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 31 Jul '12
by Bitbucket 31 Jul '12
31 Jul '12
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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commit/galaxy-central: dannon: Fix tabular display to serve raw when preview == False, which should resolve external display issues.
by Bitbucket 30 Jul '12
by Bitbucket 30 Jul '12
30 Jul '12
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 27 Jul '12
by Bitbucket 27 Jul '12
27 Jul '12
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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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 27 Jul '12
by Bitbucket 27 Jul '12
27 Jul '12
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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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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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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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 25 Jul '12
by Bitbucket 25 Jul '12
25 Jul '12
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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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
by Bitbucket 23 Jul '12
by Bitbucket 23 Jul '12
23 Jul '12
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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