commit/galaxy-central: jgoecks: Trackster bug fixes: (a) fix 1-base offset bug in LineTracks; (b) fix overview track resolution calculation; and (c) code cleanup via JSHint.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/fd21bfd6d257/
changeset: fd21bfd6d257
user: jgoecks
date: 2012-07-31 17:55:41
summary: Trackster bug fixes: (a) fix 1-base offset bug in LineTracks; (b) fix overview track resolution calculation; and (c) code cleanup via JSHint.
affected #: 1 file
diff -r eb4206636dd9b385cc84f20b81d61f9ea11727c5 -r fd21bfd6d2577090013e005f20e174b2a1d9f128 static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -3325,8 +3325,7 @@
var TiledTrack = function(view, container, obj_dict) {
Track.call(this, view, container, obj_dict);
- var track = this,
- view = track.view;
+ var track = this;
// Make track moveable.
moveable(track.container_div, track.drag_handle_class, ".group", track);
@@ -3506,8 +3505,8 @@
if (this.is_overview) {
low = this.view.max_low;
high = this.view.max_high;
- resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / TILE_SIZE ) / Math.log(RESOLUTION) ));
- w_scale = width / (view.max_high - view.max_low);
+ resolution = ( view.max_high - view.max_low ) / width;
+ w_scale = 1 / resolution;
}
this.before_draw();
@@ -3558,8 +3557,6 @@
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
- var track = this;
-
//
// If some tiles have icons, set padding of tiles without icons so features and rows align.
//
@@ -3995,19 +3992,19 @@
this.tile_predraw_init();
- var
- canvas = track.view.canvas_manager.new_canvas(),
+ var canvas = track.view.canvas_manager.new_canvas(),
tile_bounds = track._get_tile_bounds(tile_index, resolution),
tile_low = region.get('start'),
tile_high = region.get('end'),
all_data_index = 0,
width = Math.ceil( (tile_high - tile_low) * w_scale ) + this.left_offset,
height = 0,
- track_modes = [];
+ track_modes = [],
+ i;
// Get max height for all tracks and record track modes.
var track_canvas_height = 0;
- for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) {
+ for (i = 0; i < this.drawables.length; i++, all_data_index += 2) {
track = this.drawables[i];
tile_data = all_data[ all_data_index ];
@@ -4035,7 +4032,7 @@
ctx.translate(this.left_offset, 0);
ctx.globalAlpha = 0.5;
ctx.globalCompositeOperation = "source-over";
- for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) {
+ for (i = 0; i < this.drawables.length; i++, all_data_index += 2) {
track = this.drawables[i];
tile_data = all_data[ all_data_index ];
seq_data = all_data[ all_data_index + 1 ];
@@ -4509,12 +4506,13 @@
postdraw_actions: function(tiles, width, w_scale, clear_after) {
TiledTrack.prototype.postdraw_actions.call(this, tiles, clear_after);
- var track = this;
+ var track = this,
+ i;
// If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max.
if (track.mode === "Histogram") {
// Get global max.
- var i, global_max = -1;
+ var global_max = -1;
for (i = 0; i < tiles.length; i++) {
var cur_max = tiles[i].max_val;
if (cur_max > global_max) {
@@ -4547,7 +4545,7 @@
var filters_available = false,
example_feature,
filter;
- for (var i = 0; i < tiles.length; i++) {
+ 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++) {
@@ -4597,7 +4595,7 @@
//
if (first_tile instanceof FeatureTrackTile) {
var all_slotted = true;
- for (var i = 0; i < tiles.length; i++) {
+ for (i = 0; i < tiles.length; i++) {
if (!tiles[i].all_slotted) {
all_slotted = false;
break;
@@ -4671,8 +4669,7 @@
data_interval,
bin_index = 0,
bin_interval = [],
- cur_bin,
- overlap;
+ cur_bin;
// Set bin interval.
var set_bin_interval = function(interval, low, bin_index, bin_size) {
@@ -4790,7 +4787,6 @@
canvas = ctx.canvas,
tile_low = region.get('start'),
tile_high = region.get('end'),
- min_height = 25,
left_offset = this.left_offset;
// Drawing the summary tree (feature coverage histogram)
@@ -5213,7 +5209,7 @@
// Drawing prefs
this.prefs = extend( {}, this.default_prefs, prefs );
this.mode = mode;
-}
+};
Painter.prototype.default_prefs = {};
@@ -5229,13 +5225,12 @@
*/
var SummaryTreePainter = function(data, view_start, view_end, prefs, mode) {
Painter.call(this, data, view_start, view_end, prefs, mode);
-}
+};
SummaryTreePainter.prototype.default_prefs = { show_counts: false };
SummaryTreePainter.prototype.draw = function(ctx, width, height, w_scale) {
var view_start = this.view_start,
- view_range = this.view_end - this.view_start,
points = this.data.data,
max = (this.prefs.histogram_max ? this.prefs.histogram_max : this.data.max),
// Set base Y so that max label and data do not overlap. Base Y is where rectangle bases
@@ -5266,20 +5261,21 @@
}
ctx.restore();
-}
+};
var LinePainter = function(data, view_start, view_end, prefs, mode) {
Painter.call( this, data, view_start, view_end, prefs, mode );
+ var i, len;
if ( this.prefs.min_value === undefined ) {
var min_value = Infinity;
- for (var i = 0, len = this.data.length; i < len; i++) {
+ for (i = 0, len = this.data.length; i < len; i++) {
min_value = Math.min( min_value, this.data[i][1] );
}
this.prefs.min_value = min_value;
}
if ( this.prefs.max_value === undefined ) {
var max_value = -Infinity;
- for (var i = 0, len = this.data.length; i < len; i++) {
+ for (i = 0, len = this.data.length; i < len; i++) {
max_value = Math.max( max_value, this.data[i][1] );
}
this.prefs.max_value = max_value;
@@ -5296,7 +5292,6 @@
vertical_range = max_value - min_value,
height_px = height,
view_start = this.view_start,
- view_range = this.view_end - this.view_start,
mode = this.mode,
data = this.data;
@@ -5329,7 +5324,9 @@
// Paint track.
for (var i = 0, len = data.length; i < len; i++) {
ctx.fillStyle = ctx.strokeStyle = this.prefs.color;
- x_scaled = Math.round((data[i][0] - view_start) * w_scale);
+ // -1 because LineTrack data uses 1-based coordinate system but painter
+ // uses 0-based system.
+ x_scaled = Math.round((data[i][0] - view_start - 1) * w_scale);
y = data[i][1];
var top_overflow = false, bot_overflow = false;
if (y === null) {
@@ -5471,7 +5468,9 @@
extend(FeaturePainter.prototype, {
get_required_height: function(rows_required, width) {
// y_scale is the height per row
- var required_height = y_scale = this.get_row_height(), mode = this.mode;
+ var required_height = this.get_row_height(),
+ y_scale = required_height,
+ mode = this.mode;
// If using a packing mode, need to multiply by the number of slots used
if (mode === "no_detail" || mode === "Squish" || mode === "Pack") {
required_height = rows_required * y_scale;
@@ -5485,7 +5484,7 @@
/** Extra padding after last row of features */
get_bottom_padding: function(width) {
// Pad bottom by half a row, at least 5 px
- return Math.max( Math.round( this.get_row_height() / 2 ), 5 )
+ return Math.max( Math.round( this.get_row_height() / 2 ), 5 );
},
/**
* Draw data on ctx using slots and within the rectangle defined by width and height. Returns
@@ -5499,8 +5498,7 @@
ctx.fillStyle = this.prefs.block_color;
ctx.textAlign = "right";
- var view_range = this.view_end - this.view_start,
- y_scale = this.get_row_height(),
+ var y_scale = this.get_row_height(),
feature_mapper = new FeaturePositionMapper(y_scale),
x_draw_coords;
@@ -5595,7 +5593,7 @@
thickness, y_start, thick_start = null, thick_end = null,
// TODO: is there any reason why block, label color cannot be set at the Painter level?
// For now, assume '.' === '+'
- block_color = block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color);
+ block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color);
label_color = this.prefs.label_color;
// Set global alpha.
@@ -5821,8 +5819,7 @@
*/
draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) {
ctx.textAlign = "center";
- var track = this,
- tile_region = [tile_low, tile_high],
+ var tile_region = [tile_low, tile_high],
base_offset = 0,
seq_offset = 0,
gap = 0,
@@ -5839,7 +5836,7 @@
}
if (!cigar) {
// If no cigar string, then assume all matches
- cigar = [ [0, orig_seq.length] ]
+ cigar = [ [0, orig_seq.length] ];
}
for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) {
var cig = cigar[cig_id],
@@ -6001,8 +5998,8 @@
var item, type, data;
for (var i = 0; i < draw_last.length; i++) {
item = draw_last[i];
- type = item["type"];
- data = item["data"];
+ type = item.type;
+ data = item.data;
if (type === "text") {
ctx.save();
ctx.font = "bold " + ctx.font;
@@ -6154,7 +6151,7 @@
this.alpha = typeof(a) === 'number' ? a : 1;
};
Color.prototype = {
- eval: function () { return this },
+ eval: function () { return this; },
//
// If we have some transparency, the only way to represent it
@@ -6241,7 +6238,8 @@
this.start_value = start_value;
this.end_value = end_value;
this.value_range = end_value - start_value;
-}
+};
+
LinearRamp.prototype.map_value = function( value ) {
value = Math.max( value, this.start_value );
value = Math.min( value, this.end_value );
@@ -6249,7 +6247,7 @@
// HACK: just red for now
// return "hsl(0,100%," + (value * 100) + "%)"
return this.start_color.mix( this.end_color, 1 - value ).toCSS();
-}
+};
var SplitRamp = function( start_color, middle_color, end_color, start_value, end_value ) {
/**
@@ -6259,29 +6257,31 @@
this.negative_ramp = new LinearRamp( middle_color, start_color, 0, -start_value );
this.start_value = start_value;
this.end_value = end_value;
-}
+};
+
SplitRamp.prototype.map_value = function( value ) {
value = Math.max( value, this.start_value );
value = Math.min( value, this.end_value );
if ( value >= 0 ) {
- return this.positive_ramp.map_value( value )
+ return this.positive_ramp.map_value( value );
} else {
- return this.negative_ramp.map_value( -value )
+ return this.negative_ramp.map_value( -value );
}
-}
+};
var DiagonalHeatmapPainter = function(data, view_start, view_end, prefs, mode) {
Painter.call( this, data, view_start, view_end, prefs, mode );
+ var i, len;
if ( this.prefs.min_value === undefined ) {
var min_value = Infinity;
- for (var i = 0, len = this.data.length; i < len; i++) {
+ for (i = 0, len = this.data.length; i < len; i++) {
min_value = Math.min( min_value, this.data[i][5] );
}
this.prefs.min_value = min_value;
}
if ( this.prefs.max_value === undefined ) {
var max_value = -Infinity;
- for (var i = 0, len = this.data.length; i < len; i++) {
+ for (i = 0, len = this.data.length; i < len; i++) {
max_value = Math.max( max_value, this.data[i][5] );
}
this.prefs.max_value = max_value;
@@ -6303,7 +6303,6 @@
value_range = max_value - min_value,
height_px = height,
view_start = this.view_start,
- view_range = this.view_end - this.view_start,
mode = this.mode,
data = this.data,
invsqrt2 = 1 / Math.sqrt(2);
@@ -6312,7 +6311,7 @@
var d, s1, e1, s2, e2, value;
- var scale = function( p ) { return ( p - view_start ) * w_scale };
+ var scale = function( p ) { return ( p - view_start ) * w_scale; };
ctx.save();
@@ -6334,7 +6333,7 @@
e2 = scale( d[5] );
value = d[6];
- ctx.fillStyle = ( ramp.map_value( value ) )
+ ctx.fillStyle = ( ramp.map_value( value ) );
ctx.fillRect( s1, s2, ( e1 - s1 ), ( e2 - s2 ) );
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 2 months
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commit/galaxy-central: dannon: Fix tabular display to serve raw when preview == False, which should resolve external display issues.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/eb4206636dd9/
changeset: eb4206636dd9
user: dannon
date: 2012-07-30 21:54:34
summary: Fix tabular display to serve raw when preview == False, which should resolve external display issues.
affected #: 1 file
diff -r cdf84aee000b28bd73bbae56b31480e9ce5a6a86 -r eb4206636dd9b385cc84f20b81d61f9ea11727c5 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -264,7 +264,7 @@
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None):
#TODO Prevent failure when displaying extremely long > 50kb lines.
- if to_ext:
+ if to_ext or not preview:
return self._serve_raw(trans, dataset, to_ext)
if chunk:
return self.get_chunk(trans, dataset, chunk)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Handle the varying sample ID param name ('id' or 'sample_id') in /requests_admin/manage_datasets
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/cdf84aee000b/
changeset: cdf84aee000b
user: natefoo
date: 2012-07-27 18:39:24
summary: Handle the varying sample ID param name ('id' or 'sample_id') in /requests_admin/manage_datasets
affected #: 1 file
diff -r aedb20d3dd7e9a1e0638c7ffb85d0993c501c30f -r cdf84aee000b28bd73bbae56b31480e9ce5a6a86 lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -198,7 +198,13 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
+ # When this method is called due to a grid operation, the sample ID
+ # will be in the param 'id'. But when this method is called via a
+ # redirect from another method, the ID will be in 'sample_id'. So,
+ # check for 'id' if 'sample_id' is not provided.
sample_id = params.get( 'sample_id', None )
+ if sample_id is None:
+ sample_id = params.get( 'id', None )
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) )
except:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Document user_job_limit
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/aedb20d3dd7e/
changeset: aedb20d3dd7e
user: natefoo
date: 2012-07-27 16:57:29
summary: Document user_job_limit
affected #: 1 file
diff -r 099692958fcaaf9ade3c1fb430aca6860f114fe9 -r aedb20d3dd7e9a1e0638c7ffb85d0993c501c30f universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -640,6 +640,12 @@
# bytes). 0 for no limit.
#output_size_limit = 0
+# Jobs can be held back from submission to a runner if a user already has more
+# jobs queued or running than the number specified below. This prevents a
+# single user from stuffing the queue and preventing other users from being
+# able to run jobs.
+#user_job_limit = None
+
# Clustering Galaxy is not a straightforward process and requires some
# pre-configuration. See the the wiki before attempting to set any of these
# options:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Correct size abbreviation to use uppercase B for bytes.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/099692958fca/
changeset: 099692958fca
user: jgoecks
date: 2012-07-27 11:08:01
summary: Correct size abbreviation to use uppercase B for bytes.
affected #: 1 file
diff -r e3a62476b0cd6eacdff24311860507311fb03808 -r 099692958fcaaf9ade3c1fb430aca6860f114fe9 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -571,13 +571,13 @@
>>> nice_size(100)
'100 bytes'
>>> nice_size(10000)
- '9.8 Kb'
+ '9.8 KB'
>>> nice_size(1000000)
- '976.6 Kb'
+ '976.6 KB'
>>> nice_size(100000000)
- '95.4 Mb'
+ '95.4 MB'
"""
- words = [ 'bytes', 'Kb', 'Mb', 'Gb', 'Tb' ]
+ words = [ 'bytes', 'KB', 'MB', 'GB', 'TB' ]
try:
size = float( size )
except:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 2 new changesets
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5be1bf4605c3/
changeset: 5be1bf4605c3
user: takadonet
date: 2012-06-26 21:16:25
summary: Check for 'run_as' argument in dictionary 'payload' instead of kwargs
affected #: 1 file
diff -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 -r 5be1bf4605c34a96f19c1a49352ad6769e7fb020 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -134,15 +134,15 @@
return error
trans.response.set_content_type( "application/json" )
# Perform api_run_as processing, possibly changing identity
- if 'run_as' in kwargs:
+ if 'payload' in kwargs and 'run_as' in kwargs['payload']:
if not trans.user_can_do_run_as():
error_message = 'User does not have permissions to run jobs as another user'
return error
try:
- decoded_user_id = trans.security.decode_id( kwargs['run_as'] )
+ decoded_user_id = trans.security.decode_id( kwargs['payload']['run_as'] )
except TypeError:
trans.response.status = 400
- return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['run_as'] )
+ return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['payload']['run_as'] )
try:
user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
trans.api_inherit_admin = trans.user_is_admin()
https://bitbucket.org/galaxy/galaxy-central/changeset/e3a62476b0cd/
changeset: e3a62476b0cd
user: natefoo
date: 2012-07-27 08:14:52
summary: Merged in takadonet/galaxy-central (pull request #50)
affected #: 1 file
diff -r 594b69416e8ce8bac101cedc662240d46ac90031 -r e3a62476b0cd6eacdff24311860507311fb03808 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -134,15 +134,15 @@
return error
trans.response.set_content_type( "application/json" )
# Perform api_run_as processing, possibly changing identity
- if 'run_as' in kwargs:
+ if 'payload' in kwargs and 'run_as' in kwargs['payload']:
if not trans.user_can_do_run_as():
error_message = 'User does not have permissions to run jobs as another user'
return error
try:
- decoded_user_id = trans.security.decode_id( kwargs['run_as'] )
+ decoded_user_id = trans.security.decode_id( kwargs['payload']['run_as'] )
except TypeError:
trans.response.status = 400
- return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['run_as'] )
+ return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['payload']['run_as'] )
try:
user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
trans.api_inherit_admin = trans.user_is_admin()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 2 new changesets
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ce3500d71226/
changeset: ce3500d71226
user: JaimeFrey
date: 2012-06-28 21:03:46
summary: Add Condor task runner module, which runs tasks in a local Condor pool.
affected #: 1 file
diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r ce3500d712269f72f1c75a8b618c74d9f030fe82 lib/galaxy/jobs/runners/condor.py
--- /dev/null
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -0,0 +1,387 @@
+import os, sys, logging, threading, time, subprocess, re
+from Queue import Queue, Empty
+
+from galaxy import model
+from galaxy.jobs.runners import BaseJobRunner
+
+from paste.deploy.converters import asbool
+
+import pkg_resources
+
+if sys.version_info[:2] == ( 2, 4 ):
+ pkg_resources.require( "ctypes" )
+
+log = logging.getLogger( __name__ )
+
+__all__ = [ 'CondorJobRunner' ]
+
+drm_template = """#!/bin/sh
+GALAXY_LIB="%s"
+if [ "$GALAXY_LIB" != "None" ]; then
+ if [ -n "$PYTHONPATH" ]; then
+ PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
+ else
+ PYTHONPATH="$GALAXY_LIB"
+ fi
+ export PYTHONPATH
+fi
+cd %s
+%s
+"""
+
+class CondorJobState( object ):
+ def __init__( self ):
+ """
+ Encapsulates state related to a job that is being run via the DRM and
+ that we need to monitor.
+ """
+ self.job_wrapper = None
+ self.job_id = None
+ self.running = False
+ self.failed = False
+ self.job_file = None
+ self.ofile = None
+ self.efile = None
+ self.user_log = None
+ self.user_log_size = 0
+ self.runner_url = None
+
+class CondorJobRunner( BaseJobRunner ):
+ """
+ Job runner backed by a finite pool of worker threads. FIFO scheduling
+ """
+ STOP_SIGNAL = object()
+ def __init__( self, app ):
+ """Initialize this job runner and start the monitor thread"""
+ # Check if drmaa was importable, fail if not
+ self.app = app
+ self.sa_session = app.model.context
+ # 'watched' and 'queue' are both used to keep track of jobs to watch.
+ # 'queue' is used to add new watched jobs, and can be called from
+ # any thread (usually by the 'queue_job' method). 'watched' must only
+ # be modified by the monitor thread, which will move items from 'queue'
+ # to 'watched' and then manage the watched jobs.
+ self.watched = []
+ self.monitor_queue = Queue()
+ self.monitor_thread = threading.Thread( target=self.monitor )
+ self.monitor_thread.start()
+ self.work_queue = Queue()
+ self.work_threads = []
+ nworkers = app.config.cluster_job_queue_workers
+ for i in range( nworkers ):
+ worker = threading.Thread( target=self.run_next )
+ worker.start()
+ self.work_threads.append( worker )
+ log.debug( "%d workers ready" % nworkers )
+
+ def get_native_spec( self, url ):
+ """Get any native DRM arguments specified by the site configuration"""
+ try:
+ return url.split('/')[2] or None
+ except:
+ return None
+
+ def run_next( self ):
+ """
+ Run the next item in the queue (a job waiting to run or finish )
+ """
+ while 1:
+ ( op, obj ) = self.work_queue.get()
+ if op is self.STOP_SIGNAL:
+ return
+ try:
+ if op == 'queue':
+ self.queue_job( obj )
+ elif op == 'finish':
+ self.finish_job( obj )
+ elif op == 'fail':
+ self.fail_job( obj )
+ except:
+ log.exception( "Uncaught exception %sing job" % op )
+ if op == 'queue':
+ obj.fail( "Uncaught exception queueing job", exception=True )
+
+ def queue_job( self, job_wrapper ):
+ """Create job script and submit it to the DRM"""
+
+ try:
+ job_wrapper.prepare()
+ command_line = self.build_command_line( job_wrapper, include_metadata=True )
+ except:
+ job_wrapper.fail( "failure preparing job", exception=True )
+ log.exception("failure running job %s" % job_wrapper.get_id_tag())
+ return
+
+ runner_url = job_wrapper.get_job_runner()
+
+ # This is silly, why would we queue a job with no command line?
+ if not command_line:
+ job_wrapper.finish( '', '' )
+ return
+
+ if job_wrapper.get_state() == model.Job.states.DELETED:
+ log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
+ job_wrapper.cleanup()
+ return
+
+ # Change to queued state immediately
+ job_wrapper.change_state( model.Job.states.QUEUED )
+
+ # define job attributes
+ ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ user_log = "%s/%s.condor.log" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ executable = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ submit_desc = [ ]
+ submit_desc.append( 'universe = vanilla' )
+ submit_desc.append( 'getenv = true' )
+ submit_desc.append( 'executable = ' + executable )
+ submit_desc.append( 'output = ' + ofile )
+ submit_desc.append( 'error = ' + efile )
+ submit_desc.append( 'log = ' + user_log )
+ submit_desc.append( 'notification = NEVER' )
+ submit_desc.append( 'queue' )
+ submit_file = "%s/%s.condor.desc" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+
+ script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line)
+ try:
+ fh = file( executable, "w" )
+ fh.write( script )
+ fh.close()
+ os.chmod( executable, 0750 )
+ except:
+ job_wrapper.fail( "failure preparing job script", exception=True )
+ log.exception("failure running job %s" % job_wrapper.get_id_tag())
+ return
+
+ try:
+ fh = file( submit_file, 'w' )
+ for line in submit_desc:
+ fh.write( line + '\n' )
+ fh.close()
+ except:
+ job_wrapper.fail( "failure writing submit file", exception=True )
+ log.exception("failure running job %s" % job_wrapper.get_id_tag())
+ self.cleanup( ( executable, submit_file ) )
+ return
+
+ # job was deleted while we were preparing it
+ if job_wrapper.get_state() == model.Job.states.DELETED:
+ log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
+ self.cleanup( ( executable, submit_file ) )
+ job_wrapper.cleanup()
+ return
+
+ # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
+ galaxy_id_tag = job_wrapper.get_id_tag()
+
+ log.debug("(%s) submitting file %s" % ( galaxy_id_tag, executable ) )
+ log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) )
+ s_out = ''
+ job_id = None
+ try:
+ submit = subprocess.Popen( ( 'condor_submit', submit_file ), stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
+ s_out, s_err = submit.communicate()
+ if submit.returncode == 0:
+ match = re.search( 'submitted to cluster (\\d+).', s_out )
+ if match is None:
+ s_out = 'Failed to find job id from condor_submit'
+ else:
+ job_id = match.group( 1 )
+ except Exception, e:
+ # TODO Add extra except for OSError?
+ s_out = str(e)
+
+ if job_id is None:
+ log.debug( "condor_submit failed for job %s: %s" % (job_wrapper.get_id_tag(), s_out) )
+ self.cleanup( ( submit_file, executable ) )
+ job_wrapper.fail( "condor_submit failed", exception=True )
+ return
+
+ log.info("(%s) queued as %s" % ( galaxy_id_tag, job_id ) )
+
+ self.cleanup( ( submit_file, ) )
+
+ # store runner information for tracking if Galaxy restarts
+ job_wrapper.set_runner( runner_url, job_id )
+
+ # Store DRM related state information for job
+ drm_job_state = CondorJobState()
+ drm_job_state.job_wrapper = job_wrapper
+ drm_job_state.job_id = job_id
+ drm_job_state.ofile = ofile
+ drm_job_state.efile = efile
+ drm_job_state.job_file = executable
+ drm_job_state.user_log = user_log
+ drm_job_state.running = False
+ drm_job_state.runner_url = runner_url
+
+ # Add to our 'queue' of jobs to monitor
+ self.monitor_queue.put( drm_job_state )
+
+ def monitor( self ):
+ """
+ Watches jobs currently in the PBS queue and deals with state changes
+ (queued to running) and job completion
+ """
+ while 1:
+ # Take any new watched jobs and put them on the monitor list
+ try:
+ while 1:
+ drm_job_state = self.monitor_queue.get_nowait()
+ if drm_job_state is self.STOP_SIGNAL:
+ # TODO: This is where any cleanup would occur
+ #self.ds.exit()
+ # Do we need any cleanup here?
+ return
+ self.watched.append( drm_job_state )
+ except Empty:
+ pass
+ # Iterate over the list of watched jobs and check state
+ self.check_watched_items()
+ # Sleep a bit before the next state check
+ time.sleep( 1 )
+
+ def check_watched_items( self ):
+ """
+ Called by the monitor thread to look at each watched job and deal
+ with state changes.
+ """
+ new_watched = []
+ for drm_job_state in self.watched:
+ job_id = drm_job_state.job_id
+ log_job_id = job_id.zfill(3)
+ galaxy_job_id = drm_job_state.job_wrapper.job_id
+ job_running = False;
+ job_complete = False;
+ job_failed = False;
+ try:
+ if os.stat( drm_job_state.user_log ).st_size == drm_job_state.user_log_size:
+ new_watched.append( drm_job_state )
+ continue
+ with open(drm_job_state.user_log, 'r') as fh:
+ for line in fh:
+ if '001 (' + log_job_id + '.' in line:
+ job_running = True
+ if '004 (' + log_job_id + '.' in line:
+ job_running = False
+ if '007 (' + log_job_id + '.' in line:
+ job_running = False
+ if '005 (' + log_job_id + '.' in line:
+ job_complete = True
+ if '009 (' + log_job_id + '.' in line:
+ job_failed = True
+ drm_job_state.user_log_size = fh.tell()
+ except Exception, e:
+ # so we don't kill the monitor thread
+ log.exception("(%s/%s) Unable to check job status" % ( galaxy_job_id, job_id ) )
+ log.warning("(%s/%s) job will now be errored" % ( galaxy_job_id, job_id ) )
+ drm_job_state.fail_message = "Cluster could not complete job"
+ self.work_queue.put( ( 'fail', drm_job_state ) )
+ continue
+ if job_running and not drm_job_state.running:
+ log.debug("(%s/%s) job is now running" % ( galaxy_job_id, job_id ) )
+ drm_job_state.job_wrapper.change_state( model.Job.states.RUNNING )
+ if not job_running and drm_job_state.running:
+ log.debug("(%s/%s) job has stopped running" % ( galaxy_job_id, job_id ) )
+ # Will switching from RUNNING to QUEUED confuse Galaxy?
+ #drm_job_state.job_wrapper.change_state( model.Job.states.QUEUED )
+ if job_complete:
+ log.debug("(%s/%s) job has completed" % ( galaxy_job_id, job_id ) )
+ self.work_queue.put( ( 'finish', drm_job_state ) )
+ continue
+ if job_failed:
+ log.debug("(%s/%s) job failed" % ( galaxy_job_id, job_id ) )
+ drm_job_state.failed = True
+ self.work_queue.put( ( 'finish', drm_job_state ) )
+ continue
+ drm_job_state.runnning = job_running
+ new_watched.append( drm_job_state )
+ # Replace the watch list with the updated version
+ self.watched = new_watched
+
+ def finish_job( self, drm_job_state ):
+ """
+ Get the output/error for a finished job, pass to `job_wrapper.finish`
+ and cleanup all the DRM temporary files.
+ """
+ ofile = drm_job_state.ofile
+ efile = drm_job_state.efile
+ job_file = drm_job_state.job_file
+ # collect the output
+ try:
+ ofh = file(ofile, "r")
+ efh = file(efile, "r")
+ stdout = ofh.read( 32768 )
+ stderr = efh.read( 32768 )
+ except:
+ stdout = ''
+ stderr = 'Job output not returned from cluster'
+ log.debug(stderr)
+
+ try:
+ drm_job_state.job_wrapper.finish( stdout, stderr )
+ except:
+ log.exception("Job wrapper finish method failed")
+
+ # clean up the drm files
+ self.cleanup( ( ofile, efile, job_file, drm_job_state.user_log ) )
+
+ def fail_job( self, drm_job_state ):
+ """
+ Seperated out so we can use the worker threads for it.
+ """
+ self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) )
+ drm_job_state.job_wrapper.fail( drm_job_state.fail_message )
+ self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file, drm_job_state.user_log ) )
+
+ def cleanup( self, files ):
+ if not asbool( self.app.config.get( 'debug', False ) ):
+ for file in files:
+ if os.access( file, os.R_OK ):
+ os.unlink( file )
+
+ def put( self, job_wrapper ):
+ """Add a job to the queue (by job identifier)"""
+ # Change to queued state before handing to worker thread so the runner won't pick it up again
+ job_wrapper.change_state( model.Job.states.QUEUED )
+ self.work_queue.put( ( 'queue', job_wrapper ) )
+
+ def shutdown( self ):
+ """Attempts to gracefully shut down the monitor thread"""
+ log.info( "sending stop signal to worker threads" )
+ self.monitor_queue.put( self.STOP_SIGNAL )
+ for i in range( len( self.work_threads ) ):
+ self.work_queue.put( ( self.STOP_SIGNAL, None ) )
+ log.info( "condor job runner stopped" )
+
+ def stop_job( self, job ):
+ """Attempts to delete a job from the DRM queue"""
+ try:
+ subprocess.check_call( ( 'condor_rm', job.job_runner_external_id ) )
+ log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) )
+ except subprocess.CalledProcessError:
+ log.debug( "(%s/%s) User killed running job, but condor_rm failed" % ( job.id, job.job_runner_external_id ) )
+ except Exception, e:
+ log.debug( "(%s/%s) User killed running job, but error encountered removing from Condor queue: %s" % ( job.id, job.job_runner_external_id, e ) )
+
+ def recover( self, job, job_wrapper ):
+ """Recovers jobs stuck in the queued/running state when Galaxy started"""
+ # TODO Check if we need any changes here
+ drm_job_state = CondorJobState()
+ drm_job_state.ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job.id)
+ drm_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id)
+ drm_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id)
+ drm_job_state.job_id = str( job.job_runner_external_id )
+ drm_job_state.runner_url = job_wrapper.get_job_runner()
+ job_wrapper.command_line = job.command_line
+ drm_job_state.job_wrapper = job_wrapper
+ drm_job_state.user_log = "%s/%s.condor.log" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ if job.state == model.Job.states.RUNNING:
+ log.debug( "(%s/%s) is still in running state, adding to the DRM queue" % ( job.id, job.job_runner_external_id ) )
+ drm_job_state.running = True
+ self.monitor_queue.put( drm_job_state )
+ elif job.state == model.Job.states.QUEUED:
+ log.debug( "(%s/%s) is still in DRM queued state, adding to the DRM queue" % ( job.id, job.job_runner_external_id ) )
+ drm_job_state.running = False
+ self.monitor_queue.put( drm_job_state )
https://bitbucket.org/galaxy/galaxy-central/changeset/594b69416e8c/
changeset: 594b69416e8c
user: natefoo
date: 2012-07-26 19:11:05
summary: Merged in JaimeFrey/galaxy-condor (pull request #51)
affected #: 1 file
diff -r 6d23049609a995e2ef7371aa63a7cb8bf6536403 -r 594b69416e8ce8bac101cedc662240d46ac90031 lib/galaxy/jobs/runners/condor.py
--- /dev/null
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -0,0 +1,387 @@
+import os, sys, logging, threading, time, subprocess, re
+from Queue import Queue, Empty
+
+from galaxy import model
+from galaxy.jobs.runners import BaseJobRunner
+
+from paste.deploy.converters import asbool
+
+import pkg_resources
+
+if sys.version_info[:2] == ( 2, 4 ):
+ pkg_resources.require( "ctypes" )
+
+log = logging.getLogger( __name__ )
+
+__all__ = [ 'CondorJobRunner' ]
+
+drm_template = """#!/bin/sh
+GALAXY_LIB="%s"
+if [ "$GALAXY_LIB" != "None" ]; then
+ if [ -n "$PYTHONPATH" ]; then
+ PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
+ else
+ PYTHONPATH="$GALAXY_LIB"
+ fi
+ export PYTHONPATH
+fi
+cd %s
+%s
+"""
+
+class CondorJobState( object ):
+ def __init__( self ):
+ """
+ Encapsulates state related to a job that is being run via the DRM and
+ that we need to monitor.
+ """
+ self.job_wrapper = None
+ self.job_id = None
+ self.running = False
+ self.failed = False
+ self.job_file = None
+ self.ofile = None
+ self.efile = None
+ self.user_log = None
+ self.user_log_size = 0
+ self.runner_url = None
+
+class CondorJobRunner( BaseJobRunner ):
+ """
+ Job runner backed by a finite pool of worker threads. FIFO scheduling
+ """
+ STOP_SIGNAL = object()
+ def __init__( self, app ):
+ """Initialize this job runner and start the monitor thread"""
+ # Check if drmaa was importable, fail if not
+ self.app = app
+ self.sa_session = app.model.context
+ # 'watched' and 'queue' are both used to keep track of jobs to watch.
+ # 'queue' is used to add new watched jobs, and can be called from
+ # any thread (usually by the 'queue_job' method). 'watched' must only
+ # be modified by the monitor thread, which will move items from 'queue'
+ # to 'watched' and then manage the watched jobs.
+ self.watched = []
+ self.monitor_queue = Queue()
+ self.monitor_thread = threading.Thread( target=self.monitor )
+ self.monitor_thread.start()
+ self.work_queue = Queue()
+ self.work_threads = []
+ nworkers = app.config.cluster_job_queue_workers
+ for i in range( nworkers ):
+ worker = threading.Thread( target=self.run_next )
+ worker.start()
+ self.work_threads.append( worker )
+ log.debug( "%d workers ready" % nworkers )
+
+ def get_native_spec( self, url ):
+ """Get any native DRM arguments specified by the site configuration"""
+ try:
+ return url.split('/')[2] or None
+ except:
+ return None
+
+ def run_next( self ):
+ """
+ Run the next item in the queue (a job waiting to run or finish )
+ """
+ while 1:
+ ( op, obj ) = self.work_queue.get()
+ if op is self.STOP_SIGNAL:
+ return
+ try:
+ if op == 'queue':
+ self.queue_job( obj )
+ elif op == 'finish':
+ self.finish_job( obj )
+ elif op == 'fail':
+ self.fail_job( obj )
+ except:
+ log.exception( "Uncaught exception %sing job" % op )
+ if op == 'queue':
+ obj.fail( "Uncaught exception queueing job", exception=True )
+
+ def queue_job( self, job_wrapper ):
+ """Create job script and submit it to the DRM"""
+
+ try:
+ job_wrapper.prepare()
+ command_line = self.build_command_line( job_wrapper, include_metadata=True )
+ except:
+ job_wrapper.fail( "failure preparing job", exception=True )
+ log.exception("failure running job %s" % job_wrapper.get_id_tag())
+ return
+
+ runner_url = job_wrapper.get_job_runner()
+
+ # This is silly, why would we queue a job with no command line?
+ if not command_line:
+ job_wrapper.finish( '', '' )
+ return
+
+ if job_wrapper.get_state() == model.Job.states.DELETED:
+ log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
+ job_wrapper.cleanup()
+ return
+
+ # Change to queued state immediately
+ job_wrapper.change_state( model.Job.states.QUEUED )
+
+ # define job attributes
+ ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ user_log = "%s/%s.condor.log" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ executable = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ submit_desc = [ ]
+ submit_desc.append( 'universe = vanilla' )
+ submit_desc.append( 'getenv = true' )
+ submit_desc.append( 'executable = ' + executable )
+ submit_desc.append( 'output = ' + ofile )
+ submit_desc.append( 'error = ' + efile )
+ submit_desc.append( 'log = ' + user_log )
+ submit_desc.append( 'notification = NEVER' )
+ submit_desc.append( 'queue' )
+ submit_file = "%s/%s.condor.desc" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+
+ script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line)
+ try:
+ fh = file( executable, "w" )
+ fh.write( script )
+ fh.close()
+ os.chmod( executable, 0750 )
+ except:
+ job_wrapper.fail( "failure preparing job script", exception=True )
+ log.exception("failure running job %s" % job_wrapper.get_id_tag())
+ return
+
+ try:
+ fh = file( submit_file, 'w' )
+ for line in submit_desc:
+ fh.write( line + '\n' )
+ fh.close()
+ except:
+ job_wrapper.fail( "failure writing submit file", exception=True )
+ log.exception("failure running job %s" % job_wrapper.get_id_tag())
+ self.cleanup( ( executable, submit_file ) )
+ return
+
+ # job was deleted while we were preparing it
+ if job_wrapper.get_state() == model.Job.states.DELETED:
+ log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
+ self.cleanup( ( executable, submit_file ) )
+ job_wrapper.cleanup()
+ return
+
+ # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
+ galaxy_id_tag = job_wrapper.get_id_tag()
+
+ log.debug("(%s) submitting file %s" % ( galaxy_id_tag, executable ) )
+ log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) )
+ s_out = ''
+ job_id = None
+ try:
+ submit = subprocess.Popen( ( 'condor_submit', submit_file ), stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
+ s_out, s_err = submit.communicate()
+ if submit.returncode == 0:
+ match = re.search( 'submitted to cluster (\\d+).', s_out )
+ if match is None:
+ s_out = 'Failed to find job id from condor_submit'
+ else:
+ job_id = match.group( 1 )
+ except Exception, e:
+ # TODO Add extra except for OSError?
+ s_out = str(e)
+
+ if job_id is None:
+ log.debug( "condor_submit failed for job %s: %s" % (job_wrapper.get_id_tag(), s_out) )
+ self.cleanup( ( submit_file, executable ) )
+ job_wrapper.fail( "condor_submit failed", exception=True )
+ return
+
+ log.info("(%s) queued as %s" % ( galaxy_id_tag, job_id ) )
+
+ self.cleanup( ( submit_file, ) )
+
+ # store runner information for tracking if Galaxy restarts
+ job_wrapper.set_runner( runner_url, job_id )
+
+ # Store DRM related state information for job
+ drm_job_state = CondorJobState()
+ drm_job_state.job_wrapper = job_wrapper
+ drm_job_state.job_id = job_id
+ drm_job_state.ofile = ofile
+ drm_job_state.efile = efile
+ drm_job_state.job_file = executable
+ drm_job_state.user_log = user_log
+ drm_job_state.running = False
+ drm_job_state.runner_url = runner_url
+
+ # Add to our 'queue' of jobs to monitor
+ self.monitor_queue.put( drm_job_state )
+
+ def monitor( self ):
+ """
+ Watches jobs currently in the PBS queue and deals with state changes
+ (queued to running) and job completion
+ """
+ while 1:
+ # Take any new watched jobs and put them on the monitor list
+ try:
+ while 1:
+ drm_job_state = self.monitor_queue.get_nowait()
+ if drm_job_state is self.STOP_SIGNAL:
+ # TODO: This is where any cleanup would occur
+ #self.ds.exit()
+ # Do we need any cleanup here?
+ return
+ self.watched.append( drm_job_state )
+ except Empty:
+ pass
+ # Iterate over the list of watched jobs and check state
+ self.check_watched_items()
+ # Sleep a bit before the next state check
+ time.sleep( 1 )
+
+ def check_watched_items( self ):
+ """
+ Called by the monitor thread to look at each watched job and deal
+ with state changes.
+ """
+ new_watched = []
+ for drm_job_state in self.watched:
+ job_id = drm_job_state.job_id
+ log_job_id = job_id.zfill(3)
+ galaxy_job_id = drm_job_state.job_wrapper.job_id
+ job_running = False;
+ job_complete = False;
+ job_failed = False;
+ try:
+ if os.stat( drm_job_state.user_log ).st_size == drm_job_state.user_log_size:
+ new_watched.append( drm_job_state )
+ continue
+ with open(drm_job_state.user_log, 'r') as fh:
+ for line in fh:
+ if '001 (' + log_job_id + '.' in line:
+ job_running = True
+ if '004 (' + log_job_id + '.' in line:
+ job_running = False
+ if '007 (' + log_job_id + '.' in line:
+ job_running = False
+ if '005 (' + log_job_id + '.' in line:
+ job_complete = True
+ if '009 (' + log_job_id + '.' in line:
+ job_failed = True
+ drm_job_state.user_log_size = fh.tell()
+ except Exception, e:
+ # so we don't kill the monitor thread
+ log.exception("(%s/%s) Unable to check job status" % ( galaxy_job_id, job_id ) )
+ log.warning("(%s/%s) job will now be errored" % ( galaxy_job_id, job_id ) )
+ drm_job_state.fail_message = "Cluster could not complete job"
+ self.work_queue.put( ( 'fail', drm_job_state ) )
+ continue
+ if job_running and not drm_job_state.running:
+ log.debug("(%s/%s) job is now running" % ( galaxy_job_id, job_id ) )
+ drm_job_state.job_wrapper.change_state( model.Job.states.RUNNING )
+ if not job_running and drm_job_state.running:
+ log.debug("(%s/%s) job has stopped running" % ( galaxy_job_id, job_id ) )
+ # Will switching from RUNNING to QUEUED confuse Galaxy?
+ #drm_job_state.job_wrapper.change_state( model.Job.states.QUEUED )
+ if job_complete:
+ log.debug("(%s/%s) job has completed" % ( galaxy_job_id, job_id ) )
+ self.work_queue.put( ( 'finish', drm_job_state ) )
+ continue
+ if job_failed:
+ log.debug("(%s/%s) job failed" % ( galaxy_job_id, job_id ) )
+ drm_job_state.failed = True
+ self.work_queue.put( ( 'finish', drm_job_state ) )
+ continue
+ drm_job_state.runnning = job_running
+ new_watched.append( drm_job_state )
+ # Replace the watch list with the updated version
+ self.watched = new_watched
+
+ def finish_job( self, drm_job_state ):
+ """
+ Get the output/error for a finished job, pass to `job_wrapper.finish`
+ and cleanup all the DRM temporary files.
+ """
+ ofile = drm_job_state.ofile
+ efile = drm_job_state.efile
+ job_file = drm_job_state.job_file
+ # collect the output
+ try:
+ ofh = file(ofile, "r")
+ efh = file(efile, "r")
+ stdout = ofh.read( 32768 )
+ stderr = efh.read( 32768 )
+ except:
+ stdout = ''
+ stderr = 'Job output not returned from cluster'
+ log.debug(stderr)
+
+ try:
+ drm_job_state.job_wrapper.finish( stdout, stderr )
+ except:
+ log.exception("Job wrapper finish method failed")
+
+ # clean up the drm files
+ self.cleanup( ( ofile, efile, job_file, drm_job_state.user_log ) )
+
+ def fail_job( self, drm_job_state ):
+ """
+ Seperated out so we can use the worker threads for it.
+ """
+ self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) )
+ drm_job_state.job_wrapper.fail( drm_job_state.fail_message )
+ self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file, drm_job_state.user_log ) )
+
+ def cleanup( self, files ):
+ if not asbool( self.app.config.get( 'debug', False ) ):
+ for file in files:
+ if os.access( file, os.R_OK ):
+ os.unlink( file )
+
+ def put( self, job_wrapper ):
+ """Add a job to the queue (by job identifier)"""
+ # Change to queued state before handing to worker thread so the runner won't pick it up again
+ job_wrapper.change_state( model.Job.states.QUEUED )
+ self.work_queue.put( ( 'queue', job_wrapper ) )
+
+ def shutdown( self ):
+ """Attempts to gracefully shut down the monitor thread"""
+ log.info( "sending stop signal to worker threads" )
+ self.monitor_queue.put( self.STOP_SIGNAL )
+ for i in range( len( self.work_threads ) ):
+ self.work_queue.put( ( self.STOP_SIGNAL, None ) )
+ log.info( "condor job runner stopped" )
+
+ def stop_job( self, job ):
+ """Attempts to delete a job from the DRM queue"""
+ try:
+ subprocess.check_call( ( 'condor_rm', job.job_runner_external_id ) )
+ log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) )
+ except subprocess.CalledProcessError:
+ log.debug( "(%s/%s) User killed running job, but condor_rm failed" % ( job.id, job.job_runner_external_id ) )
+ except Exception, e:
+ log.debug( "(%s/%s) User killed running job, but error encountered removing from Condor queue: %s" % ( job.id, job.job_runner_external_id, e ) )
+
+ def recover( self, job, job_wrapper ):
+ """Recovers jobs stuck in the queued/running state when Galaxy started"""
+ # TODO Check if we need any changes here
+ drm_job_state = CondorJobState()
+ drm_job_state.ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job.id)
+ drm_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id)
+ drm_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id)
+ drm_job_state.job_id = str( job.job_runner_external_id )
+ drm_job_state.runner_url = job_wrapper.get_job_runner()
+ job_wrapper.command_line = job.command_line
+ drm_job_state.job_wrapper = job_wrapper
+ drm_job_state.user_log = "%s/%s.condor.log" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
+ if job.state == model.Job.states.RUNNING:
+ log.debug( "(%s/%s) is still in running state, adding to the DRM queue" % ( job.id, job.job_runner_external_id ) )
+ drm_job_state.running = True
+ self.monitor_queue.put( drm_job_state )
+ elif job.state == model.Job.states.QUEUED:
+ log.debug( "(%s/%s) is still in DRM queued state, adding to the DRM queue" % ( job.id, job.job_runner_external_id ) )
+ drm_job_state.running = False
+ self.monitor_queue.put( drm_job_state )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 2 months
- 1
- 0
commit/galaxy-central: james_taylor: tooltips: use a special even to remove tooltips automatically when their element is deleted. fix the bug deleting datasets from this history.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/6d23049609a9/
changeset: 6d23049609a9
user: james_taylor
date: 2012-07-25 23:08:38
summary: tooltips: use a special even to remove tooltips automatically when their element is deleted. fix the bug deleting datasets from this history.
affected #: 2 files
diff -r 51992bf52e0c6f1931256903f678b13ed2d373b6 -r 6d23049609a995e2ef7371aa63a7cb8bf6536403 static/scripts/bootstrap.js
--- a/static/scripts/bootstrap.js
+++ b/static/scripts/bootstrap.js
@@ -1,3 +1,4 @@
+
/* ===================================================
* bootstrap-transition.js v2.0.4
* http://twitter.github.com/bootstrap/javascript.html#transitions
@@ -221,6 +222,16 @@
"use strict"; // jshint ;_;
+ // Add a special event that is called when an element is destroyed
+ (function($){
+ jQuery.event.special.destroyed = {
+ remove: function(o) {
+ if (o.handler) {
+ o.handler()
+ }
+ }
+ }
+ })(jQuery)
/* TOOLTIP PUBLIC CLASS DEFINITION
* =============================== */
@@ -249,6 +260,9 @@
this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this))
}
+ // Make sure tooltip is hidden when element is destroyed
+ this.$element.on( 'destroyed', $.proxy( this.hide, this ) );
+
this.options.selector ?
(this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) :
this.fixTitle()
@@ -298,6 +312,8 @@
, actualWidth
, actualHeight
, placement
+ , placementPosition
+ , $window
, tp
if (this.hasContent() && this.enabled) {
@@ -312,6 +328,8 @@
this.options.placement.call(this, $tip[0], this.$element[0]) :
this.options.placement
+ placementPosition = inside ? placement.split(' ')[1] : placement;
+
inside = /in/.test(placement)
$tip
@@ -324,7 +342,7 @@
actualWidth = $tip[0].offsetWidth
actualHeight = $tip[0].offsetHeight
- switch (inside ? placement.split(' ')[1] : placement) {
+ switch (placementPosition) {
case 'bottom':
tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2}
break
@@ -339,28 +357,21 @@
break
}
- // BEGIN GALAXY MODIFICATION
-
// Shift if off screen
- var $w = $(window),
- p = inside ? placement.split(' ')[1] : placement;
+ $window = $(window)
// If off the top of the screen, flip
- if ( tp.top < $w.scrollTop() && placement == 'top' ) {
+ if ( tp.top < $window.scrollTop() && placementPosition == 'top' ) {
tp.top = pos.top + pos.height;
placement = inside ? 'inside bottom' : 'bottom';
}
- // If off bottom, just shift for now
- tp.top = Math.min( tp.top, $w.scrollTop() + $w.height() - $tip.outerHeight() );
-
-
// Shift left or right
var leftShift = 0;
- if ( tp.left < $w.scrollLeft() ) {
- leftShift = tp.left - $w.scrollLeft();
+ if ( tp.left < $window.scrollLeft() ) {
+ leftShift = tp.left - $window.scrollLeft();
}
- var t = $w.scrollLeft() + $w.width() - $tip.outerWidth();
+ var t = $window.scrollLeft() + $window.width() - $tip.outerWidth();
if ( tp.left > t ) {
leftShift = tp.left - t;
}
@@ -384,7 +395,6 @@
// END GALAXY MODIFICATION
-
$tip
.css(tp)
.addClass(placement)
@@ -516,4 +526,4 @@
, delay: 0
}
-}(window.jQuery);
\ No newline at end of file
+}(window.jQuery);
diff -r 51992bf52e0c6f1931256903f678b13ed2d373b6 -r 6d23049609a995e2ef7371aa63a7cb8bf6536403 templates/root/history.mako
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -138,7 +138,6 @@
}
});
%endif
- $(".tooltip").remove();
} else {
render_message( "Dataset deletion failed", "error" );
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 3 months
- 1
- 0
commit/galaxy-central: 3 new changesets
by Bitbucket
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/10829b9c5086/
changeset: 10829b9c5086
user: jgoecks
date: 2012-07-24 20:07:06
summary: Trackster: only draw connector when both mates of a read are drawn; this prevents spurious connectors from being drawn but prevents connectors from being drawn across tile boundaries.
affected #: 1 file
diff -r cb9272041d954762664dd12f917619dbd6a48356 -r 10829b9c5086a09b80b0c592d9a289b65d723fcf static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -6042,18 +6042,30 @@
var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ),
b1_end = Math.ceil( Math.min(width, Math.max(0, (feature[4][1] - tile_low) * w_scale)) ),
b2_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ),
- b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) );
+ b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ),
+ connector = true;
// Draw left/forward read.
if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
}
+ else {
+ connector = false;
+ }
+
// Draw right/reverse read.
if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) {
this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
}
- // Draw connector.
- if (b2_start > b1_end) {
+ else {
+ connector = false;
+ }
+
+ // Draw connector if both reads were drawn.
+ // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager
+ // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would
+ // make it possible to put together more easily.
+ if (connector && b2_start > b1_end) {
ctx.fillStyle = CONNECTOR_COLOR;
dashedLine(ctx, b1_end - gap, y_center + 5, b2_start - gap, y_center + 5);
}
https://bitbucket.org/galaxy/galaxy-central/changeset/339f886d3ffa/
changeset: 339f886d3ffa
user: jgoecks
date: 2012-07-24 20:21:40
summary: Rename paramamonster as sweepster and use bootstrap tooltips in sweepster.
affected #: 8 files
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -476,9 +476,9 @@
return self.tracks_grid( trans, **kwargs )
@web.expose
- def paramamonster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ):
+ def sweepster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ):
"""
- Creates a paramamonster visualization using the incoming parameters. If id is available,
+ Creates a sweepster visualization using the incoming parameters. If id is available,
get the visualization with the given id; otherwise, create a new visualization using
a given dataset and regions.
"""
@@ -505,7 +505,7 @@
viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True )
viz_config[ 'dataset' ] = dataset.get_api_value()
- return trans.fill_template_mako( "visualization/paramamonster.mako", config=viz_config )
+ return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config )
@web.expose
def circster( self, trans, id, **kwargs ):
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 static/scripts/packed/viz/paramamonster.js
--- a/static/scripts/packed/viz/paramamonster.js
+++ /dev/null
@@ -1,1 +0,0 @@
-var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var ParamaMonsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:ParamaMonsterTrack});var ParamaMonsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"ParamaMonsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"paramamonster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var ParamaMonsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".tooltip").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");if(!a){return}$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i=b.model.get("mode");$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1],m=$("#center").position().left;h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+m))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var ParamaMonsterVisualizationView=Backbone.View.extend({className:"paramamonster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a});this.block_color=get_random_color();this.reverse_strand_color=get_random_color([this.block_color,"#ffffff"])},render:function(){var g=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(g.$el);var j=this,d=j.model.get("regions"),h=$("<tr/>").appendTo(this.track_collection_container);d.each(function(k){h.append($("<th>").text(k.toString()))});h.children().first().attr("colspan",2);var e=$("<div>").addClass("tiles");$("#right").append(e.append(this.track_collection_container));j.model.get("tracks").each(function(k){j.add_track(k)});var i=$(this.helpText).addClass("help"),f=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tooltip").remove();i.remove()}}]);i.prepend(f.$el.css("float","right"));$("#center").append(i);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var c=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var b=["Squish","Pack"],a={};_.each(b,function(k){a[k]=function(){j.model.set("default_mode",k);j.model.get("tracks").each(function(l){l.set("mode",k)})}});make_popupmenu(c.$el.find(".chevron-expand"),a);c.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(c.$el)},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new ParamaMonsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new ParamaMonsterTrack({settings:m,regions:d,mode:a.model.get("default_mode")});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);o.prefs.block_color=a.block_color;o.prefs.reverse_strand_color=a.reverse_strand_color;n.set("track",o)})},m*10000)})})})}});
\ No newline at end of file
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 static/scripts/viz/paramamonster.js
--- a/static/scripts/viz/paramamonster.js
+++ /dev/null
@@ -1,939 +0,0 @@
-/**
- * Visualization and components for ParamaMonster, a visualization for exploring a tool's parameter space via
- * genomic visualization.
- */
-
-/**
- * A collection of tool input settings. Object is useful for keeping a list of settings
- * for future use without changing the input's value and for preserving inputs order.
- */
-var ToolInputsSettings = Backbone.Model.extend({
- defaults: {
- inputs: null,
- values: null
- }
-});
-
-/**
- * Tree for a tool's parameters.
- */
-var ToolParameterTree = Backbone.RelationalModel.extend({
- defaults: {
- tool: null,
- tree_data: null
- },
-
- initialize: function(options) {
- // Set up tool parameters to work with tree.
- var self = this;
- this.get('tool').get('inputs').each(function(input) {
- if (!input.get_samples()) { return; }
-
- // Listen for changes to input's attributes.
- input.on('change:min change:max change:num_samples', function(input) {
- if (input.get('in_ptree')) {
- self.set_tree_data();
- }
- }, self);
- input.on('change:in_ptree', function(input) {
- if (input.get('in_ptree')) {
- self.add_param(input);
- }
- else {
- self.remove_param(input);
- }
- self.set_tree_data();
- }, self);
- });
-
- // If there is a config, use it.
- if (options.config) {
- _.each(options.config, function(input_config) {
- var input = self.get('tool').get('inputs').find(function(input) {
- return input.get('name') === input_config.name;
- });
- self.add_param(input);
- input.set(input_config);
- });
- }
- },
-
- add_param: function(param) {
- // If parameter already present, do not add it.
- if (param.get('ptree_index')) { return; }
-
- param.set('in_ptree', true);
- param.set('ptree_index', this.get_tree_params().length);
- },
-
- remove_param: function(param) {
- // Remove param from tree.
- param.set('in_ptree', false);
- param.set('ptree_index', null);
-
- // Update ptree indices for remaining params.
- _(this.get_tree_params()).each(function(input, index) {
- // +1 to use 1-based indexing.
- input.set('ptree_index', index + 1);
- });
- },
-
- /**
- * Sets tree data using tool's inputs.
- */
- set_tree_data: function() {
- // Get samples for each parameter.
- var params_samples = _.map(this.get_tree_params(), function(param) {
- return {
- param: param,
- samples: param.get_samples()
- };
- });
- var node_id = 0,
- // Creates tree data recursively.
- create_tree_data = function(params_samples, index) {
- var param_samples = params_samples[index],
- param = param_samples.param,
- param_label = param.get('label'),
- settings = param_samples.samples;
-
- // Create leaves when last parameter setting is reached.
- if (params_samples.length - 1 === index) {
- return _.map(settings, function(setting) {
- return {
- id: node_id++,
- name: setting,
- param: param,
- value: setting
- };
- });
- }
-
- // Recurse to handle other parameters.
- return _.map(settings, function(setting) {
- return {
- id: node_id++,
- name: setting,
- param: param,
- value: setting,
- children: create_tree_data(params_samples, index + 1)
- };
- });
- };
-
- this.set('tree_data', {
- name: 'Root',
- id: node_id++,
- children: (params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null)
- });
- },
-
- get_tree_params: function() {
- // Filter and sort parameters to get list in tree.
- return _(this.get('tool').get('inputs').where( {in_ptree: true} ))
- .sortBy( function(input) { return input.get('ptree_index'); } );
- },
-
- /**
- * Returns number of leaves in tree.
- */
- get_num_leaves: function() {
- return this.get_tree_params().reduce(function(memo, param) { return memo * param.get_samples().length; }, 1);
- },
-
- /**
- * Returns array of ToolInputsSettings objects based on a node and its subtree.
- */
- get_node_settings: function(target_node) {
- // -- Get fixed settings from tool and parent nodes.
-
- // Start with tool's settings.
- var fixed_settings = this.get('tool').get_inputs_dict();
-
- // Get fixed settings using node's parents.
- var cur_node = target_node.parent;
- if (cur_node) {
- while(cur_node.depth !== 0) {
- fixed_settings[cur_node.param.get('name')] = cur_node.value;
- cur_node = cur_node.parent;
- }
- }
-
- // Walk subtree starting at clicked node to get full list of settings.
- var self = this,
- get_settings = function(node, settings) {
- // Add setting for this node. Root node does not have a param,
- // however.
- if (node.param) {
- settings[node.param.get('name')] = node.value;
- }
-
- if (!node.children) {
- // At leaf node, so return settings.
- return new ToolInputsSettings({
- inputs: self.get('tool').get('inputs'),
- values: settings
- });
- }
- else {
- // At interior node: return list of subtree settings.
- return _.flatten( _.map(node.children, function(c) { return get_settings(c, _.clone(settings)); }) );
- }
- },
- all_settings = get_settings(target_node, fixed_settings);
-
- // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.
- if (!_.isArray(all_settings)) { all_settings = [ all_settings ]; }
-
- return all_settings;
- },
-
- /**
- * Returns all nodes connected a particular node; this includes parents and children of the node.
- */
- get_connected_nodes: function(node) {
- var get_subtree_nodes = function(a_node) {
- if (!a_node.children) {
- return a_node;
- }
- else {
- // At interior node: return subtree nodes.
- return _.flatten( [a_node, _.map(a_node.children, function(c) { return get_subtree_nodes(c); })] );
- }
- };
-
- // Get node's parents.
- var parents = [],
- cur_parent = node.parent;
- while(cur_parent) {
- parents.push(cur_parent);
- cur_parent = cur_parent.parent;
- }
-
- return _.flatten([parents, get_subtree_nodes(node)]);
- },
-
- /**
- * Returns the leaf that corresponds to a settings collection.
- */
- get_leaf: function(settings) {
- var cur_node = this.get('tree_data'),
- find_child = function(children) {
- return _.find(children, function(child) {
- return settings[child.param.get('name')] === child.value;
- });
- };
-
- while (cur_node.children) {
- cur_node = find_child(cur_node.children);
- }
- return cur_node;
- },
-
- /**
- * Returns a list of parameters used in tree.
- */
- toJSON: function() {
- // FIXME: returning and jsonifying complete param causes trouble on the server side,
- // so just use essential attributes for now.
- return this.get_tree_params().map(function(param) {
- return {
- name: param.get('name'),
- min: param.get('min'),
- max: param.get('max'),
- num_samples: param.get('num_samples')
- };
- });
- }
-});
-
-var ParamaMonsterTrack = Backbone.RelationalModel.extend({
- defaults: {
- track: null,
- mode: 'Pack',
- settings: null,
- regions: null
- },
-
- relations: [
- {
- type: Backbone.HasMany,
- key: 'regions',
- relatedModel: 'GenomeRegion'
- }
- ],
-
- initialize: function(options) {
- if (options.track) {
- // FIXME: find a better way to deal with needed URLs:
- var track_config = _.extend({
- data_url: galaxy_paths.get('raw_data_url'),
- converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
- }, options.track);
- this.set('track', object_from_template(track_config, {}, null));
- }
- },
-
- same_settings: function(a_track) {
- var this_settings = this.get('settings'),
- other_settings = a_track.get('settings');
- for (var prop in this_settings) {
- if (!other_settings[prop] ||
- this_settings[prop] !== other_settings[prop]) {
- return false;
- }
- }
- return true;
- },
-
- toJSON: function() {
- return {
- track: this.get('track').to_dict(),
- settings: this.get('settings'),
- regions: this.get('regions')
- };
- }
-});
-
-var TrackCollection = Backbone.Collection.extend({
- model: ParamaMonsterTrack
-});
-
-/**
- * ParamaMonster visualization model.
- */
-var ParamaMonsterVisualization = Visualization.extend({
- defaults: _.extend({}, Visualization.prototype.defaults, {
- dataset: null,
- tool: null,
- parameter_tree: null,
- regions: null,
- tracks: null,
- default_mode: 'Pack'
- }),
-
- relations: [
- {
- type: Backbone.HasOne,
- key: 'dataset',
- relatedModel: 'Dataset'
- },
- {
- type: Backbone.HasOne,
- key: 'tool',
- relatedModel: 'Tool'
- },
- {
- type: Backbone.HasMany,
- key: 'regions',
- relatedModel: 'GenomeRegion'
- },
- {
- type: Backbone.HasMany,
- key: 'tracks',
- relatedModel: 'ParamaMonsterTrack'
- }
- // NOTE: cannot use relationship for parameter tree because creating tree is complex.
- ],
-
- initialize: function(options) {
- var tool_with_samplable_inputs = this.get('tool').copy(true);
- this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);
-
- this.set('parameter_tree', new ToolParameterTree({
- tool: tool_with_samplable_inputs,
- config: options.tree_config
- }));
- },
-
- add_track: function(track) {
- this.get('tracks').add(track);
- },
-
- toJSON: function() {
- // TODO: could this be easier by using relational models?
- return {
- id: this.get('id'),
- title: 'Parameter exploration for dataset \'' + this.get('dataset').get('name') + '\'',
- type: 'paramamonster',
- dataset_id: this.get('dataset').id,
- tool_id: this.get('tool').id,
- regions: this.get('regions').toJSON(),
- tree_config: this.get('parameter_tree').toJSON(),
- tracks: this.get('tracks').toJSON()
- };
- }
-});
-
-/**
- * --- Views ---
- */
-
-/**
- * ParamaMonster track view.
- */
-var ParamaMonsterTrackView = Backbone.View.extend({
- tagName: 'tr',
-
- TILE_LEN: 250,
-
- initialize: function(options) {
- this.canvas_manager = options.canvas_manager;
- this.render();
- this.model.on('change:track change:mode', this.draw_tiles, this);
- },
-
- render: function() {
- // Render settings icon and popup.
- // TODO: use template.
- var settings = this.model.get('settings'),
- values = settings.get('values'),
- settings_td = $('<td/>').addClass('settings').appendTo(this.$el),
- settings_div = $('<div/>').addClass('track-info').hide().appendTo(settings_td);
- settings_div.append( $('<div/>').css('font-weight', 'bold').text('Track Settings') );
- settings.get('inputs').each(function(input) {
- settings_div.append( input.get('label') + ': ' + values[input.get('name')] + '<br/>');
- });
- var self = this,
- run_on_dataset_button = $('<button/>').appendTo(settings_div).text('Run on complete dataset').click(function() {
- settings_div.toggle();
- self.trigger('run_on_dataset', settings);
- });
- var icon_menu = create_icon_buttons_menu([
- {
- title: 'Settings',
- icon_class: 'gear track-settings',
- on_click: function() {
- settings_div.toggle();
- }
- },
- {
- title: 'Remove',
- icon_class: 'cross-circle',
- on_click: function() {
- self.$el.remove();
- $('.tooltip').remove();
- // TODO: remove track from viz collection.
- }
- }
- ]);
- settings_td.prepend(icon_menu.$el);
-
- // Render tile placeholders.
- this.model.get('regions').each(function() {
- self.$el.append($('<td/>').addClass('tile').html(
- $('<img/>').attr('src', galaxy_paths.get('image_path') + '/loading_large_white_bg.gif')
- ));
- });
-
- if (this.model.get('track')) {
- this.draw_tiles();
- }
- },
-
- /**
- * Draw tiles for regions.
- */
- draw_tiles: function() {
- var self = this,
- track = this.model.get('track'),
- regions = this.model.get('regions'),
- tile_containers = this.$el.find('td.tile');
-
- // Do nothing if track is not defined.
- if (!track) { return; }
-
- // When data is ready, draw tiles.
- $.when(track.data_manager.data_is_ready()).then(function(data_ok) {
- // Draw tile for each region.
- regions.each(function(region, index) {
- var resolution = region.length() / self.TILE_LEN,
- w_scale = 1/resolution,
- mode = self.model.get('mode');
- $.when(track.data_manager.get_data(region, mode, resolution, {})).then(function(tile_data) {
- var canvas = self.canvas_manager.new_canvas();
- canvas.width = self.TILE_LEN;
- canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width);
- track.draw_tile(tile_data, canvas.getContext('2d'), mode, resolution, region, w_scale);
- $(tile_containers[index]).empty().append(canvas);
- });
- });
- });
- }
-});
-
-/**
- * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as
- * it augments an existing input form row rather than creates a completely new HTML element.
- */
-var ToolInputValOrSweepView = Backbone.View.extend({
-
- // Template for rendering sweep inputs:
- number_input_template: '<div class="form-row-input sweep">' +
- '<input class="min" type="text" size="6" value="<%= min %>"> - ' +
- '<input class="max" type="text" size="6" value="<%= max %>">' +
- ' samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>">' +
- '</div>',
-
- select_input_template: '<div class="form-row-input sweep"><%= options %></div>',
-
- initialize: function(options) {
- this.$el = options.tool_row;
- this.render();
- },
-
- render: function() {
- var input = this.model,
- type = input.get('type'),
- single_input_row = this.$el.find('.form-row-input'),
- sweep_inputs_row = null;
-
- // Update tool inputs as single input changes.
- single_input_row.find(':input').change(function() {
- input.set('value', $(this).val());
- });
-
- // Add row for parameter sweep inputs.
- if (type === 'number') {
- sweep_inputs_row = $(_.template(this.number_input_template, this.model.toJSON()));
- }
- else if (type === 'select') {
- var options = _.map(this.$el.find('select option'), function(option) {
- return $(option).val();
- }),
- options_text = options.join(', ');
- sweep_inputs_row = $(_.template(this.select_input_template, {
- options: options_text
- }));
- }
- sweep_inputs_row.insertAfter(single_input_row);
-
- // Add buttons for adding/removing parameter.
- var self = this,
- menu = create_icon_buttons_menu([
- {
- title: 'Add parameter to tree',
- icon_class: 'plus-button',
- on_click: function () {
- input.set('in_ptree', true);
- single_input_row.hide();
- sweep_inputs_row.show();
- $(this).hide();
- self.$el.find('.icon-button.toggle').show();
- }
-
- },
- {
- title: 'Remove parameter from tree',
- icon_class: 'toggle',
- on_click: function() {
- // Remove parameter from tree params where name matches clicked paramter.
- input.set('in_ptree', false);
- sweep_inputs_row.hide();
- single_input_row.show();
- $(this).hide();
- self.$el.find('.icon-button.plus-button').show();
- }
- }
- ],
- {
-
- });
- this.$el.prepend(menu.$el);
-
- // Show/hide input rows and icons depending on whether parameter is in the tree.
- if (input.get('in_ptree')) {
- single_input_row.hide();
- self.$el.find('.icon-button.plus-button').hide();
- }
- else {
- self.$el.find('.icon-button.toggle').hide();
- sweep_inputs_row.hide();
- }
-
- // Update input's min, max, number of samples as values change.
- _.each(['min', 'max', 'num_samples'], function(attr) {
- sweep_inputs_row.find('.' + attr).change(function() {
- input.set(attr, parseFloat( $(this).val() ));
- });
- });
- }
-});
-
-var ToolParameterTreeDesignView = Backbone.View.extend({
- className: 'tree-design',
-
- initialize: function(options) {
- this.render();
- },
-
- render: function() {
- // Start with tool form view.
- var tool_form_view = new ToolFormView({
- model: this.model.get('tool')
- });
- tool_form_view.render();
- this.$el.append(tool_form_view.$el);
-
- // Set up views for each tool input.
- var self = this,
- inputs = self.model.get('tool').get('inputs');
- this.$el.find('.form-row').not('.form-actions').each(function(i) {
- var input_view = new ToolInputValOrSweepView({
- model: inputs.at(i),
- tool_row: $(this)
- });
- });
- }
-});
-
-/**
- * Displays and updates parameter tree.
- */
-var ToolParameterTreeView = Backbone.View.extend({
- className: 'tool-parameter-tree',
-
- initialize: function(options) {
- // When tree data changes, re-render.
- this.model.on('change:tree_data', this.render, this);
- },
-
- render: function() {
- // Start fresh.
- this.$el.children().remove();
-
- var tree_params = this.model.get_tree_params();
- if (!tree_params.length) {
- return;
- }
-
- // Set width, height based on params and samples.
- this.width = 100 * (2 + tree_params.length);
- this.height = 15 * this.model.get_num_leaves();
-
- var self = this;
-
- // Layout tree.
- var cluster = d3.layout.cluster()
- .size([this.height, this.width - 160]);
-
- var diagonal = d3.svg.diagonal()
- .projection(function(d) { return [d.y, d.x]; });
-
- // Layout nodes.
- var nodes = cluster.nodes(this.model.get('tree_data'));
-
- // Setup and add labels for tree levels.
- var param_depths = _.uniq(_.pluck(nodes, "y"));
- _.each(tree_params, function(param, index) {
- var x = param_depths[index+1],
- center_left = $('#center').position().left;
- self.$el.append( $('<div>').addClass('label')
- .text(param.get('label'))
- .css('left', x + center_left) );
- });
-
- // Set up vis element.
- var vis = d3.select(this.$el[0])
- .append("svg")
- .attr("width", this.width)
- .attr("height", this.height + 30)
- .append("g")
- .attr("transform", "translate(40, 20)");
-
- // Draw links.
- var link = vis.selectAll("path.link")
- .data(cluster.links(nodes))
- .enter().append("path")
- .attr("class", "link")
- .attr("d", diagonal);
-
- // Draw nodes.
- var node = vis.selectAll("g.node")
- .data(nodes)
- .enter().append("g")
- .attr("class", "node")
- .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; })
- .on('mouseover', function(a_node) {
- var connected_node_ids = _.pluck(self.model.get_connected_nodes(a_node), 'id');
- // TODO: probably can use enter() to do this more easily.
- node.filter(function(d) {
- return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;
- }).style('fill', '#f00');
- })
- .on('mouseout', function() {
- node.style('fill', '#000');
- });
-
- node.append("circle")
- .attr("r", 9);
-
- node.append("text")
- .attr("dx", function(d) { return d.children ? -12 : 12; })
- .attr("dy", 3)
- .attr("text-anchor", function(d) { return d.children ? "end" : "start"; })
- .text(function(d) { return d.name; });
- }
-});
-
-/**
- * ParamaMonster visualization view. View requires rendering in 3-panel setup for now.
- */
-var ParamaMonsterVisualizationView = Backbone.View.extend({
- className: 'paramamonster',
-
- helpText:
- '<div><h4>Getting Started</h4>' +
- '<ol><li>Create a parameter tree by using the icons next to the tool\'s parameter names to add or remove parameters.' +
- '<li>Adjust the tree by using parameter inputs to select min, max, and number of samples' +
- '<li>Run the tool with different settings by clicking on tree nodes' +
- '</ol></div>',
-
- initialize: function(options) {
- this.canvas_manager = new CanvasManager(this.$el.parents('body'));
- this.tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') });
- this.track_collection_container = $('<table/>').addClass('tracks');
-
- // Handle node clicks for tree data.
- this.model.get('parameter_tree').on('change:tree_data', this.handle_node_clicks, this);
-
- // Each track must have a view so it has a canvas manager.
- var self = this;
- this.model.get('tracks').each(function(track) {
- track.get('track').view = self;
- });
-
- // Set block, reverse strand block colors; these colors will be used for all tracks.
- this.block_color = get_random_color();
- this.reverse_strand_color = get_random_color( [ this.block_color, "#ffffff" ] );
- },
-
- render: function() {
- // Render tree design view in left panel.
- var tree_design_view = new ToolParameterTreeDesignView({
- model: this.model.get('parameter_tree')
- });
-
- $('#left').append(tree_design_view.$el);
-
- // Render track collection container/view in right panel.
- var self = this,
- regions = self.model.get('regions'),
- tr = $('<tr/>').appendTo(this.track_collection_container);
-
- regions.each(function(region) {
- tr.append( $('<th>').text(region.toString()) );
- });
- tr.children().first().attr('colspan', 2);
-
- var tracks_div = $('<div>').addClass('tiles');
- $('#right').append( tracks_div.append(this.track_collection_container) );
-
- self.model.get('tracks').each(function(track) {
- self.add_track(track);
- });
-
- // -- Render help and tool parameter tree in center panel. --
-
- // Help includes text and a close button.
- var help_div = $(this.helpText).addClass('help'),
- close_button = create_icon_buttons_menu([
- {
- title: 'Close',
- icon_class: 'cross-circle',
- on_click: function() {
- $('.tooltip').remove();
- help_div.remove();
- }
- }
- ]);
-
- help_div.prepend(close_button.$el.css('float', 'right'));
- $('#center').append(help_div);
-
- // Parameter tree:
- this.tool_param_tree_view.render();
- $('#center').append(this.tool_param_tree_view.$el);
-
- // Set up handler for tree node clicks.
- this.handle_node_clicks();
-
- // Set up visualization menu.
- var menu = create_icon_buttons_menu(
- [
- // Save.
- /*
- { icon_class: 'disk--arrow', title: 'Save', on_click: function() {
- // Show saving dialog box
- show_modal("Saving...", "progress");
-
- viz.save().success(function(vis_info) {
- hide_modal();
- viz.set({
- 'id': vis_info.vis_id,
- 'has_changes': false
- });
- })
- .error(function() {
- show_modal( "Could Not Save", "Could not save visualization. Please try again later.",
- { "Close" : hide_modal } );
- });
- } },
- */
- // Change track modes.
- {
- icon_class: 'chevron-expand',
- title: 'Set display mode'
- },
- // Close viz.
- {
- icon_class: 'cross-circle',
- title: 'Close',
- on_click: function() {
- window.location = "${h.url_for( controller='visualization', action='list' )}";
- }
- }
- ],
- {
- tooltip_config: {placement: 'bottom'}
- });
-
- // Create mode selection popup. Mode selection changes default mode and mode for all tracks.
- var modes = ['Squish', 'Pack'],
- mode_mapping = {};
- _.each(modes, function(mode) {
- mode_mapping[mode] = function() {
- self.model.set('default_mode', mode);
- self.model.get('tracks').each(function(track) {
- track.set('mode', mode);
- });
- };
- });
-
- make_popupmenu(menu.$el.find('.chevron-expand'), mode_mapping);
-
- menu.$el.attr("style", "float: right");
- $("#right .unified-panel-header-inner").append(menu.$el);
- },
-
- run_tool_on_dataset: function(settings) {
- var tool = this.model.get('tool'),
- tool_name = tool.get('name'),
- dataset = this.model.get('dataset');
- tool.set_input_values(settings.get('values'));
- $.when(tool.rerun(dataset)).then(function(outputs) {
- // TODO.
- });
-
- show_modal('Running ' + tool_name + ' on complete dataset',
- tool_name + ' is running on dataset \'' +
- dataset.get('name') + '\'. Outputs are in the dataset\'s history.',
- {
- 'Ok': function() { hide_modal(); }
- });
- },
-
- /**
- * Add track to model and view.
- */
- add_track: function(pm_track) {
- var self = this,
- param_tree = this.model.get('parameter_tree');
-
- // Add track to model.
- self.model.add_track(pm_track);
-
- var track_view = new ParamaMonsterTrackView({
- model: pm_track,
- canvas_manager: self.canvas_manager
- });
- track_view.on('run_on_dataset', self.run_tool_on_dataset, self);
- self.track_collection_container.append(track_view.$el);
- track_view.$el.hover(function() {
- var settings_leaf = param_tree.get_leaf(pm_track.get('settings').get('values'));
- var connected_node_ids = _.pluck(param_tree.get_connected_nodes(settings_leaf), 'id');
-
- // TODO: can do faster with enter?
- d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node")
- .filter(function(d) {
- return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;
- }).style('fill', '#f00');
- },
- function() {
- d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node").style('fill', '#000');
- });
- return pm_track;
- },
-
- /**
- * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of
- * the settings defined by the node's subtree and tracks are added for each run.
- */
- handle_node_clicks: function() {
- // When node clicked in tree, run tool and add tracks to model.
- var self = this,
- param_tree = this.model.get('parameter_tree'),
- regions = this.model.get('regions'),
- node = d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");
- node.on("click", function(d, i) {
- // Get all settings corresponding to node.
- var tool = self.model.get('tool'),
- dataset = self.model.get('dataset'),
- all_settings = param_tree.get_node_settings(d),
- run_jobs_deferred = $.Deferred();
-
- // Do not allow 10+ jobs to be run.
- if (all_settings.length >= 10) {
- show_modal("Whoa there cowboy!",
- "You clicked on a node to try " + self.model.get('tool').get('name') +
- " with " + all_settings.length +
- " different combinations of settings. You can only run 10 jobs at a time.",
- {
- "Ok": function() { hide_modal(); run_jobs_deferred.resolve(false); }
- });
- }
- else {
- run_jobs_deferred.resolve(true);
- }
-
- // Take action when deferred resolves.
- $.when(run_jobs_deferred).then(function(run_jobs) {
- if (!run_jobs) { return; }
-
- // Create and add tracks for each settings group.
- var tracks = _.map(all_settings, function(settings) {
- var pm_track = new ParamaMonsterTrack({
- settings: settings,
- regions: regions,
- mode: self.model.get('default_mode')
- });
- self.add_track(pm_track);
- return pm_track;
- });
-
- // For each track, run tool using track's settings and update track.
- _.each(tracks, function(pm_track, index) {
- setTimeout(function() {
- // Set inputs and run tool.
- // console.log('running with settings', pm_track.get('settings'));
- tool.set_input_values(pm_track.get('settings').get('values'));
- $.when(tool.rerun(dataset, regions)).then(function(output) {
- // Create and add track for output dataset.
- var track_config = _.extend({
- data_url: galaxy_paths.get('raw_data_url'),
- converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
- }, output.first().get('track_config')),
- track_obj = object_from_template(track_config, self, null);
-
- // Set track block colors.
- track_obj.prefs.block_color = self.block_color;
- track_obj.prefs.reverse_strand_color = self.reverse_strand_color;
-
- pm_track.set('track', track_obj);
- });
- }, index * 10000);
- });
- });
- });
- }
-});
\ No newline at end of file
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 static/scripts/viz/sweepster.js
--- /dev/null
+++ b/static/scripts/viz/sweepster.js
@@ -0,0 +1,939 @@
+/**
+ * Visualization and components for Sweepster, a visualization for exploring a tool's parameter space via
+ * genomic visualization.
+ */
+
+/**
+ * A collection of tool input settings. Object is useful for keeping a list of settings
+ * for future use without changing the input's value and for preserving inputs order.
+ */
+var ToolInputsSettings = Backbone.Model.extend({
+ defaults: {
+ inputs: null,
+ values: null
+ }
+});
+
+/**
+ * Tree for a tool's parameters.
+ */
+var ToolParameterTree = Backbone.RelationalModel.extend({
+ defaults: {
+ tool: null,
+ tree_data: null
+ },
+
+ initialize: function(options) {
+ // Set up tool parameters to work with tree.
+ var self = this;
+ this.get('tool').get('inputs').each(function(input) {
+ if (!input.get_samples()) { return; }
+
+ // Listen for changes to input's attributes.
+ input.on('change:min change:max change:num_samples', function(input) {
+ if (input.get('in_ptree')) {
+ self.set_tree_data();
+ }
+ }, self);
+ input.on('change:in_ptree', function(input) {
+ if (input.get('in_ptree')) {
+ self.add_param(input);
+ }
+ else {
+ self.remove_param(input);
+ }
+ self.set_tree_data();
+ }, self);
+ });
+
+ // If there is a config, use it.
+ if (options.config) {
+ _.each(options.config, function(input_config) {
+ var input = self.get('tool').get('inputs').find(function(input) {
+ return input.get('name') === input_config.name;
+ });
+ self.add_param(input);
+ input.set(input_config);
+ });
+ }
+ },
+
+ add_param: function(param) {
+ // If parameter already present, do not add it.
+ if (param.get('ptree_index')) { return; }
+
+ param.set('in_ptree', true);
+ param.set('ptree_index', this.get_tree_params().length);
+ },
+
+ remove_param: function(param) {
+ // Remove param from tree.
+ param.set('in_ptree', false);
+ param.set('ptree_index', null);
+
+ // Update ptree indices for remaining params.
+ _(this.get_tree_params()).each(function(input, index) {
+ // +1 to use 1-based indexing.
+ input.set('ptree_index', index + 1);
+ });
+ },
+
+ /**
+ * Sets tree data using tool's inputs.
+ */
+ set_tree_data: function() {
+ // Get samples for each parameter.
+ var params_samples = _.map(this.get_tree_params(), function(param) {
+ return {
+ param: param,
+ samples: param.get_samples()
+ };
+ });
+ var node_id = 0,
+ // Creates tree data recursively.
+ create_tree_data = function(params_samples, index) {
+ var param_samples = params_samples[index],
+ param = param_samples.param,
+ param_label = param.get('label'),
+ settings = param_samples.samples;
+
+ // Create leaves when last parameter setting is reached.
+ if (params_samples.length - 1 === index) {
+ return _.map(settings, function(setting) {
+ return {
+ id: node_id++,
+ name: setting,
+ param: param,
+ value: setting
+ };
+ });
+ }
+
+ // Recurse to handle other parameters.
+ return _.map(settings, function(setting) {
+ return {
+ id: node_id++,
+ name: setting,
+ param: param,
+ value: setting,
+ children: create_tree_data(params_samples, index + 1)
+ };
+ });
+ };
+
+ this.set('tree_data', {
+ name: 'Root',
+ id: node_id++,
+ children: (params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null)
+ });
+ },
+
+ get_tree_params: function() {
+ // Filter and sort parameters to get list in tree.
+ return _(this.get('tool').get('inputs').where( {in_ptree: true} ))
+ .sortBy( function(input) { return input.get('ptree_index'); } );
+ },
+
+ /**
+ * Returns number of leaves in tree.
+ */
+ get_num_leaves: function() {
+ return this.get_tree_params().reduce(function(memo, param) { return memo * param.get_samples().length; }, 1);
+ },
+
+ /**
+ * Returns array of ToolInputsSettings objects based on a node and its subtree.
+ */
+ get_node_settings: function(target_node) {
+ // -- Get fixed settings from tool and parent nodes.
+
+ // Start with tool's settings.
+ var fixed_settings = this.get('tool').get_inputs_dict();
+
+ // Get fixed settings using node's parents.
+ var cur_node = target_node.parent;
+ if (cur_node) {
+ while(cur_node.depth !== 0) {
+ fixed_settings[cur_node.param.get('name')] = cur_node.value;
+ cur_node = cur_node.parent;
+ }
+ }
+
+ // Walk subtree starting at clicked node to get full list of settings.
+ var self = this,
+ get_settings = function(node, settings) {
+ // Add setting for this node. Root node does not have a param,
+ // however.
+ if (node.param) {
+ settings[node.param.get('name')] = node.value;
+ }
+
+ if (!node.children) {
+ // At leaf node, so return settings.
+ return new ToolInputsSettings({
+ inputs: self.get('tool').get('inputs'),
+ values: settings
+ });
+ }
+ else {
+ // At interior node: return list of subtree settings.
+ return _.flatten( _.map(node.children, function(c) { return get_settings(c, _.clone(settings)); }) );
+ }
+ },
+ all_settings = get_settings(target_node, fixed_settings);
+
+ // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.
+ if (!_.isArray(all_settings)) { all_settings = [ all_settings ]; }
+
+ return all_settings;
+ },
+
+ /**
+ * Returns all nodes connected a particular node; this includes parents and children of the node.
+ */
+ get_connected_nodes: function(node) {
+ var get_subtree_nodes = function(a_node) {
+ if (!a_node.children) {
+ return a_node;
+ }
+ else {
+ // At interior node: return subtree nodes.
+ return _.flatten( [a_node, _.map(a_node.children, function(c) { return get_subtree_nodes(c); })] );
+ }
+ };
+
+ // Get node's parents.
+ var parents = [],
+ cur_parent = node.parent;
+ while(cur_parent) {
+ parents.push(cur_parent);
+ cur_parent = cur_parent.parent;
+ }
+
+ return _.flatten([parents, get_subtree_nodes(node)]);
+ },
+
+ /**
+ * Returns the leaf that corresponds to a settings collection.
+ */
+ get_leaf: function(settings) {
+ var cur_node = this.get('tree_data'),
+ find_child = function(children) {
+ return _.find(children, function(child) {
+ return settings[child.param.get('name')] === child.value;
+ });
+ };
+
+ while (cur_node.children) {
+ cur_node = find_child(cur_node.children);
+ }
+ return cur_node;
+ },
+
+ /**
+ * Returns a list of parameters used in tree.
+ */
+ toJSON: function() {
+ // FIXME: returning and jsonifying complete param causes trouble on the server side,
+ // so just use essential attributes for now.
+ return this.get_tree_params().map(function(param) {
+ return {
+ name: param.get('name'),
+ min: param.get('min'),
+ max: param.get('max'),
+ num_samples: param.get('num_samples')
+ };
+ });
+ }
+});
+
+var SweepsterTrack = Backbone.RelationalModel.extend({
+ defaults: {
+ track: null,
+ mode: 'Pack',
+ settings: null,
+ regions: null
+ },
+
+ relations: [
+ {
+ type: Backbone.HasMany,
+ key: 'regions',
+ relatedModel: 'GenomeRegion'
+ }
+ ],
+
+ initialize: function(options) {
+ if (options.track) {
+ // FIXME: find a better way to deal with needed URLs:
+ var track_config = _.extend({
+ data_url: galaxy_paths.get('raw_data_url'),
+ converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
+ }, options.track);
+ this.set('track', object_from_template(track_config, {}, null));
+ }
+ },
+
+ same_settings: function(a_track) {
+ var this_settings = this.get('settings'),
+ other_settings = a_track.get('settings');
+ for (var prop in this_settings) {
+ if (!other_settings[prop] ||
+ this_settings[prop] !== other_settings[prop]) {
+ return false;
+ }
+ }
+ return true;
+ },
+
+ toJSON: function() {
+ return {
+ track: this.get('track').to_dict(),
+ settings: this.get('settings'),
+ regions: this.get('regions')
+ };
+ }
+});
+
+var TrackCollection = Backbone.Collection.extend({
+ model: SweepsterTrack
+});
+
+/**
+ * Sweepster visualization model.
+ */
+var SweepsterVisualization = Visualization.extend({
+ defaults: _.extend({}, Visualization.prototype.defaults, {
+ dataset: null,
+ tool: null,
+ parameter_tree: null,
+ regions: null,
+ tracks: null,
+ default_mode: 'Pack'
+ }),
+
+ relations: [
+ {
+ type: Backbone.HasOne,
+ key: 'dataset',
+ relatedModel: 'Dataset'
+ },
+ {
+ type: Backbone.HasOne,
+ key: 'tool',
+ relatedModel: 'Tool'
+ },
+ {
+ type: Backbone.HasMany,
+ key: 'regions',
+ relatedModel: 'GenomeRegion'
+ },
+ {
+ type: Backbone.HasMany,
+ key: 'tracks',
+ relatedModel: 'SweepsterTrack'
+ }
+ // NOTE: cannot use relationship for parameter tree because creating tree is complex.
+ ],
+
+ initialize: function(options) {
+ var tool_with_samplable_inputs = this.get('tool').copy(true);
+ this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);
+
+ this.set('parameter_tree', new ToolParameterTree({
+ tool: tool_with_samplable_inputs,
+ config: options.tree_config
+ }));
+ },
+
+ add_track: function(track) {
+ this.get('tracks').add(track);
+ },
+
+ toJSON: function() {
+ // TODO: could this be easier by using relational models?
+ return {
+ id: this.get('id'),
+ title: 'Parameter exploration for dataset \'' + this.get('dataset').get('name') + '\'',
+ type: 'sweepster',
+ dataset_id: this.get('dataset').id,
+ tool_id: this.get('tool').id,
+ regions: this.get('regions').toJSON(),
+ tree_config: this.get('parameter_tree').toJSON(),
+ tracks: this.get('tracks').toJSON()
+ };
+ }
+});
+
+/**
+ * --- Views ---
+ */
+
+/**
+ * Sweepster track view.
+ */
+var SweepsterTrackView = Backbone.View.extend({
+ tagName: 'tr',
+
+ TILE_LEN: 250,
+
+ initialize: function(options) {
+ this.canvas_manager = options.canvas_manager;
+ this.render();
+ this.model.on('change:track change:mode', this.draw_tiles, this);
+ },
+
+ render: function() {
+ // Render settings icon and popup.
+ // TODO: use template.
+ var settings = this.model.get('settings'),
+ values = settings.get('values'),
+ settings_td = $('<td/>').addClass('settings').appendTo(this.$el),
+ settings_div = $('<div/>').addClass('track-info').hide().appendTo(settings_td);
+ settings_div.append( $('<div/>').css('font-weight', 'bold').text('Track Settings') );
+ settings.get('inputs').each(function(input) {
+ settings_div.append( input.get('label') + ': ' + values[input.get('name')] + '<br/>');
+ });
+ var self = this,
+ run_on_dataset_button = $('<button/>').appendTo(settings_div).text('Run on complete dataset').click(function() {
+ settings_div.toggle();
+ self.trigger('run_on_dataset', settings);
+ });
+ var icon_menu = create_icon_buttons_menu([
+ {
+ title: 'Settings',
+ icon_class: 'gear track-settings',
+ on_click: function() {
+ settings_div.toggle();
+ }
+ },
+ {
+ title: 'Remove',
+ icon_class: 'cross-circle',
+ on_click: function() {
+ self.$el.remove();
+ $('.bs-tooltip').remove();
+ // TODO: remove track from viz collection.
+ }
+ }
+ ]);
+ settings_td.prepend(icon_menu.$el);
+
+ // Render tile placeholders.
+ this.model.get('regions').each(function() {
+ self.$el.append($('<td/>').addClass('tile').html(
+ $('<img/>').attr('src', galaxy_paths.get('image_path') + '/loading_large_white_bg.gif')
+ ));
+ });
+
+ if (this.model.get('track')) {
+ this.draw_tiles();
+ }
+ },
+
+ /**
+ * Draw tiles for regions.
+ */
+ draw_tiles: function() {
+ var self = this,
+ track = this.model.get('track'),
+ regions = this.model.get('regions'),
+ tile_containers = this.$el.find('td.tile');
+
+ // Do nothing if track is not defined.
+ if (!track) { return; }
+
+ // When data is ready, draw tiles.
+ $.when(track.data_manager.data_is_ready()).then(function(data_ok) {
+ // Draw tile for each region.
+ regions.each(function(region, index) {
+ var resolution = region.length() / self.TILE_LEN,
+ w_scale = 1/resolution,
+ mode = self.model.get('mode');
+ $.when(track.data_manager.get_data(region, mode, resolution, {})).then(function(tile_data) {
+ var canvas = self.canvas_manager.new_canvas();
+ canvas.width = self.TILE_LEN;
+ canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width);
+ track.draw_tile(tile_data, canvas.getContext('2d'), mode, resolution, region, w_scale);
+ $(tile_containers[index]).empty().append(canvas);
+ });
+ });
+ });
+ }
+});
+
+/**
+ * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as
+ * it augments an existing input form row rather than creates a completely new HTML element.
+ */
+var ToolInputValOrSweepView = Backbone.View.extend({
+
+ // Template for rendering sweep inputs:
+ number_input_template: '<div class="form-row-input sweep">' +
+ '<input class="min" type="text" size="6" value="<%= min %>"> - ' +
+ '<input class="max" type="text" size="6" value="<%= max %>">' +
+ ' samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>">' +
+ '</div>',
+
+ select_input_template: '<div class="form-row-input sweep"><%= options %></div>',
+
+ initialize: function(options) {
+ this.$el = options.tool_row;
+ this.render();
+ },
+
+ render: function() {
+ var input = this.model,
+ type = input.get('type'),
+ single_input_row = this.$el.find('.form-row-input'),
+ sweep_inputs_row = null;
+
+ // Update tool inputs as single input changes.
+ single_input_row.find(':input').change(function() {
+ input.set('value', $(this).val());
+ });
+
+ // Add row for parameter sweep inputs.
+ if (type === 'number') {
+ sweep_inputs_row = $(_.template(this.number_input_template, this.model.toJSON()));
+ }
+ else if (type === 'select') {
+ var options = _.map(this.$el.find('select option'), function(option) {
+ return $(option).val();
+ }),
+ options_text = options.join(', ');
+ sweep_inputs_row = $(_.template(this.select_input_template, {
+ options: options_text
+ }));
+ }
+ sweep_inputs_row.insertAfter(single_input_row);
+
+ // Add buttons for adding/removing parameter.
+ var self = this,
+ menu = create_icon_buttons_menu([
+ {
+ title: 'Add parameter to tree',
+ icon_class: 'plus-button',
+ on_click: function () {
+ input.set('in_ptree', true);
+ single_input_row.hide();
+ sweep_inputs_row.show();
+ $(this).hide();
+ self.$el.find('.icon-button.toggle').show();
+ }
+
+ },
+ {
+ title: 'Remove parameter from tree',
+ icon_class: 'toggle',
+ on_click: function() {
+ // Remove parameter from tree params where name matches clicked paramter.
+ input.set('in_ptree', false);
+ sweep_inputs_row.hide();
+ single_input_row.show();
+ $(this).hide();
+ self.$el.find('.icon-button.plus-button').show();
+ }
+ }
+ ],
+ {
+
+ });
+ this.$el.prepend(menu.$el);
+
+ // Show/hide input rows and icons depending on whether parameter is in the tree.
+ if (input.get('in_ptree')) {
+ single_input_row.hide();
+ self.$el.find('.icon-button.plus-button').hide();
+ }
+ else {
+ self.$el.find('.icon-button.toggle').hide();
+ sweep_inputs_row.hide();
+ }
+
+ // Update input's min, max, number of samples as values change.
+ _.each(['min', 'max', 'num_samples'], function(attr) {
+ sweep_inputs_row.find('.' + attr).change(function() {
+ input.set(attr, parseFloat( $(this).val() ));
+ });
+ });
+ }
+});
+
+var ToolParameterTreeDesignView = Backbone.View.extend({
+ className: 'tree-design',
+
+ initialize: function(options) {
+ this.render();
+ },
+
+ render: function() {
+ // Start with tool form view.
+ var tool_form_view = new ToolFormView({
+ model: this.model.get('tool')
+ });
+ tool_form_view.render();
+ this.$el.append(tool_form_view.$el);
+
+ // Set up views for each tool input.
+ var self = this,
+ inputs = self.model.get('tool').get('inputs');
+ this.$el.find('.form-row').not('.form-actions').each(function(i) {
+ var input_view = new ToolInputValOrSweepView({
+ model: inputs.at(i),
+ tool_row: $(this)
+ });
+ });
+ }
+});
+
+/**
+ * Displays and updates parameter tree.
+ */
+var ToolParameterTreeView = Backbone.View.extend({
+ className: 'tool-parameter-tree',
+
+ initialize: function(options) {
+ // When tree data changes, re-render.
+ this.model.on('change:tree_data', this.render, this);
+ },
+
+ render: function() {
+ // Start fresh.
+ this.$el.children().remove();
+
+ var tree_params = this.model.get_tree_params();
+ if (!tree_params.length) {
+ return;
+ }
+
+ // Set width, height based on params and samples.
+ this.width = 100 * (2 + tree_params.length);
+ this.height = 15 * this.model.get_num_leaves();
+
+ var self = this;
+
+ // Layout tree.
+ var cluster = d3.layout.cluster()
+ .size([this.height, this.width - 160]);
+
+ var diagonal = d3.svg.diagonal()
+ .projection(function(d) { return [d.y, d.x]; });
+
+ // Layout nodes.
+ var nodes = cluster.nodes(this.model.get('tree_data'));
+
+ // Setup and add labels for tree levels.
+ var param_depths = _.uniq(_.pluck(nodes, "y"));
+ _.each(tree_params, function(param, index) {
+ var x = param_depths[index+1],
+ center_left = $('#center').position().left;
+ self.$el.append( $('<div>').addClass('label')
+ .text(param.get('label'))
+ .css('left', x + center_left) );
+ });
+
+ // Set up vis element.
+ var vis = d3.select(this.$el[0])
+ .append("svg")
+ .attr("width", this.width)
+ .attr("height", this.height + 30)
+ .append("g")
+ .attr("transform", "translate(40, 20)");
+
+ // Draw links.
+ var link = vis.selectAll("path.link")
+ .data(cluster.links(nodes))
+ .enter().append("path")
+ .attr("class", "link")
+ .attr("d", diagonal);
+
+ // Draw nodes.
+ var node = vis.selectAll("g.node")
+ .data(nodes)
+ .enter().append("g")
+ .attr("class", "node")
+ .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; })
+ .on('mouseover', function(a_node) {
+ var connected_node_ids = _.pluck(self.model.get_connected_nodes(a_node), 'id');
+ // TODO: probably can use enter() to do this more easily.
+ node.filter(function(d) {
+ return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;
+ }).style('fill', '#f00');
+ })
+ .on('mouseout', function() {
+ node.style('fill', '#000');
+ });
+
+ node.append("circle")
+ .attr("r", 9);
+
+ node.append("text")
+ .attr("dx", function(d) { return d.children ? -12 : 12; })
+ .attr("dy", 3)
+ .attr("text-anchor", function(d) { return d.children ? "end" : "start"; })
+ .text(function(d) { return d.name; });
+ }
+});
+
+/**
+ * Sweepster visualization view. View requires rendering in 3-panel setup for now.
+ */
+var SweepsterVisualizationView = Backbone.View.extend({
+ className: 'Sweepster',
+
+ helpText:
+ '<div><h4>Getting Started</h4>' +
+ '<ol><li>Create a parameter tree by using the icons next to the tool\'s parameter names to add or remove parameters.' +
+ '<li>Adjust the tree by using parameter inputs to select min, max, and number of samples' +
+ '<li>Run the tool with different settings by clicking on tree nodes' +
+ '</ol></div>',
+
+ initialize: function(options) {
+ this.canvas_manager = new CanvasManager(this.$el.parents('body'));
+ this.tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') });
+ this.track_collection_container = $('<table/>').addClass('tracks');
+
+ // Handle node clicks for tree data.
+ this.model.get('parameter_tree').on('change:tree_data', this.handle_node_clicks, this);
+
+ // Each track must have a view so it has a canvas manager.
+ var self = this;
+ this.model.get('tracks').each(function(track) {
+ track.get('track').view = self;
+ });
+
+ // Set block, reverse strand block colors; these colors will be used for all tracks.
+ this.block_color = get_random_color();
+ this.reverse_strand_color = get_random_color( [ this.block_color, "#ffffff" ] );
+ },
+
+ render: function() {
+ // Render tree design view in left panel.
+ var tree_design_view = new ToolParameterTreeDesignView({
+ model: this.model.get('parameter_tree')
+ });
+
+ $('#left').append(tree_design_view.$el);
+
+ // Render track collection container/view in right panel.
+ var self = this,
+ regions = self.model.get('regions'),
+ tr = $('<tr/>').appendTo(this.track_collection_container);
+
+ regions.each(function(region) {
+ tr.append( $('<th>').text(region.toString()) );
+ });
+ tr.children().first().attr('colspan', 2);
+
+ var tracks_div = $('<div>').addClass('tiles');
+ $('#right').append( tracks_div.append(this.track_collection_container) );
+
+ self.model.get('tracks').each(function(track) {
+ self.add_track(track);
+ });
+
+ // -- Render help and tool parameter tree in center panel. --
+
+ // Help includes text and a close button.
+ var help_div = $(this.helpText).addClass('help'),
+ close_button = create_icon_buttons_menu([
+ {
+ title: 'Close',
+ icon_class: 'cross-circle',
+ on_click: function() {
+ $('.bs-tooltip').remove();
+ help_div.remove();
+ }
+ }
+ ]);
+
+ help_div.prepend(close_button.$el.css('float', 'right'));
+ $('#center').append(help_div);
+
+ // Parameter tree:
+ this.tool_param_tree_view.render();
+ $('#center').append(this.tool_param_tree_view.$el);
+
+ // Set up handler for tree node clicks.
+ this.handle_node_clicks();
+
+ // Set up visualization menu.
+ var menu = create_icon_buttons_menu(
+ [
+ // Save.
+ /*
+ { icon_class: 'disk--arrow', title: 'Save', on_click: function() {
+ // Show saving dialog box
+ show_modal("Saving...", "progress");
+
+ viz.save().success(function(vis_info) {
+ hide_modal();
+ viz.set({
+ 'id': vis_info.vis_id,
+ 'has_changes': false
+ });
+ })
+ .error(function() {
+ show_modal( "Could Not Save", "Could not save visualization. Please try again later.",
+ { "Close" : hide_modal } );
+ });
+ } },
+ */
+ // Change track modes.
+ {
+ icon_class: 'chevron-expand',
+ title: 'Set display mode'
+ },
+ // Close viz.
+ {
+ icon_class: 'cross-circle',
+ title: 'Close',
+ on_click: function() {
+ window.location = "${h.url_for( controller='visualization', action='list' )}";
+ }
+ }
+ ],
+ {
+ tooltip_config: {placement: 'bottom'}
+ });
+
+ // Create mode selection popup. Mode selection changes default mode and mode for all tracks.
+ var modes = ['Squish', 'Pack'],
+ mode_mapping = {};
+ _.each(modes, function(mode) {
+ mode_mapping[mode] = function() {
+ self.model.set('default_mode', mode);
+ self.model.get('tracks').each(function(track) {
+ track.set('mode', mode);
+ });
+ };
+ });
+
+ make_popupmenu(menu.$el.find('.chevron-expand'), mode_mapping);
+
+ menu.$el.attr("style", "float: right");
+ $("#right .unified-panel-header-inner").append(menu.$el);
+ },
+
+ run_tool_on_dataset: function(settings) {
+ var tool = this.model.get('tool'),
+ tool_name = tool.get('name'),
+ dataset = this.model.get('dataset');
+ tool.set_input_values(settings.get('values'));
+ $.when(tool.rerun(dataset)).then(function(outputs) {
+ // TODO.
+ });
+
+ show_modal('Running ' + tool_name + ' on complete dataset',
+ tool_name + ' is running on dataset \'' +
+ dataset.get('name') + '\'. Outputs are in the dataset\'s history.',
+ {
+ 'Ok': function() { hide_modal(); }
+ });
+ },
+
+ /**
+ * Add track to model and view.
+ */
+ add_track: function(pm_track) {
+ var self = this,
+ param_tree = this.model.get('parameter_tree');
+
+ // Add track to model.
+ self.model.add_track(pm_track);
+
+ var track_view = new SweepsterTrackView({
+ model: pm_track,
+ canvas_manager: self.canvas_manager
+ });
+ track_view.on('run_on_dataset', self.run_tool_on_dataset, self);
+ self.track_collection_container.append(track_view.$el);
+ track_view.$el.hover(function() {
+ var settings_leaf = param_tree.get_leaf(pm_track.get('settings').get('values'));
+ var connected_node_ids = _.pluck(param_tree.get_connected_nodes(settings_leaf), 'id');
+
+ // TODO: can do faster with enter?
+ d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node")
+ .filter(function(d) {
+ return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;
+ }).style('fill', '#f00');
+ },
+ function() {
+ d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node").style('fill', '#000');
+ });
+ return pm_track;
+ },
+
+ /**
+ * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of
+ * the settings defined by the node's subtree and tracks are added for each run.
+ */
+ handle_node_clicks: function() {
+ // When node clicked in tree, run tool and add tracks to model.
+ var self = this,
+ param_tree = this.model.get('parameter_tree'),
+ regions = this.model.get('regions'),
+ node = d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");
+ node.on("click", function(d, i) {
+ // Get all settings corresponding to node.
+ var tool = self.model.get('tool'),
+ dataset = self.model.get('dataset'),
+ all_settings = param_tree.get_node_settings(d),
+ run_jobs_deferred = $.Deferred();
+
+ // Do not allow 10+ jobs to be run.
+ if (all_settings.length >= 10) {
+ show_modal("Whoa there cowboy!",
+ "You clicked on a node to try " + self.model.get('tool').get('name') +
+ " with " + all_settings.length +
+ " different combinations of settings. You can only run 10 jobs at a time.",
+ {
+ "Ok": function() { hide_modal(); run_jobs_deferred.resolve(false); }
+ });
+ }
+ else {
+ run_jobs_deferred.resolve(true);
+ }
+
+ // Take action when deferred resolves.
+ $.when(run_jobs_deferred).then(function(run_jobs) {
+ if (!run_jobs) { return; }
+
+ // Create and add tracks for each settings group.
+ var tracks = _.map(all_settings, function(settings) {
+ var pm_track = new SweepsterTrack({
+ settings: settings,
+ regions: regions,
+ mode: self.model.get('default_mode')
+ });
+ self.add_track(pm_track);
+ return pm_track;
+ });
+
+ // For each track, run tool using track's settings and update track.
+ _.each(tracks, function(pm_track, index) {
+ setTimeout(function() {
+ // Set inputs and run tool.
+ // console.log('running with settings', pm_track.get('settings'));
+ tool.set_input_values(pm_track.get('settings').get('values'));
+ $.when(tool.rerun(dataset, regions)).then(function(output) {
+ // Create and add track for output dataset.
+ var track_config = _.extend({
+ data_url: galaxy_paths.get('raw_data_url'),
+ converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
+ }, output.first().get('track_config')),
+ track_obj = object_from_template(track_config, self, null);
+
+ // Set track block colors.
+ track_obj.prefs.block_color = self.block_color;
+ track_obj.prefs.reverse_strand_color = self.reverse_strand_color;
+
+ pm_track.set('track', track_obj);
+ });
+ }, index * 10000);
+ });
+ });
+ });
+ }
+});
\ No newline at end of file
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -3074,7 +3074,7 @@
// Go to visualization.
window.location.href =
- galaxy_paths.get('paramamonster_url') + "?" +
+ galaxy_paths.get('sweepster_url') + "?" +
$.param({
dataset_id: track.dataset_id,
hda_ldda: track.hda_ldda,
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 templates/base_panels.mako
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -60,7 +60,7 @@
converted_datasets_state_url: '${h.url_for( controller="/tracks", action="converted_datasets_state" )}',
dataset_state_url: '${h.url_for( controller="/tracks", action="dataset_state" )}',
visualization_url: '${h.url_for( controller="/visualization", action="save" )}',
- paramamonster_url: '${h.url_for( controller="/tracks", action="paramamonster" )}'
+ sweepster_url: '${h.url_for( controller="/tracks", action="sweepster" )}'
});
</script></%def>
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 templates/visualization/paramamonster.mako
--- a/templates/visualization/paramamonster.mako
+++ /dev/null
@@ -1,137 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
- self.has_left_panel=True
- self.has_right_panel=True
- self.active_view="visualization"
- self.message_box_visible=False
-%>
-</%def>
-
-<%def name="stylesheets()">
- ${parent.stylesheets()}
- <style>
- .link {
- fill: none;
- stroke: #ccc;
- stroke-width: 1.5px;
- }
- .node {
- font: 10px sans-serif;
- }
- .node circle {
- fill: #fff;
- stroke: steelblue;
- stroke-width: 1.5px;
- cursor: pointer;
- }
- .node:hover {
- fill: #f00;
- }
- .node:hover circle {
- fill: #ccc;
- stroke: #f00;
- }
- table.tracks {
- border-collapse: separate;
- border-spacing: 5px;
- }
- .tile {
- border: solid 1px #DDD;
- margin: 2px;
- border-radius: 10px;
- margin: 3px;
- }
- .label {
- position: fixed;
- font: 10px sans-serif;
- font-weight: bold;
- background-color: #DDD;
- border-radius: 5px;
- padding: 1px;
- }
- th,td {
- text-align: center;
- }
- td.settings {
- vertical-align: top;
- }
- .icon-button.track-settings {
- float: none;
- }
- .track-info {
- text-align: left;
- font: 10px sans-serif;
- position: fixed;
- background-color: #CCC;
- border: solid 1px #AAA;
- border-radius: 2px;
- padding: 2px;
- }
- .btn-primary, .btn-primary:hover {
- color: #EEE;
- background-color: #DDD;
- background-image: none;
- border-radius: 12px;
- }
- #left {
- width: 300px;
- }
- #center {
- left: 300px;
- right: 600px;
- overflow: auto;
- }
- #right {
- width: 600px;
- }
- .tiles {
- overflow: auto;
- position: absolute;
- top: 30px;
- bottom: 25px;
- left: 0;
- right: 0;
- }
- .help {
- border-radius: 15px;
- border: solid 1px #CCC;
- padding: 0px 2px;
- margin: 10px;
- }
- </style>
-</%def>
-
-<%def name="javascripts()">
- ${parent.javascripts()}
-
- ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )}
- ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/paramamonster",
- "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider" )}
-
- <script type="text/javascript">
- var viz;
- $(function() {
- // -- Viz set up. --
- var viz = new ParamaMonsterVisualization(
- ${ h.to_json_string( config ).replace('\\', '\\\\' )}
- );
- var viz_view = new ParamaMonsterVisualizationView({ model: viz });
- viz_view.render();
- });
- </script>
-</%def>
-
-<%def name="center_panel()">
-</%def>
-
-<%def name="left_panel()">
-</%def>
-
-<%def name="right_panel()">
- <div class="unified-panel-header" unselectable="on">
- <div class="unified-panel-header-inner">
- </div>
- </div>
-</%def>
\ No newline at end of file
diff -r 10829b9c5086a09b80b0c592d9a289b65d723fcf -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 templates/visualization/sweepster.mako
--- /dev/null
+++ b/templates/visualization/sweepster.mako
@@ -0,0 +1,137 @@
+<%inherit file="/webapps/galaxy/base_panels.mako"/>
+
+<%def name="init()">
+<%
+ self.has_left_panel=True
+ self.has_right_panel=True
+ self.active_view="visualization"
+ self.message_box_visible=False
+%>
+</%def>
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .link {
+ fill: none;
+ stroke: #ccc;
+ stroke-width: 1.5px;
+ }
+ .node {
+ font: 10px sans-serif;
+ }
+ .node circle {
+ fill: #fff;
+ stroke: steelblue;
+ stroke-width: 1.5px;
+ cursor: pointer;
+ }
+ .node:hover {
+ fill: #f00;
+ }
+ .node:hover circle {
+ fill: #ccc;
+ stroke: #f00;
+ }
+ table.tracks {
+ border-collapse: separate;
+ border-spacing: 5px;
+ }
+ .tile {
+ border: solid 1px #DDD;
+ margin: 2px;
+ border-radius: 10px;
+ margin: 3px;
+ }
+ .label {
+ position: fixed;
+ font: 10px sans-serif;
+ font-weight: bold;
+ background-color: #DDD;
+ border-radius: 5px;
+ padding: 1px;
+ }
+ th,td {
+ text-align: center;
+ }
+ td.settings {
+ vertical-align: top;
+ }
+ .icon-button.track-settings {
+ float: none;
+ }
+ .track-info {
+ text-align: left;
+ font: 10px sans-serif;
+ position: fixed;
+ background-color: #CCC;
+ border: solid 1px #AAA;
+ border-radius: 2px;
+ padding: 2px;
+ }
+ .btn-primary, .btn-primary:hover {
+ color: #EEE;
+ background-color: #DDD;
+ background-image: none;
+ border-radius: 12px;
+ }
+ #left {
+ width: 300px;
+ }
+ #center {
+ left: 300px;
+ right: 600px;
+ overflow: auto;
+ }
+ #right {
+ width: 600px;
+ }
+ .tiles {
+ overflow: auto;
+ position: absolute;
+ top: 30px;
+ bottom: 25px;
+ left: 0;
+ right: 0;
+ }
+ .help {
+ border-radius: 15px;
+ border: solid 1px #CCC;
+ padding: 0px 2px;
+ margin: 10px;
+ }
+ </style>
+</%def>
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+
+ ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )}
+ ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/sweepster",
+ "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider" )}
+
+ <script type="text/javascript">
+ var viz;
+ $(function() {
+ // -- Viz set up. --
+ var viz = new SweepsterVisualization(
+ ${ h.to_json_string( config ).replace('\\', '\\\\' )}
+ );
+ var viz_view = new SweepsterVisualizationView({ model: viz });
+ viz_view.render();
+ });
+ </script>
+</%def>
+
+<%def name="center_panel()">
+</%def>
+
+<%def name="left_panel()">
+</%def>
+
+<%def name="right_panel()">
+ <div class="unified-panel-header" unselectable="on">
+ <div class="unified-panel-header-inner">
+ </div>
+ </div>
+</%def>
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/changeset/51992bf52e0c/
changeset: 51992bf52e0c
user: jgoecks
date: 2012-07-24 20:28:08
summary: Add bigwig/bigbed support to Circster. Pack scripts.
affected #: 7 files
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -105,6 +105,17 @@
"""
iterator = self.get_iterator( chrom, start, end )
return self.process_data( iterator, start_val, max_vals, **kwargs )
+
+ def get_genome_data( self, chroms_info, **kwargs ):
+ """
+ Returns data for complete genome.
+ """
+ dataset_summary = []
+ for chrom_info in chroms_info[ 'chrom_info' ]:
+ summary = self.get_data( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], **kwargs )
+ dataset_summary.append( summary )
+
+ return dataset_summary
def get_filters( self ):
"""
@@ -617,20 +628,8 @@
def valid_chroms( self ):
st = summary_tree_from_file( self.converted_dataset.file_name )
return st.chrom_blocks.keys()
-
- def get_genome_data( self, chroms_info ):
- """
- Returns summary tree data for complete genome.
- """
- dataset_summary = []
- for chrom_info in chroms_info[ 'chrom_info' ]:
- summary = self.get_summary( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], level=3, detail_cutoff=0, draw_cutoff=0 )
- dataset_summary.append( summary )
-
- return dataset_summary
- # TODO: rename to get_data to match other providers.
- def get_summary( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None ):
+ def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None ):
"""
Returns summary tree data for a given genomic region.
"""
@@ -899,7 +898,7 @@
all_dat = bbi.query(chrom, 0, 2147483647, 1)
f.close()
return all_dat is not None
-
+
def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
# Bigwig can be a standalone bigwig file, in which case we use
# original_dataset, or coming from wig->bigwig conversion in
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -380,7 +380,7 @@
tracks_dataset_type = data_sources['index']['name']
converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset )
- summary = indexer.get_summary( chrom, low, high, resolution=kwargs[ 'resolution' ] )
+ summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] )
if summary is None:
return { 'dataset_type': tracks_dataset_type, 'data': None }
@@ -528,7 +528,8 @@
# Get converted dataset and append track's genome data.
converted_dataset = dataset.get_converted_dataset( trans, indexed_type )
data_provider = get_data_provider( indexed_type )( converted_dataset, dataset )
- track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info ) }
+ # HACK: pass in additional params, which are only used for summary tree data, not BBI data.
+ track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) }
return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome )
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 static/scripts/packed/bootstrap.js
--- a/static/scripts/packed/bootstrap.js
+++ b/static/scripts/packed/bootstrap.js
@@ -1,1 +1,1 @@
-!function(b){var a=function(c){this.element=b(c)};a.prototype={constructor:a,show:function(){var i=this.element,f=i.closest("ul:not(.dropdown-menu)"),d=i.attr("data-target"),g,c,h;if(!d){d=i.attr("href");d=d&&d.replace(/.*(?=#[^\s]*$)/,"")}if(i.parent("li").hasClass("active")){return}g=f.find(".active a").last()[0];h=b.Event("show",{relatedTarget:g});i.trigger(h);if(h.isDefaultPrevented()){return}c=b(d);this.activate(i.parent("li"),f);this.activate(c,c.parent(),function(){i.trigger({type:"shown",relatedTarget:g})})},activate:function(e,d,h){var c=d.find("> .active"),g=h&&b.support.transition&&c.hasClass("fade");function f(){c.removeClass("active").find("> .dropdown-menu > .active").removeClass("active");e.addClass("active");if(g){e[0].offsetWidth;e.addClass("in")}else{e.removeClass("fade")}if(e.parent(".dropdown-menu")){e.closest("li.dropdown").addClass("active")}h&&h()}g?c.one(b.support.transition.end,f):f();c.removeClass("in")}};b.fn.tab=function(c){return this.each(function(){var e=b(this),d=e.data("tab");if(!d){e.data("tab",(d=new a(this)))}if(typeof c=="string"){d[c]()}})};b.fn.tab.Constructor=a;b(function(){b("body").on("click.tab.data-api",'[data-toggle="tab"], [data-toggle="pill"]',function(c){c.preventDefault();b(this).tab("show")})})}(window.jQuery);!function(b){var a=function(d,c){this.init("tooltip",d,c)};a.prototype={constructor:a,init:function(f,e,d){var g,c;this.type=f;this.$element=b(e);this.options=this.getOptions(d);this.enabled=true;if(this.options.trigger!="manual"){g=this.options.trigger=="hover"?"mouseenter":"focus";c=this.options.trigger=="hover"?"mouseleave":"blur";this.$element.on(g,this.options.selector,b.proxy(this.enter,this));this.$element.on(c,this.options.selector,b.proxy(this.leave,this))}this.options.selector?(this._options=b.extend({},this.options,{trigger:"manual",selector:""})):this.fixTitle()},getOptions:function(c){c=b.extend({},b.fn[this.type].defaults,c,this.$element.data());if(c.delay&&typeof 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\ No newline at end of file
+!function(a){a(function(){a.support.transition=(function(){var b=(function(){var e=document.createElement("bootstrap"),d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in d){if(e.style[c]!==undefined){return d[c]}}}());return b&&{end:b}})()})}(window.jQuery);!function(b){var a=function(c){this.element=b(c)};a.prototype={constructor:a,show:function(){var i=this.element,f=i.closest("ul:not(.dropdown-menu)"),d=i.attr("data-target"),g,c,h;if(!d){d=i.attr("href");d=d&&d.replace(/.*(?=#[^\s]*$)/,"")}if(i.parent("li").hasClass("active")){return}g=f.find(".active a").last()[0];h=b.Event("show",{relatedTarget:g});i.trigger(h);if(h.isDefaultPrevented()){return}c=b(d);this.activate(i.parent("li"),f);this.activate(c,c.parent(),function(){i.trigger({type:"shown",relatedTarget:g})})},activate:function(e,d,h){var c=d.find("> 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\ No newline at end of file
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 static/scripts/packed/viz/sweepster.js
--- /dev/null
+++ b/static/scripts/packed/viz/sweepster.js
@@ -0,0 +1,1 @@
+var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var SweepsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:SweepsterTrack});var SweepsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"SweepsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var SweepsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".bs-tooltip").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");if(!a){return}$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i=b.model.get("mode");$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1],m=$("#center").position().left;h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+m))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var SweepsterVisualizationView=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a});this.block_color=get_random_color();this.reverse_strand_color=get_random_color([this.block_color,"#ffffff"])},render:function(){var g=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(g.$el);var j=this,d=j.model.get("regions"),h=$("<tr/>").appendTo(this.track_collection_container);d.each(function(k){h.append($("<th>").text(k.toString()))});h.children().first().attr("colspan",2);var e=$("<div>").addClass("tiles");$("#right").append(e.append(this.track_collection_container));j.model.get("tracks").each(function(k){j.add_track(k)});var i=$(this.helpText).addClass("help"),f=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();i.remove()}}]);i.prepend(f.$el.css("float","right"));$("#center").append(i);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var c=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var b=["Squish","Pack"],a={};_.each(b,function(k){a[k]=function(){j.model.set("default_mode",k);j.model.get("tracks").each(function(l){l.set("mode",k)})}});make_popupmenu(c.$el.find(".chevron-expand"),a);c.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(c.$el)},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new SweepsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new SweepsterTrack({settings:m,regions:d,mode:a.model.get("default_mode")});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);o.prefs.block_color=a.block_color;o.prefs.reverse_strand_color=a.reverse_strand_color;n.set("track",o)})},m*10000)})})})}});
\ No newline at end of file
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 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 class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.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(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.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(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;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 Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}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 Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.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.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});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(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);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(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: 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Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aa.manager.alpha_filter!==aa){aa.manager.alpha_filter=aa;aa.manager.parent_div.find(".layer-transparent").removeClass("active").hide();aa.transparency_icon.addClass("active").show()}else{aa.manager.alpha_filter=null;aa.transparency_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aa.manager.height_filter!==aa){aa.manager.height_filter=aa;aa.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();aa.height_icon.addClass("active").show()}else{aa.manager.height_filter=null;aa.height_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();aa.parent_div.hover(function(){aa.transparency_icon.show();aa.height_icon.show()},function(){if(aa.manager.alpha_filter!==aa){aa.transparency_icon.hide()}if(aa.manager.height_filter!==aa){aa.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){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(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("paramamonster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.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 W){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this,ab=Z.view;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;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(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.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(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/P)/Math.log(RESOLUTION)));am=ab/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ac,ad,af,Z){var ab=this;var ae=false;for(var aa=0;aa<ac.length;aa++){if(ac[aa].has_icons){ae=true;break}}if(ae){for(var aa=0;aa<ac.length;aa++){tile=ac[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[];var Z=0;for(var av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(var av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value: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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{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:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",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:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;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()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this;if(ai.mode==="Histogram"){var al,aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(var al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(var al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){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(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_summary_tree_data:function(ad,ag,ab,ao){if(ao>ab-ag){ao=ab-ag}var ak=Math.floor((ab-ag)/ao),an=[],ac=0;var ae=0,af=0,aj,am=0,ah=[],al,ai;var aa=function(ar,aq,at,ap){ar[0]=aq+at*ap;ar[1]=aq+(at+1)*ap};while(am<ao&&ae!==ad.length){var Z=false;for(;am<ao&&!Z;am++){aa(ah,ag,am,ak);for(af=ae;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){Z=true;break}}if(Z){break}}data_start_index=af;an[an.length]=al=[ah[0],0];for(;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){al[1]++}else{break}}if(al[1]>ac){ac=al[1]}am++}return{max:ac,delta:ak,data:an}},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Histogram"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(ak,ao,am,ap,ac,ag,ab){var an=this,aa=ao.canvas,aw=ac.get("start"),Z=ac.get("end"),aB=25,ad=this.left_offset;if(am==="summary_tree"||am==="Histogram"){if(ak.dataset_type!=="summary_tree"){var ah=this.get_summary_tree_data(ak.data,aw,Z,200);if(ak.max){ah.max=ak.max}ak=ah}var ay=new I.SummaryTreePainter(ak,aw,Z,this.prefs);ay.draw(ao,aa.width,aa.height,ag);return new j(an,ac,ap,aa,ak.data,ak.max)}var af=[],al=this.slotters[ag].slots;all_slotted=true;if(ak.data){var ai=this.filters_manager.filters;for(var aq=0,at=ak.data.length;aq<at;aq++){var ae=ak.data[aq];var ar=false;var aj;for(var av=0,aA=ai.length;av<aA;av++){aj=ai[av];aj.update_attrs(ae);if(!aj.keep(ae)){ar=true;break}}if(!ar){af.push(ae);if(!(ae[0] in al)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var ax=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ay=new (this.painter)(af,aw,Z,this.prefs,am,az,ax,ab);var au=null;ao.fillStyle=this.prefs.block_color;ao.font=ao.canvas.manager.default_font;ao.textAlign="right";if(ak.data){au=ay.draw(ao,aa.width,aa.height,ag,al);au.translation=-ad}return new L(an,ac,ap,aa,ak.data,ag,am,ak.message,all_slotted,au)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value: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_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({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:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,view_range=this.view_end-this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){var min_value=Infinity;for(var i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(var i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,view_range=this.view_end-this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=y_scale=this.get_row_height(),mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var view_range=this.view_end-this.view_start,y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var track=this,tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale)));if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}if(b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){var min_value=Infinity;for(var i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(var i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,view_range=this.view_end-this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.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(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.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(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;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 Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}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 Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.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.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});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(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);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(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);Z.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()});if("visible" in ac&&ac.visible){this.parent_div.show()}};o(q.prototype,{update_params:function(){for(var Z=0;Z<this.params.length;Z++){this.params[Z].update_value()}},state_dict:function(){var aa={};for(var Z=0;Z<this.params.length;Z++){aa[this.params[Z].name]=this.params[Z].value}aa.visible=this.parent_div.is(":visible");return aa},get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=ab});return Z},get_param_values:function(){var Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aa.manager.alpha_filter!==aa){aa.manager.alpha_filter=aa;aa.manager.parent_div.find(".layer-transparent").removeClass("active").hide();aa.transparency_icon.addClass("active").show()}else{aa.manager.alpha_filter=null;aa.transparency_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aa.manager.height_filter!==aa){aa.manager.height_filter=aa;aa.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();aa.height_icon.addClass("active").show()}else{aa.manager.height_filter=null;aa.height_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();aa.parent_div.hover(function(){aa.transparency_icon.show();aa.height_icon.show()},function(){if(aa.manager.alpha_filter!==aa){aa.transparency_icon.hide()}if(aa.manager.height_filter!==aa){aa.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){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(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.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 W){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this,ab=Z.view;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;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(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.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(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/P)/Math.log(RESOLUTION)));am=ab/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ac,ad,af,Z){var ab=this;var ae=false;for(var aa=0;aa<ac.length;aa++){if(ac[aa].has_icons){ae=true;break}}if(ae){for(var aa=0;aa<ac.length;aa++){tile=ac[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[];var Z=0;for(var av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(var av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value: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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{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:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",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:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;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()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this;if(ai.mode==="Histogram"){var al,aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(var al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(var al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){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(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_summary_tree_data:function(ad,ag,ab,ao){if(ao>ab-ag){ao=ab-ag}var ak=Math.floor((ab-ag)/ao),an=[],ac=0;var ae=0,af=0,aj,am=0,ah=[],al,ai;var aa=function(ar,aq,at,ap){ar[0]=aq+at*ap;ar[1]=aq+(at+1)*ap};while(am<ao&&ae!==ad.length){var Z=false;for(;am<ao&&!Z;am++){aa(ah,ag,am,ak);for(af=ae;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){Z=true;break}}if(Z){break}}data_start_index=af;an[an.length]=al=[ah[0],0];for(;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){al[1]++}else{break}}if(al[1]>ac){ac=al[1]}am++}return{max:ac,delta:ak,data:an}},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Histogram"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(ak,ao,am,ap,ac,ag,ab){var an=this,aa=ao.canvas,aw=ac.get("start"),Z=ac.get("end"),aB=25,ad=this.left_offset;if(am==="summary_tree"||am==="Histogram"){if(ak.dataset_type!=="summary_tree"){var ah=this.get_summary_tree_data(ak.data,aw,Z,200);if(ak.max){ah.max=ak.max}ak=ah}var ay=new I.SummaryTreePainter(ak,aw,Z,this.prefs);ay.draw(ao,aa.width,aa.height,ag);return new j(an,ac,ap,aa,ak.data,ak.max)}var af=[],al=this.slotters[ag].slots;all_slotted=true;if(ak.data){var ai=this.filters_manager.filters;for(var aq=0,at=ak.data.length;aq<at;aq++){var ae=ak.data[aq];var ar=false;var aj;for(var av=0,aA=ai.length;av<aA;av++){aj=ai[av];aj.update_attrs(ae);if(!aj.keep(ae)){ar=true;break}}if(!ar){af.push(ae);if(!(ae[0] in al)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var ax=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ay=new (this.painter)(af,aw,Z,this.prefs,am,az,ax,ab);var au=null;ao.fillStyle=this.prefs.block_color;ao.font=ao.canvas.manager.default_font;ao.textAlign="right";if(ak.data){au=ay.draw(ao,aa.width,aa.height,ag,al);au.translation=-ad}return new L(an,ac,ap,aa,ak.data,ag,am,ak.message,all_slotted,au)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value: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_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({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:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,view_range=this.view_end-this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){var min_value=Infinity;for(var i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(var i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,view_range=this.view_end-this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=y_scale=this.get_row_height(),mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var view_range=this.view_end-this.view_start,y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var track=this,tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){var min_value=Infinity;for(var i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(var i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,view_range=this.view_end-this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,genome_wide_summary_data:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({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.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var GenomeWideSummaryData=Backbone.RelationalModel.extend({defaults:{data:null,max:0},initialize:function(b){var a=_.max(this.get("data"),function(c){if(!c||typeof c==="string"){return 0}return c[1]});this.attributes.max=(a&&typeof a!=="string"?a[1]:0)}});var BackboneTrack=Dataset.extend({initialize:function(a){this.set("id",a.dataset_id)},relations:[{type:Backbone.HasOne,key:"genome_wide_data",relatedModel:"GenomeWideSummaryData"}]});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:"BackboneTrack"}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var GenomeVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{bookmarks:null,viewport:null})});var TrackConfig=Backbone.Model.extend({});var CircsterHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height;this.track_gap=5},render:function(){var b=this,c=this.dataset_arc_height;var a=d3.select(b.$el[0]).append("svg").attr("width",b.width).attr("height",b.height).append("g").attr("transform","translate("+b.width/2+","+b.height/2+")");this.model.get("tracks").each(function(e,j){var g=e.get("genome_wide_data");var i=b.radius_start+j*(c+b.track_gap),o=new CircsterHistogramDatasetLayout({genome:b.genome,total_gap:b.total_gap}),n=o.chroms_layout(),l=_.zip(n,g.get("data")),m=g.get("max"),f=_.map(l,function(s){var t=s[0],r=s[1];return o.chrom_data_layout(t,r,i,i+c,m)});var p=a.append("g").attr("id","inner-arc"),k=d3.svg.arc().innerRadius(i).outerRadius(i+c),d=p.selectAll("#inner-arc>path").data(n).enter().append("path").attr("d",k).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(r){return r.data.chrom});var q=e.get("prefs"),h=q.block_color;_.each(f,function(r){if(!r){return}var u=a.append("g"),t=d3.svg.arc().innerRadius(i),s=u.selectAll("path").data(r).enter().append("path").attr("d",t).style("stroke",h).style("fill",h)})})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})};
\ No newline at end of file
+var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"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")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,genome_wide_summary_data:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({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.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var GenomeWideBigWigData=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.flatten(_.map(this.get("data"),function(c){if(c.data.length!==0){return _.map(c.data,function(d){return d[1]})}else{return 0}}));this.set("max",_.max(a));this.set("min",_.min(a))}});var GenomeWideSummaryTreeData=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.max(this.get("data"),function(c){if(!c||typeof c==="string"){return 0}return c[1]});this.attributes.max=(a&&typeof a!=="string"?a[1]:0)}});var BackboneTrack=Dataset.extend({initialize:function(a){this.set("id",a.dataset_id);var c=this.get("genome_wide_data");if(c){var b=(this.get("track_type")==="LineTrack"?GenomeWideBigWigData:GenomeWideSummaryTreeData);this.set("genome_wide_data",new b(c))}}});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:"BackboneTrack"}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var GenomeVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{bookmarks:null,viewport:null})});var TrackConfig=Backbone.Model.extend({});var CircsterDataLayout=Backbone.Model.extend({defaults:{genome:null,dataset:null,total_gap:null},chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(d,c,b,e,a){},genome_data_layout:function(){var b=this,a=this.chroms_layout(),f=this.get("track").get("genome_wide_data"),e=this.get("radius_start"),c=this.get("radius_end"),d=_.zip(a,f.get("data")),g=_.map(d,function(i){var j=i[0],h=i[1];return b.chrom_data_layout(j,h,e,c,f.get("min"),f.get("max"))});return g}});var CircsterSummaryTreeLayout=CircsterDataLayout.extend({chrom_data_layout:function(k,b,h,g,d,i){if(!b||typeof b==="string"){return null}var e=b[0],j=b[3],c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l){return j}).startAngle(k.startAngle).endAngle(k.endAngle),a=f(e);_.each(e,function(l,m){a[m].outerRadius=c(l[1])});return a}});var CircsterBigWigLayout=CircsterDataLayout.extend({chrom_data_layout:function(j,b,h,g,d,i){var e=b.data;if(e.length===0){return}var c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l,k){if(k+1===e.length){return 0}return e[k+1][0]-e[k][0]}).startAngle(j.startAngle).endAngle(j.endAngle),a=f(e);_.each(e,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height;this.track_gap=5},render:function(){var b=this,c=this.dataset_arc_height;var a=d3.select(b.$el[0]).append("svg").attr("width",b.width).attr("height",b.height).append("g").attr("transform","translate("+b.width/2+","+b.height/2+")");this.model.get("tracks").each(function(f,l){var g=f.get("genome_wide_data"),k=b.radius_start+l*(c+b.track_gap),h=(g instanceof GenomeWideBigWigData?CircsterBigWigLayout:CircsterSummaryTreeLayout),n=new h({track:f,radius_start:k,radius_end:k+c,genome:b.genome,total_gap:b.total_gap}),d=n.chroms_layout(),i=n.genome_data_layout();var o=a.append("g").attr("id","inner-arc"),m=d3.svg.arc().innerRadius(k).outerRadius(k+c),e=o.selectAll("#inner-arc>path").data(d).enter().append("path").attr("d",m).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(q){return q.data.chrom});var p=f.get("prefs"),j=p.block_color;_.each(i,function(q){if(!q){return}var t=a.append("g"),s=d3.svg.arc().innerRadius(k),r=t.selectAll("path").data(q).enter().append("path").attr("d",s).style("stroke",j).style("fill",j)})})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})};
\ No newline at end of file
diff -r 339f886d3ffadcb8cd5eb63029a141a55c9b2fd1 -r 51992bf52e0c6f1931256903f678b13ed2d373b6 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -549,13 +549,40 @@
model: BrowserBookmark
});
-/**
- * Genome-wide summary data.
- */
-var GenomeWideSummaryData = Backbone.RelationalModel.extend({
+var GenomeWideBigWigData = Backbone.Model.extend({
defaults: {
data: null,
- max: 0
+ min: 0,
+ max: 0
+ },
+
+ initialize: function(options) {
+ // Set max across dataset by extracting all values, flattening them into a
+ // single array, and getting the min and max.
+ var values = _.flatten( _.map(this.get('data'), function(d) {
+ if (d.data.length !== 0) {
+ // Each data point has the form [position, value], so return all values.
+ return _.map(d.data, function(p) {
+ return p[1];
+ });
+ }
+ else {
+ return 0;
+ }
+ }) );
+ this.set('max', _.max(values));
+ this.set('min', _.min(values));
+ }
+});
+
+/**
+ * Genome-wide summary tree dataset.
+ */
+var GenomeWideSummaryTreeData = Backbone.RelationalModel.extend({
+ defaults: {
+ data: null,
+ min: 0,
+ max: 0
},
initialize: function(options) {
@@ -577,15 +604,15 @@
initialize: function(options) {
// Dataset id is unique ID for now.
this.set('id', options.dataset_id);
- },
- relations: [
- {
- type: Backbone.HasOne,
- key: 'genome_wide_data',
- relatedModel: 'GenomeWideSummaryData'
+ // Create genome-wide dataset if available.
+ var genome_wide_data = this.get('genome_wide_data');
+ if (genome_wide_data) {
+ var gwd_class = (this.get('track_type') === 'LineTrack' ?
+ GenomeWideBigWigData : GenomeWideSummaryTreeData);
+ this.set('genome_wide_data', new gwd_class(genome_wide_data));
}
- ]
+ }
});
/**
@@ -649,12 +676,14 @@
});
-/**
- * Layout for a histogram dataset in a circster visualization.
- */
-var CircsterHistogramDatasetLayout = Backbone.Model.extend({
- // TODO: should accept genome and dataset and use these to generate layout data.
-
+
+var CircsterDataLayout = Backbone.Model.extend({
+ defaults: {
+ genome: null,
+ dataset: null,
+ total_gap: null
+ },
+
/**
* Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle
* separated by gaps.
@@ -671,16 +700,45 @@
arc.endAngle = (new_endAngle > arc.startAngle ? new_endAngle : arc.startAngle);
return arc;
});
-
- // TODO: remove arcs for chroms that are too small and recompute?
-
return chrom_arcs;
},
+
+ /**
+ * Returns layouts for drawing a chromosome's data.
+ */
+ chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) {
+ },
+
+ genome_data_layout: function() {
+ var self = this,
+ chrom_arcs = this.chroms_layout(),
+ dataset = this.get('track').get('genome_wide_data'),
+ r_start = this.get('radius_start'),
+ r_end = this.get('radius_end'),
+
+ // Merge chroms layout with data.
+ layout_and_data = _.zip(chrom_arcs, dataset.get('data')),
+
+ // Do dataset layout for each chromosome's data using pie layout.
+ chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
+ var chrom_arc = chrom_info[0],
+ chrom_data = chrom_info[1];
+ return self.chrom_data_layout(chrom_arc, chrom_data, r_start, r_end, dataset.get('min'), dataset.get('max'));
+ });
+
+ return chroms_data_layout;
+ }
+});
+
+/**
+ * Layout for summary tree data in a circster visualization.
+ */
+var CircsterSummaryTreeLayout = CircsterDataLayout.extend({
/**
- * Returns layouts for drawing a chromosome's data. For now, only works with summary tree data.
+ * Returns layouts for drawing a chromosome's data.
*/
- chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) {
+ chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) {
// If no chrom data, return null.
if (!chrom_data || typeof chrom_data === "string") {
return null;
@@ -689,8 +747,8 @@
var data = chrom_data[0],
delta = chrom_data[3],
scale = d3.scale.linear()
- .domain( [0, max] )
- .range( [inner_radius, outer_radius] ),
+ .domain( [min, max] )
+ .range( [inner_radius, outer_radius] ),
arc_layout = d3.layout.pie().value(function(d) {
return delta;
})
@@ -705,7 +763,42 @@
return arcs;
}
-
+});
+
+/**
+ * Layout for BigWig data in a circster visualization.
+ */
+var CircsterBigWigLayout = CircsterDataLayout.extend({
+
+ /**
+ * Returns layouts for drawing a chromosome's data.
+ */
+ chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) {
+ var data = chrom_data.data;
+ if (data.length === 0) { return; }
+
+ var scale = d3.scale.linear()
+ .domain( [min, max] )
+ .range( [inner_radius, outer_radius] ),
+ arc_layout = d3.layout.pie().value(function(d, i) {
+ // If at end of data, draw nothing.
+ if (i + 1 === data.length) { return 0; }
+
+ // Layout is from current position to next position.
+ return data[i+1][0] - data[i][0];
+ })
+ .startAngle(chrom_arc.startAngle)
+ .endAngle(chrom_arc.endAngle),
+ arcs = arc_layout(data);
+
+ // Use scale to assign outer radius.
+ _.each(data, function(datum, index) {
+ arcs[index].outerRadius = scale(datum[1]);
+ });
+
+ return arcs;
+ }
+
});
/**
@@ -739,27 +832,20 @@
// -- Render each dataset in the visualization. --
this.model.get('tracks').each(function(track, index) {
- var dataset = track.get('genome_wide_data');
-
- var radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap),
+ var dataset = track.get('genome_wide_data'),
+ radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap),
// Layout chromosome arcs.
- arcs_layout = new CircsterHistogramDatasetLayout({
+ layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ),
+ arcs_layout = new layout_class({
+ track: track,
+ radius_start: radius_start,
+ radius_end: radius_start + dataset_arc_height,
genome: self.genome,
total_gap: self.total_gap
}),
- chrom_arcs = arcs_layout.chroms_layout(),
+ genome_arcs = arcs_layout.chroms_layout(),
+ chroms_arcs = arcs_layout.genome_data_layout();
- // Merge chroms layout with data.
- layout_and_data = _.zip(chrom_arcs, dataset.get('data')),
- dataset_max = dataset.get('max'),
-
- // Do dataset layout for each chromosome's data using pie layout.
- chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
- var chrom_arc = chrom_info[0],
- chrom_data = chrom_info[1];
- return arcs_layout.chrom_data_layout(chrom_arc, chrom_data, radius_start, radius_start + dataset_arc_height, dataset_max);
- });
-
// -- Render. --
// Draw background arcs for each chromosome.
@@ -769,7 +855,7 @@
.outerRadius(radius_start + dataset_arc_height),
// Draw arcs.
chroms_elts = base_arc.selectAll("#inner-arc>path")
- .data(chrom_arcs).enter().append("path")
+ .data(genome_arcs).enter().append("path")
.attr("d", arc_gen)
.style("stroke", "#ccc")
.style("fill", "#ccc")
@@ -778,7 +864,7 @@
// For each chromosome, draw dataset.
var prefs = track.get('prefs'),
block_color = prefs.block_color;
- _.each(chroms_data_layout, function(chrom_layout) {
+ _.each(chroms_arcs, function(chrom_layout) {
if (!chrom_layout) { return; }
var group = svg.append("g"),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: rmarenco: Added eXpress sam format support + 5 parameters (-B, -O, --calc-covar, -m, -s) with their associated tests
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/cb9272041d95/
changeset: cb9272041d95
user: rmarenco
date: 2012-07-23 20:17:23
summary: Added eXpress sam format support + 5 parameters (-B, -O, --calc-covar, -m, -s) with their associated tests
affected #: 15 files
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Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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