(af){var ah=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ah.min,ai=ah.max;ag=Math.floor(Math.min(0,Math.max(ag,ah.mean-2*ah.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ah.mean+2*ah.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ai}})},change_mode:function(af){var ae=this;ae.mode=af;ae.config.get("values")["mode"]=af;if(af==="Auto"){this.data_manager.clear()}ae.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ae){return af+"_"+ae},request_draw:function(ae){if(ae&&ae.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ae,this)},before_draw:function(){this.max_height_px=0},_draw:function(at){if(!this.can_draw()){return}var ap=at&&at.clear_after,an=this.view.low,ai=this.view.high,al=ai-an,af=this.view.container.width(),ar=this.view.resolution_px_b,ah=1/ar;if(this.is_overview){an=this.view.max_low;ai=this.view.max_high;ar=af/(view.max_high-view.max_low);ah=1/ar}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ah*T)),am,ao,aj,ak=[],aq=[];while((ae*T*ah)<ai){am=Math.floor(ae*T*ah);ao=new y.GenomeRegion({chrom:this.view.chrom,start:am,end:Math.min(am+Math.ceil(T*ah),this.view.max_high)});aj=this.draw_helper(ao,ar,at);ak.push(aj);$.when(aj).then(function(au){aq.push(au)});ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ag=this;$.when.apply($,ak).then(function(){ag.tiles_div.children(".remove").remove();aq=ad.filter(aq,function(au){return au!==null});if(aq.length!==0){ag.postdraw_actions(aq,af,ar,ap)}})},_add_yaxis_label:function(ah,aj){var af=this,ai=(ah==="max"?"top":"bottom"),ak=(ah==="max"?"max":"min"),ae=(ah==="max"?"max_value":"min_value"),aj=aj||function(){af.request_draw({clear_tile_cache:true})},ag=this.container_div.find(".yaxislabel."+ai);if(ag.length!==0){ag.text(af.prefs[ae])}else{ag=$("<div/>").text(af.prefs[ae]).make_text_editable({num_cols:12,on_finish:function(al){$(".tooltip").remove();af.config.set_param_value(ae,al);aj()},help_text:"Set "+ak+" value"}).addClass("yaxislabel "+ai).css("color",this.prefs.label_color);this.container_div.prepend(ag)}},postdraw_actions:function(ah,ai,ak,ae){var ag=ad.filter(ah,function(al){return(al instanceof N)});if(ag.length>0){this.max_height_px=0;var af=this;ad.each(ah,function(al){if(!(al instanceof N)){al.html_elt.remove();af.draw_helper(al.region,ak,{force:true,mode:"Coverage"})}});af._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var aj=ad.find(ah,function(al){return al.has_icons});if(aj){ad.each(ah,function(al){if(!al.has_icons){al.html_elt.css("padding-top",F)}})}}},get_mode:function(ae){return this.mode},update_auto_mode:function(ae){},_get_drawables:function(){return[this]},draw_helper:function(an,aq,ar){if(!ar){ar={}}var af=ar.force,ap=!(ar.data_fetch===false),ak=ar.mode||this.mode,ah=1/aq,ag=this,ai=this._get_drawables(),ao=this._gen_tile_cache_key(aq,an),aj=function(at){return(at&&"track" in at)};var al=(af?undefined:ag.tile_cache.get_elt(ao));if(al){if(aj(al)){ag.show_tile(al,aq)}return al}if(!ap){return null}var am=function(){var at=(ad.find(C,function(av){return av===ak})?"Coverage":ak);var au=ad.map(ai,function(av){return av.data_manager.get_data(an,at,ah,ag.data_url_extra_params)});if(view.reference_track){au.push(view.reference_track.data_manager.get_data(an,ak,ah,view.reference_track.data_url_extra_params))}return au};var ae=$.Deferred();ag.tile_cache.set_elt(ao,ae);$.when.apply($,am()).then(function(){var at=am(),ay=at,aE;if(view.reference_track){aE=view.reference_track.data_manager.subset_entry(at.pop(),an)}var az=[],aw=[];ad.each(ai,function(aJ,aG){var aI=aJ.mode,aH=ay[aG];if(aI==="Auto"){aI=aJ.get_mode(aH);aJ.update_auto_mode(aI)}az.push(aI);aw.push(aJ.get_canvas_height(aH,aI,aq,au))});var ax=ag.view.canvas_manager.new_canvas(),aA=an.get("start"),aF=an.get("end"),av=0,au=Math.ceil((aF-aA)*aq)+ag.left_offset,aC=ad.max(aw),aB;ax.width=au;ax.height=(ar.height||aC);var aD=ax.getContext("2d");aD.translate(ag.left_offset,0);if(ai.length>1){aD.globalAlpha=0.5;aD.globalCompositeOperation="source-over"}ad.each(ai,function(aH,aG){aB=aH.draw_tile(ay[aG],aD,az[aG],an,aq,aE)});if(aB!==undefined){ag.tile_cache.set_elt(ao,aB);ag.show_tile(aB,aq)}ae.resolve(aB)});return ae},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},_draw_line_track_tile:function(ae,ag,aj,ai,ak){var ah=ag.canvas,af=new M.LinePainter(ae.data,ai.get("start"),ai.get("end"),this.prefs,aj);af.draw(ag,ah.width,ah.height,ak);return new N(this,ai,ak,ah,ae.data)},draw_tile:function(ae,af,ai,ah,aj,ag){},show_tile:function(ag,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ai=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ai-=this.left_offset}ae.css({position:"absolute",top:0,left:ai});if(ae.hasClass("remove")){ae.removeClass("remove")}else{this.tiles_div.append(ae)}this.max_height_px=Math.max(this.max_height_px,$(ag.canvas).height());ae.parent().children().css("height",this.max_height_px+"px");var ah=this.max_height_px;if(this.visible_height_px!==0){ah=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ah+"px")},tool_region_and_parameters_str:function(ah){var ae=this,ag=(ah!==undefined?ah.toString():"all"),af=ad.values(ae.tool.get_inputs_dict()).join(", ");return" - region=["+ag+"], parameters=["+af+"]"},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="bigwig"}else{if(ae.dataset_type==="bigwig"||ae.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ae){if(ae.message||ae.extra_info==="no_detail"){return false}else{if(ae.dataset_type==="bigwig"){return(ae.data[1][0]-ae.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var X=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ai){var ag=this.view,ah=ag.high-ag.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/al)*al,aj=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var ak=(ae-ag.low)/ah*aj;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:ak-1}));ae+=al}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){this.display_modes=C;O.call(this,af,ae,ai);this.drawables=[];if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}ad.each(this.drawables,function(aj){if(aj instanceof d||aj instanceof U){aj.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,O.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".tooltip").remove();ae.show_group()}}].concat(O.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ae){O.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ah=new Q(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw({clear_tile_cache:true})},before_draw:function(){O.prototype.before_draw.call(this);var af=ad.min(ad.map(this.drawables,function(ag){return ag.prefs.min_value})),ae=ad.max(ad.map(this.drawables,function(ag){return ag.prefs.max_value}));this.prefs.min_value=af;this.prefs.max_value=ae;ad.each(this.drawables,function(ag){ag.prefs.min_value=af;ag.prefs.max_value=ae})},update_all_min_max:function(){var ae=this;ad.each(this.drawables,function(af){af.prefs.min_value=ae.prefs.min_value;af.prefs.max_value=ae.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ak,ae,an,aj){O.prototype.postdraw_actions.call(this,ak,ae,an,aj);var ai=-1;for(var ag=0;ag<ak.length;ag++){var al=ak[ag].html_elt.find("canvas").height();if(al>ai){ai=al}}for(var ag=0;ag<ak.length;ag++){var ah=ak[ag];if(ah.html_elt.find("canvas").height()!==ai){this.draw_helper(ah.region,an,{force:true,height:ai});ah.html_elt.remove()}}var af=this,am=function(){af.update_all_min_max()};this._add_yaxis_label("min",am);this._add_yaxis_label("max",am)}});var D=function(ae){O.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});this.visible_height_px=12;this.left_offset=ae.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,O.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(af,ag,ae){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return O.prototype.draw_helper.call(this,af,ag,ae)}else{this.tiles_div.hide();return null}},can_subset:function(ae){return true},draw_tile:function(ag,am,ah,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ae=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new c(this,aj,an,ae,af)}});var h=function(ag,af,ah){var ae=this;this.display_modes=C;this.mode="Histogram";O.call(this,ag,af,ah);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.visible_height_px=this.prefs.height};q(h.prototype,r.prototype,O.prototype,{before_draw:function(){},draw_tile:function(ae,af,ah,ag,ai){return this._draw_line_track_tile(ae,af,ah,ag,ai)},can_subset:function(ae){return(ae.data[1][0]-ae.data[0][0]===1)},postdraw_actions:function(af,ag,ah,ae){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";O.call(this,ag,af,ah);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.visible_height_px=this.prefs.height};q(t.prototype,r.prototype,O.prototype,{draw_tile:function(ae,ag,aj,ai,ak){var ah=ag.canvas,af=new M.DiagonalHeatmapPainter(ae.data,ai.get("start"),ai.get("end"),this.prefs,aj);af.draw(ag,ah.width,ah.height,ak);return new c(this,ai,ak,ah,ae.data)}});var d=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];O.call(this,ah,ag,aj);var ai=l.get_random_color(),ae=l.get_random_color([ai,"#FFFFFF"]);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.set_painter_from_config();af.request_draw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.visible_height_px=this.prefs.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,O.prototype,{set_painter_from_config:function(){if(this.config.get("values")["connector_style"]==="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(ao,ag,ap,an){O.prototype.postdraw_actions.call(this,ao,ag,ap,an);var ai=this,aj;if(ai.filters_manager){var ah=ai.filters_manager.filters;for(var al=0;al<ah.length;al++){ah[al].update_ui_elt()}var ak=false,am,af;for(aj=0;aj<ao.length;aj++){if(ao[aj].data.length){am=ao[aj].data[0];for(var al=0;al<ah.length;al++){af=ah[al];if(af.applies_to(am)&&af.min!==af.max){ak=true;break}}}}if(ai.filters_available!==ak){ai.filters_available=ak;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}if(ao[0] instanceof P){var ae=true;for(aj=0;aj<ao.length;aj++){if(!ao[aj].all_slotted){ae=false;break}}if(!ae){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,B,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>J){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="Coverage"||ae.dataset_type==="bigwig"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,ah,al,ag){var ar=this,af=at.canvas,az=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(ao.dataset_type==="bigwig"){return this._draw_line_track_tile(ao,at,aq,ah,al)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var au=0,aw=ao.data.length;au<aw;au++){var aj=ao.data[au];var av=false;var an;for(var ay=0,aD=am.length;ay<aD;ay++){an=am[ay];an.update_attrs(aj);if(!an.keep(aj)){av=true;break}}if(!av){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),aB=new (this.painter)(ak,az,ae,this.prefs,aq,aC,aA,ag,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ax=aB.draw(at,af.width,af.height,al,ap);ax.translation=-ai}return new P(ar,ah,al,af,ao.data,aq,ao.message,all_slotted,ax)}});var aa=function(af,ae,ag){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];O.call(this,af,ae,ag);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.painter=M.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(aa.prototype,r.prototype,O.prototype,{draw_tile:function(ae,ah,aj,ai,ak){if(ae.dataset_type==="bigwig"){return this._draw_line_track_tile(ae,ah,"Histogram",ai,ak)}else{var ag=this.view,af=new (this.painter)(ae.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return ag.get_base_color(al)});af.draw(ah,ah.canvas.width,ah.canvas.height,ak);return new c(this,ai,ak,ah.canvas,ae.data)}},get_canvas_height:function(ae,ai,aj,ag){if(ae.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(af===0&&ae.data.length!==0){af=ae.data[0][7].match(/,/g);if(af===null){af=1}else{af=af.length+1}}var ah=new (this.painter)(null,null,null,this.prefs,ai);return ah.get_required_height(af)}},predraw_init:function(){var ae=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ae.push(this.dataset.fetch())}return ae},postdraw_actions:function(ai,aj,al,af){O.prototype.postdraw_actions.call(this,ai,aj,al,af);var ah=ad.filter(ai,function(am){return(am instanceof N)});var ag=this.dataset.get_metadata("sample_names");if(ah.length===0&&this.prefs.show_labels&&ag){var ae;if(this.container_div.find(".yaxislabel.variant").length===0){ae=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ae+"px",top:(this.prefs.summary_height-ae)/2+"px"}));if(this.prefs.show_sample_data){var ak=ag.join("<br/>");this.tiles_div.prepend($("<div/>").html(ak).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ae=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ae,"line-height":ae});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var U=function(ag,af,ai){d.call(this,ag,af,ai);var ah=l.get_random_color(),ae=l.get_random_color([ah,"#ffffff"]);this.config=new j({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.get("values");this.painter=(ag.reference_track?M.RefBasedReadPainter:M.ReadPainter);this.update_icons()};q(U.prototype,r.prototype,O.prototype,d.prototype);var e={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:U,VariantTrack:aa,VcfTrack:aa};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new e[ah](af,ae,ag)}};return{TracksterView:Z,DrawableGroup:Q,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:U,VariantTrack:aa,CompositeTrack:f,object_from_template:p}});
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){Galaxy.modal.show({title:"Select datasets for new tracks",body:y,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});Galaxy.modal.hide()}}})}})};var j=function(u){return("promise" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_config.root+"static/images"+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!j(C)){var F=this.subset_entry(C,B);this.set(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var E=this.most_recently_added(),B=B.copy();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=Backbone.RelationalModel.extend({relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:i.Dataset}],initialize:function(u){this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}});
\ No newline at end of file
+define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){Galaxy.modal.show({title:"Select datasets for new tracks",body:y,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});Galaxy.modal.hide()}}})}})};var j=function(u){return("promise" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_config.root+"static/images"+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!j(C)){var F=this.subset_entry(C,B);this.set(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){B=B.copy();var E=this.most_recently_added();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=Backbone.RelationalModel.extend({relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:i.Dataset}],initialize:function(u){this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}});
\ No newline at end of file
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/utils/galaxy.css.js
--- a/static/scripts/utils/galaxy.css.js
+++ /dev/null
@@ -1,41 +0,0 @@
-/**
- * Galaxy CSS utilities
-*/
-
-// dependencies
-define(["libs/underscore"], function(_) {
-
-// get css value
-function get_attribute (classname, name)
-{
- // place dummy element
- var el = $('<div class="' + classname + '"></div>');
-
- // required append
- el.appendTo(':eq(0)');
-
- // get value
- var value = el.css(name);
-
- // remove element
- el.remove();
-
- // return css value
- return value;
-}
-
-// load css
-function load_file (url)
-{
- // check if css is already available
- if (!$('link[href^="' + url + '"]').length)
- $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head');
-};
-
-// return
-return {
- load_file : load_file,
- get_attribute : get_attribute
-};
-
-});
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/utils/galaxy.uploadbox.js
--- a/static/scripts/utils/galaxy.uploadbox.js
+++ b/static/scripts/utils/galaxy.uploadbox.js
@@ -41,6 +41,7 @@
// indicates if queue is currently running
var queue_running = false;
+ var queue_pause = false;
// element
var el = null;
@@ -155,8 +156,9 @@
function process()
{
// validate
- if (queue_length == 0 || !queue_running)
+ if (queue_length == 0 || queue_pause)
{
+ queue_pause = false;
queue_running = false;
opts.complete();
return;
@@ -338,8 +340,8 @@
// pause upload process
function pause()
{
- // set global status variable to false
- queue_running = false;
+ // request pause
+ queue_pause = true;
}
// set options
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/scripts/utils/galaxy.utils.js
--- /dev/null
+++ b/static/scripts/utils/galaxy.utils.js
@@ -0,0 +1,73 @@
+/**
+ * Galaxy utilities comprises small functions, which at this point
+ * do not require their own classes/files
+*/
+
+// dependencies
+define(["libs/underscore"], function(_) {
+
+// generic function to recieve json from url
+function jsonFromUrl (url, successHandler, errorHandler) {
+
+ // open url
+ var xhr = new XMLHttpRequest();
+ xhr.open('GET', url, true);
+
+ // configure request
+ xhr.setRequestHeader('Accept', 'application/json');
+ xhr.setRequestHeader('Cache-Control', 'no-cache');
+ xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest');
+
+ // on completion
+ xhr.onloadend = function() {
+ var status = xhr.status;
+ if (status == 200) {
+ try
+ {
+ response = jQuery.parseJSON(xhr.responseText);
+ } catch (e) {
+ response = xhr.responseText;
+ }
+ successHandler && successHandler(response);
+ } else {
+ errorHandler && errorHandler(status);
+ }
+ };
+
+ // submit request
+ xhr.send();
+};
+
+// get css value
+function cssGetAttribute (classname, name) {
+ // place dummy element
+ var el = $('<div class="' + classname + '"></div>');
+
+ // required append
+ el.appendTo(':eq(0)');
+
+ // get value
+ var value = el.css(name);
+
+ // remove element
+ el.remove();
+
+ // return css value
+ return value;
+};
+
+// load css
+function cssLoadFile (url) {
+ // check if css is already available
+ if (!$('link[href^="' + url + '"]').length)
+ $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head');
+};
+
+// return
+return {
+ cssLoadFile : cssLoadFile,
+ cssGetAttribute : cssGetAttribute,
+ jsonFromUrl : jsonFromUrl
+};
+
+});
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1125,10 +1125,10 @@
.galaxy-frame .frame .f-pin{left:6px;top:1px}
.galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px}
.upload-info{font-weight:normal;text-align:center}
-.upload-box{width:100%;height:90%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px}.upload-box .table{width:100%}
+.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px}.upload-box .table{width:100%}
.upload-box .table th{text-align:center;white-space:nowrap}
.upload-box .table td{margin:0px;paddign:0px}
-.upload-box .title{width:150px;word-wrap:break-word;font-size:11px}
+.upload-box .title{width:120px;word-wrap:break-word;font-size:11px}
.upload-box .size{white-space:nowrap}
.upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit}
.upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff}
diff -r ac7e402af32e98cb9a0a1e5d88f75db16dc78281 -r 2157b57ca8e49985cc9c0139a9cf771115e12934 static/style/src/less/upload.less
--- a/static/style/src/less/upload.less
+++ b/static/style/src/less/upload.less
@@ -7,7 +7,7 @@
.upload-box
{
width : 100%;
- height : 90%;
+ height : 95%;
text-align : center;
overflow : scroll;
font-size : @font-size-base;
@@ -32,7 +32,7 @@
}
.title {
- width: 150px;
+ width: 120px;
word-wrap: break-word;
font-size : @font-size-small;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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