/
blast-results.js
executable file
·1181 lines (1164 loc) · 55.7 KB
/
blast-results.js
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(function () {
function decimalAdjust(type, value, exp) {
// If the exp is undefined or zero...
if (typeof exp === 'undefined' || +exp === 0) {
return Math[type](value);
}
value = +value;
exp = +exp;
// If the value is not a number or the exp is not an integer...
if (isNaN(value) || !(typeof exp === 'number' && exp % 1 === 0)) {
return NaN;
}
// Shift
value = value.toString().split('e');
value = Math[type](+(value[0] + 'e' + (value[1] ? (+value[1] - exp) : -exp)));
// Shift back
value = value.toString().split('e');
return +(value[0] + 'e' + (value[1] ? (+value[1] + exp) : exp));
}
// Decimal round
if (!Math.round10) {
Math.round10 = function (value, exp) {
return decimalAdjust('round', value, exp);
};
}
// Decimal floor
if (!Math.floor10) {
Math.floor10 = function (value, exp) {
return decimalAdjust('floor', value, exp);
};
}
// Decimal ceil
if (!Math.ceil10) {
Math.ceil10 = function (value, exp) {
return decimalAdjust('ceil', value, exp);
};
}
})();
$(function () { // document ready
//////////////////
// Prepare Data //
//////////////////
var col_idx = _.object(results_col_names, _.range(results_col_names.length));
/////////////////////////
// Hover and Selection //
/////////////////////////
// State variables
var last_focus_row_index = 0;
var State = Backbone.Model.extend({
defaults: {
'hover': null,
'selected': []
},
focus_row_index: function() {
var focus_row_index = this.get('hover');
if (focus_row_index == null) {
selected = this.get('selected');
if (selected.length > 0)
focus_row_index = selected[0];
else
focus_row_index = last_focus_row_index;
}
last_focus_row_index = focus_row_index;
return focus_row_index;
}
});
var s = new State;
//////////////////
// BLAST Report //
//////////////////
var cm_blast_report = CodeMirror($('#blast-report')[0], {
value: results_detail,
theme: 'xq-light',
tabSize: 2,
lineNumbers: true,
styleActiveLine: true,
readOnly: true,
viewportMargin: 15,
gutters: ["CodeMirror-linenumbers"]
});
$('#text-tabs a[href="#blast-report"]').on('shown.bs.tab', function (e) {
cm_blast_report.refresh();
})
// Selected line changed event
cm_blast_report.on('cursorActivity', function (instance) {
//console.log('cm_blast_report.getCursor() = ' + cm_blast_report.getCursor().line);
var filtered = results_info['line_num_list'].filter(function (i) { return i <= cm_blast_report.getCursor().line + 3 });
var i = 0;
if (filtered.length > 0)
i = filtered.length - 1;
s.set({ 'selected': [i] }, { 'set_by': instance });
})
function cm_blast_report_select_hsp(row_idx) {
cm_blast_report.operation(function () {
cm_blast_report.scrollIntoView({ line: results_info['line_num_list'][row_idx], ch: 0 }, cm_blast_report.getScrollInfo().clientHeight / 2);
cm_blast_report.setCursor({ line: results_info['line_num_list'][row_idx], ch: 0 });
cm_blast_report.curOp.cursorActivityHandlers = false; // don't fire event
});
cm_blast_report.operation(function () {
var info = cm_blast_report.getScrollInfo();
cm_blast_report.scrollTo(0, info.top + info.clientHeight / 2 - 42);
cm_blast_report.curOp.cursorActivityHandlers = false; // don't fire event
});
}
s.on('change:hover', function (model, value, options) {
if (options.set_by == this)
return;
if (value != null)
cm_blast_report_select_hsp(value);
else {
selected = s.get('selected')
if (selected.length > 0)
cm_blast_report_select_hsp(selected[0]);
}
}, cm_blast_report);
s.on('change:selected', function (model, value, options) {
if (options.set_by == this)
return;
if (value.length > 0)
cm_blast_report_select_hsp(value[0]);
}, cm_blast_report);
//////////////////
// FASTA Viewer //
//////////////////
var empty_fasta_hint = 'Select one or more rows in the table on the left to display its FASTA sequence.';
var cm_fasta_viewer = CodeMirror($('#fasta-viewer')[0], {
value: empty_fasta_hint,
theme: 'xq-light',
tabSize: 2,
lineNumbers: true,
styleActiveLine: true,
readOnly: true,
viewportMargin: 15,
gutters: ["CodeMirror-linenumbers"],
lineWrapping: true,
});
$('#text-tabs a[href="#fasta-viewer"]').on('shown.bs.tab', function (e) {
cm_fasta_viewer.refresh();
})
// Check if an ajax call is already done or underway, prevent duplicate calls to server
// Cache FASTA sequences
var fasta_cache = {};
// Flag ongoing ajax calls
var fasta_loading = {};
var url_root = /(https?:\/\/.*(?:blast)*)\/task\//g.exec(document.URL)[1];
function get_fasta(sseqid) {
// Returns a jqXHR or true if already in cache, for use with $.when
//http://localhost:8000/api/seq/gnl%7CLoxosceles_reclusa_transcript_v0.5.3%7CLREC000002-RA/?format=fasta
if (sseqid in fasta_cache)
return true;
else if (sseqid in fasta_loading)
return fasta_loading[sseqid];
else {
fasta_loading[sseqid] = $.get(url_root + '/api/seq/' + sseqid + '/?format=fasta', function (data) {
fasta_cache[sseqid] = data;
});
return fasta_loading[sseqid];
}
}
s.on('change:hover', function (model, value, options) {}, cm_fasta_viewer);
s.on('change:selected', function (model, row_indexes, options) {
if (options.set_by == this)
return;
if (row_indexes.length > 0) {
sseqids = _.uniq(row_indexes.map(function (row_index) { return results_data[row_index][col_idx['sseqid']]; }));
$.when.apply(null, sseqids.map(get_fasta)).then(function () {
//check if row_indexes in fasta_cache, row_indexes might have already changed when this is called
if (sseqids.length > 0 && _.all(sseqids.map(function (sseqid) { return sseqid in fasta_cache; }))) {
var fasta = '';
for (var i = 0; i < sseqids.length; i++) { // faster than array.join('')
fasta += fasta_cache[sseqids[i]];
}
cm_fasta_viewer.setValue(fasta);
}
});
} else {
cm_fasta_viewer.setValue(empty_fasta_hint);
}
}, cm_fasta_viewer);
///////////////////
// Results Table //
///////////////////
var toolbar_prefix = 'fg-toolbar ui-toolbar ui-widget-header ui-helper-clearfix ui-corner-';
var index_of_blastdb = col_idx['blastdb']; // -1 if not present
var index_of_sseqid = col_idx['sseqid']; // -1 if not present
var fixedColumns = 2;
// add header and footer for jbrowse if index != -1
if (index_of_blastdb != -1) {
$('#results-table thead tr').append('<th></th>');
$('#results-table tfoot tr').append('<th></th>');
fixedColumns = 3;
}
var $results_table = $('#results-table').dataTable({
scrollX: '100%',
scrollY: '200px',
dom:
'<"' + toolbar_prefix + 'tl ui-corner-tr"Rifr>' +
't' +
'<"' + toolbar_prefix + 'bl ui-corner-br"<"btn-download btn-group dropup">T>S',
tableTools: {
sRowSelect: "os",
aButtons: [],
},
colReorder: {
fixedColumns: fixedColumns,
realtime: true,
stateSave: true
},
order: [[ col_idx['qseqid'], 'asc' ]],
//responsive: true,
data: results_data,
columns: _.map(results_col_names, function (name) {
col = {
'title': name,
'name': name.toLowerCase().replace(' ', '-')
};
if (name == 'blastdb') {
col['orderable'] = false;
col['type'] = 'choice';
col['className'] = 'center-cell';
col['render'] = function (dbtitle, type, row, meta) {
if (type == "display") {
var sseqid = row[index_of_sseqid];
if (/\|\w\w\w\w\w\w_([^|]+)$/g.exec(sseqid) != null)
//>gnl|Ceratitis_capitata|cercap_Scaffold1
sseqid = /\|[^|_]+?_([^|]+)$/g.exec(sseqid)[1];
else if (/\|([^|]+)$/.exec(sseqid) != null)
//>gnl|Drosophila_ficusphila_transcript_v0.5.3|DFIC013799-RA
sseqid = /\|([^|]+)$/.exec(sseqid)[1];
if (dbtitle in results_info['db_url']) {
var start_pos = row[col_idx['sstart']];
var end_pos = row[col_idx['send']];
if (end_pos < start_pos)
end_pos = [start_pos, start_pos = end_pos][0];
start_pos -= 200;
if (start_pos < 0)
start_pos = 0;
end_pos += 200;
if (end_pos > row[col_idx['slen']])
end_pos = row[col_idx['slen']];
db_url = decodeURI( results_info['db_url'][dbtitle]);
final_url = encodeURI( db_url + '?loc=' + sseqid + ':' + start_pos + '..' + end_pos + '&addStores={"url":{"type":"JBrowse/Store/SeqFeature/GFF3","urlTemplate":"' + /^(https?:\/\/)/g.exec(results_info['db_url'][dbtitle])[1] + /https?:\/\/(.*?)\/(?:blast)+/g.exec(document.URL)[1] + '/media/blast/task/' + task_id + '/' + dbtitle + '.gff"}}&addTracks=[{"label":"BLAST+ Results","category":"Reference Assembly","type":"WebApollo/View/Track/DraggableBLASTFeatures","store":"url","style":{"renderClassName":"gray-center-30pct","subfeatureClasses":{"match_part":"blast-match_part"}}}]&tracks=BLAST+ Results');
return '<a class="btn btn-primary btn-xs" data-toggle="tooltip" data-placement="right" data-container="body" title="' + dbtitle + '\nClick to view in genome browser" target="_blank" href="' + final_url + '" role="button"><span class="glyphicon glyphicon-new-window"></span> ' + results_info['db_organism'][dbtitle] + '</a>';
} else {
return '<span data-toggle="tooltip" data-placement="right" title="' + dbtitle + '">' + results_info['db_organism'][dbtitle] + '</span>';
}
}
return dbtitle;
}
} else if (name == 'sseqid') {
col['render'] = function (sseqid, type, row, meta) {
if (type == "display") {
if (/\|\w\w\w\w\w\w_([^|]+)$/g.exec(sseqid) != null)
//>gnl|Ceratitis_capitata|cercap_Scaffold1
sseqid = /\|[^|_]+?_([^|]+)$/g.exec(sseqid)[1];
else if (/\|([^|]+)$/.exec(sseqid) != null)
//>gnl|Drosophila_ficusphila_transcript_v0.5.3|DFIC013799-RA
sseqid = /\|([^|]+)$/.exec(sseqid)[1];
var idx = meta.row;
return sseqid;
}
return sseqid;
}
}
return col;
}),
headerCallback: function (thead, data, start, end, display) {
$(thead).find('th').each(function (index) {
$(this).children().tooltip('destroy'); // remove old tooltip
$(this).html('<a data-toggle="tooltip" data-placement="top" data-container="body" title="' + results_col_names_display[col_idx[$(this).text()]] + '"><span>' + results_col_names[col_idx[$(this).text()]] + '</span></a>');
$(this).children().tooltip();
});
},
rowCallback: function (row, data) {
var $blastdb_td = $('td', row).eq(index_of_blastdb); // .addClass('center-cell')
$blastdb_td.children().tooltip();
}
});
var results_table_api = $results_table.api();
///////////////////
// Download Menu //
///////////////////
var task_path = /(https?:\/\/.*?)\/(?:blast)*/g.exec(document.URL)[1] + '/media/blast/task/' + task_id + '/' + task_id;
$('.btn-download').html('<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">\
<span class="glyphicon glyphicon-download"></span> Download <span class="caret"></span>\
</button>\
<ul class="dropdown-menu" role="menu">\
<li><a href="' + task_path + '.0"><span class="glyphicon glyphicon-file"></span> Pairwise</a></li>\
<li><a href="' + task_path + '.1"><span class="glyphicon glyphicon-file"></span> Query-anchored showing identities</a></li>\
<li><a href="' + task_path + '.3"><span class="glyphicon glyphicon-file"></span> Flat query-anchored, show identities</a></li>\
<li><a href="' + task_path + '.xml"><span class="glyphicon glyphicon-file"></span> XML</a></li>\
<li><a href="' + task_path + '.tsv"><span class="glyphicon glyphicon-file"></span> Tabular</a></li>\
<li><a href="' + task_path + '.asn"><span class="glyphicon glyphicon-file"></span> BLAST archive format (ASN.1)</a></li>\
</ul>')
///////////////////
// Table Filters //
///////////////////
var filters = {};
// Add per column filter input elements to tfoot
$('.dataTables_scrollFoot tfoot th').each(function (i) {
var col_setting = results_table_api.settings()[0].aoColumns[i];
var type = col_setting.sType
var id = 'results-table-' + i + '-filter';
var title = col_setting.sName || id;
if (type == 'choice') { // blastdb
var db_list = results_table_api.column(i).data().unique().sort();
var select = $('<select id="' + id + '" class="selectpicker dropup show-menu-arrow" data-style="btn-sm btn-default" data-width="91px" multiple data-live-search="true" data-actions-box="true" multiple data-selected-text-format="count" data-count-selected-text="{0} of {1}" title="Filter" data-icon="icon-filter" data-size="10"></select>')
.appendTo($(this).empty())
.on('change', function () {
// build search string '|'.join
var $toggle = $('#' + id + '+.bootstrap-select .dropdown-toggle');
var $title = $('#' + id + '+.bootstrap-select .title');
var selected_options = $('#' + id + ' option:selected').map(function () { return this.value; }).get();
$title.text(selected_options.length + ' of ' + db_list.length);
if (selected_options.length == db_list.length) {
$toggle.removeClass('btn-success');
results_table_api.column(i).search('', true, false).draw();
} else {
$toggle.addClass('btn-success');
results_table_api.column(i).search(selected_options.join('|') || '^$', true, false).draw();
}
});
db_list.each(function (d, j) {
select.append('<option selected value="' + d + '">' + d + '</option>')
});
select.selectpicker();
} else if (title == 'evalue') {
// use log slider for evalue
var data = results_table_api.column(i).data();
var min = _.min(data);
var max = _.max(data);
var min_log = min;
var max_log = max;
// remove 0
if (max == 0) { // all 0
min_log = -324;
max_log = -324; // Math.pow(10, -324) == 0
} else if (min == 0) {
//Math.ceil(Math.log(1e-323) / Math.log(10))
min_log = _.min(_.filter(data, function (num) { return num != 0; }));
min_log = Math.ceil(Math.log(min_log) / Math.log(10)) - 1;
max_log = Math.ceil(Math.log(max) / Math.log(10));
} else {
min_log = Math.ceil(Math.log(min) / Math.log(10)) - 1;
max_log = Math.ceil(Math.log(max) / Math.log(10));
}
min = 0;
max = Math.round10(Math.pow(10, max_log), max_log);
var input = $('<div class="btn-group dropup show-menu-arrow">\
<button id="' + id + '-toggle" type="button" class="btn btn-sm btn-default dropdown-toggle" data-toggle="dropdown">\
<span class="glyphicon glyphicon-filter">\
</span>\
<span class="caret">\
</span>\
<span class="sr-only">Toggle Dropdown</span>\
</button>\
<div class="dropdown-menu range-filter" role="menu"><div class="arrow"></div>\
<div class="popover-title">' + title + ' filter</div>\
<div class="input-group label-row">\
<label for="' + id + '-input-min">Min</label>\
<div class="input-group-addon"></div>\
<label for="' + id + '-input-max">Max</label></div>\
<div class="input-group">\
<input id="' + id + '-input-min" type="text" class="form-control col-search-input-min ' + title + '" placeholder="Min"/>\
<div class="input-group-addon">-</div>\
<input id="' + id + '-input-max" type="text" class="form-control col-search-input-max ' + title + '" placeholder="Max"/>\
</div><br>\
<div id="' + id + '-slider" class="slider"></div>\
</div></div>').appendTo($(this).empty());
var $toggle = $('#' + id + '-toggle');
var $slider = $('#' + id + '-slider');
var $input_min = $('#' + id + '-input-min');
var $input_max = $('#' + id + '-input-max');
filters['min_' + i] = {
'enabled': false,
'filter': function (rd) {
var i_min = $input_min.val() * 1;
var val = rd[i] * 1;
if (!_.isNaN(val) && (_.isNaN(i_min) || i_min <= val))
return true;
else
return false;
}
};
filters['max_' + i] = {
'enabled': false,
'filter': function (rd) {
var i_max = $input_max.val() * 1;
var val = rd[i] * 1;
if (!_.isNaN(val) && (_.isNaN(i_max) || i_max >= val))
return true;
else
return false;
}
};
var draw_table = function () {
if ($input_min.val() == min)
filters['min_' + i]['enabled'] = false;
else
filters['min_' + i]['enabled'] = true;
if ($input_max.val() == max)
filters['max_' + i]['enabled'] = false;
else
filters['max_' + i]['enabled'] = true;
if ($input_min.val() == min && $input_max.val() == max) {
$toggle.removeClass('btn-success');
} else {
$toggle.addClass('btn-success');
}
results_table_api.draw();
}
$slider.slider({
range: true,
min: min_log,
max: max_log,
values: [min_log, max_log],
change: function (event, ui) {
draw_table();
},
slide: function (event, ui) {
// check for 0
if (ui.values[0] == min_log)
$input_min.val(0);
else
$input_min.val(Math.round10(Math.pow(10, ui.values[0]), ui.values[0]));
$input_max.val(Math.round10(Math.pow(10, ui.values[1]), ui.values[1]));
//console.log(ui.values[0], Math.round10(Math.pow(10, ui.values[0]), ui.values[0]), ui.values[1], Math.round10(Math.pow(10, ui.values[1]), ui.values[1]));
}
});
$input_min.val(min);
$input_max.val(max);
$input_min.on('keyup', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_min) && min <= i_min && i_max >= i_min) {
$slider.slider("values", 0, Math.log(i_min) / Math.log(10));
}
});
$input_min.on('change', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_min) && $input_min.val() != '') {
if (i_min > i_max)
i_min = i_max;
else if (i_min < min)
i_min = min;
$input_min.val(i_min);
$slider.slider("values", 0, Math.log(i_min) / Math.log(10));
} else {
$input_min.val(min);
$slider.slider("values", 0, min_log);
}
});
$input_max.on('keyup', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_max) && i_min <= i_max && max >= i_max) {
$slider.slider("values", 1, Math.log(i_max) / Math.log(10));
}
});
$input_max.on('change', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_max) && $input_max.val() != '') {
if (i_max < i_min)
i_max = i_min;
else if (i_max > max)
i_max = max;
$input_max.val(i_max);
$slider.slider("values", 1, Math.log(i_max) / Math.log(10));
} else {
$input_max.val(max);
$slider.slider("values", 1, max_log);
}
});
} else if (type == 'num') {
//var is_last_col = i == col_idx.length - 1;
var data = results_table_api.column(i).data();
var min = Math.floor(_.min(data));
var max = Math.ceil(_.max(data));
var input = $('<div class="btn-group dropup show-menu-arrow">\
<button id="' + id + '-toggle" type="button" class="btn btn-sm btn-default dropdown-toggle" data-toggle="dropdown">\
<span class="glyphicon glyphicon-filter">\
</span>\
<span class="caret">\
</span>\
<span class="sr-only">Toggle Dropdown</span>\
</button>\
<div class="dropdown-menu range-filter" role="menu"><div class="arrow"></div>\
<div class="popover-title">' + title + ' filter</div>\
<div class="input-group label-row">\
<label for="' + id + '-input-min">Min</label>\
<div class="input-group-addon"></div>\
<label for="' + id + '-input-max">Max</label></div>\
<div class="input-group">\
<input id="' + id + '-input-min" type="number" min="' + min + '" max="' + max + '" class="form-control col-search-input-min ' + title + '" placeholder="Min" />\
<div class="input-group-addon">-</div>\
<input id="' + id + '-input-max" type="number" min="' + min + '" max="' + max + '" class="form-control col-search-input-max ' + title + '" placeholder="Max" />\
</div><br>\
<div id="' + id + '-slider" class="slider"></div>\
</div></div>').appendTo($(this).empty());
var $toggle = $('#' + id + '-toggle');
var $slider = $('#' + id + '-slider');
var $input_min = $('#' + id + '-input-min');
var $input_max = $('#' + id + '-input-max');
filters['min_' + i] = {
'enabled': false,
'filter': function (rd) {
var i_min = $input_min.val() * 1;
var val = rd[i] * 1;
if (!_.isNaN(val) && (_.isNaN(i_min) || i_min <= val))
return true;
else
return false;
}
};
filters['max_' + i] = {
'enabled': false,
'filter': function (rd) {
var i_max = $input_max.val() * 1;
var val = rd[i] * 1;
if (!_.isNaN(val) && (_.isNaN(i_max) || i_max >= val))
return true;
else
return false;
}
};
var draw_table = function () {
if ($input_min.val() == min)
filters['min_' + i]['enabled'] = false;
else
filters['min_' + i]['enabled'] = true;
if ($input_max.val() == max)
filters['max_' + i]['enabled'] = false;
else
filters['max_' + i]['enabled'] = true;
if ($input_min.val() == min && $input_max.val() == max) {
$toggle.removeClass('btn-success');
} else {
$toggle.addClass('btn-success');
}
results_table_api.draw();
}
$slider.slider({
range: true,
min: min,
max: max,
values: [min, max],
change: function (event, ui) {
draw_table();
},
slide: function (event, ui) {
$input_min.val(ui.values[0]);
$input_max.val(ui.values[1]);
}
});
$input_min.val(min);
$input_max.val(max);
$input_min.on('keyup', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_min) && min <= i_min && i_max >= i_min) {
$slider.slider("values", 0, i_min);
}
});
$input_min.on('change', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_min) && $input_min.val() != '') {
if (i_min > i_max)
i_min = i_max;
else if (i_min < min)
i_min = min;
$input_min.val(i_min);
$slider.slider("values", 0, i_min);
} else {
$input_min.val(min);
$slider.slider("values", 0, min);
}
});
$input_max.on('keyup', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_max) && i_min <= i_max && max >= i_max) {
$slider.slider("values", 1, i_max);
}
});
$input_max.on('change', function () {
var i_min = $input_min.val() * 1;
var i_max = $input_max.val() * 1;
if (!_.isNaN(i_max) && $input_max.val() != '') {
if (i_max < i_min)
i_max = i_min;
else if (i_max > max)
i_max = max;
$input_max.val(i_max);
$slider.slider("values", 1, i_max);
} else {
$input_max.val(max);
$slider.slider("values", 1, max);
}
});
} else {
var input = $('<div id="' + id + '" class="input-group input-group-sm"><div class="input-group-addon"><span class="glyphicon glyphicon-search"></div><input type="text" class="form-control col-search-input ' + title + '" placeholder="' + title + ' filter" /></div></div>').appendTo($(this).empty());
$('input', input).on('keyup change', function () {
//console.log(colIdx);
if (this.value == '') {
$('#' + id).removeClass('has-success');
} else {
$('#' + id).addClass('has-success');
}
results_table_api.column(i).search(this.value).draw();
});
}
$(this).addClass('center-cell');
});
$("#result-container").kendoSplitter({
orientation: "vertical",
panes: [
{ collapsible: true, size: '38%' },
{ collapsible: false }
]
});
$results_table.dataTableExt.afnFiltering.push(
function (oSettings, aData, iDataIndex) {
return _.every(_.map(_.filter(filters, function (f) { return f['enabled']; }), function (f, key) { return f['filter'](this); }, aData));
}
);
// Fix input element click problem
$('.dropdown-menu.range-filter').click(function (e) {
e.stopPropagation();
});
//////////////////
// Resize Event //
//////////////////
// Calculate dataTables_scrollBody height
var $table_container = $('#table-container');
var $ui_corner_tr = $('.ui-corner-tr');
var $ui_corner_br = $('.ui-corner-br');
var $dataTables_scrollHead = $('.dataTables_scrollHead');
var $dataTables_scrollBody = $('.dataTables_scrollBody');
var $dataTables_scrollFoot = $('.dataTables_scrollFoot');
function updateDataTableHeight() {
// table_panel_div - top_bar - bottom_bar - table_header
var h = $table_container.height() - $ui_corner_tr.outerHeight() - $ui_corner_br.outerHeight() - $dataTables_scrollHead.outerHeight() - $dataTables_scrollFoot.outerHeight();
$dataTables_scrollBody.css('height', h);
// trigger dataTables.scroller to recalculate how many rows its showing
$(window).trigger('resize.DTS');
};
// only the horizontal-splitter changes height
$("#result-container").data("kendoSplitter").bind('resize', function () {
updateDataTableHeight();
});
// Draw initial graph with first row
var row_data = results_table_api.row(0).data();
// Selected
var oTT = TableTools.fnGetInstance('results-table');
$results_table.on('click', 'tr', function () {
s.set({ 'selected': oTT.fnGetSelectedIndexes() }, { 'set_by': $results_table });
});
// Hover
$results_table.on('mouseover', 'tr', function () {
var this_row = results_table_api.row(this);
s.set({ 'hover': this_row.index() }, { 'set_by': $results_table });
});
$('.dataTables_scrollBody').mouseleave(function () {
s.set({ 'hover': null }, { 'set_by': $results_table });
});
s.on('change:hover', function (model, hover_index, options) {
$(results_table_api.rows().nodes()).removeClass('highlight');
if (options.set_by == this)
return;
// scroll to
var scroll_index = s.focus_row_index();
// get row
var row = results_table_api.row(scroll_index);
var row_data = row.data();
// is filtered?
// Get data as ordered and filtered in datatable
var table_data = results_table_api.rows({ search: 'applied' }).data();
var i = _.indexOf(table_data, row_data);
results_table_api.scroller().scrollToRow(i, false);
// highlight row
if (hover_index != null) {
var $row = $(results_table_api.rows({ search: 'applied' }).nodes()[i]);
$row.addClass('highlight');
}
}, $results_table);
s.on('change:selected', function (model, selected_indexes, options) {
if (options.set_by == this)
return;
if (selected_indexes.length > 0) {
// get row
var row = results_table_api.row(selected_indexes[0]);
var row_data = row.data();
// is filtered?
// Get data as ordered and filtered in datatable
var table_data = results_table_api.rows({ search: 'applied' }).data();
var i = _.indexOf(table_data, row_data);
results_table_api.scroller().scrollToRow(i, false);
}
oTT.fnSelectNone();
$.each(selected_indexes, function (key, value) {
oTT.fnSelect(results_table_api.row(value).node());
});
}, $results_table);
//////////////////////////////
// Order, Search and Filter //
//////////////////////////////
var order = results_table_api.order();
$results_table.on('order.dt', function () {
//console.log('order.dt');
});
// Search event
$results_table.on('search.dt', function () {
//console.log('search.dt');
});
$results_table.on('draw.dt', function () {
//console.log('draw.dt');
var focus_row_index = s.get('hover')
if (focus_row_index == null) {
selected = s.get('selected')
if (selected.length > 0)
focus_row_index = selected[0];
else
focus_row_index = 0;
}
renderAlignmentGraph('query-canvas', focus_row_index);
renderAlignmentGraph('subject-canvas', focus_row_index);
});
/////////////////////
// Alignment Graph //
/////////////////////
function num_asc(a, b) { return (a - b); }
var sorted_score_data = results_table_api.column(col_idx['bitscore']).data().sort(num_asc);
var dynamic_min_score = Math.round(sorted_score_data[Math.round((sorted_score_data.length - 1) * 0.1)] - 1); // if there is only one score value
var dynamic_max_score = Math.round(sorted_score_data[Math.round((sorted_score_data.length - 1) * 0.9)] + 1);
var light_color_list = ['#fc9272', '#bcbddc', '#a1d99b', '#9ecae1', '#bdbdbd'].reverse();
var dark_color_list = ['#7f0000', '#4d004b', '#004529', '#081d58', '#000000'].reverse();
var selected_color_gradient = ['#fee6ce', '#f8bb5d', '#ee7d45']; // orange
var hover_color_gradient = ['#f1e5bf', '#ffcc00', '#d4af37']; // yellow
var min_score = dynamic_min_score;
var max_score = dynamic_max_score;
// #fc9272, #bcbddc, #a1d99b, #9ecae1, #bdbdbd
var light_color_interpolator = chroma.scale(light_color_list).domain([min_score, max_score], 50);
// #7f0000, #4d004b, #004529, #081d58, #000000
var dark_color_interpolator = chroma.scale(dark_color_list).domain([min_score, max_score], 50);
// build color lookup tables
var score_to_color_light = {};
var score_to_color_dark = {};
for (var i = min_score; i <= max_score; i++) {
score_to_color_light[i] = light_color_interpolator(i).hex();
score_to_color_dark[i] = dark_color_interpolator(i).hex();
}
// Graph legend
var legend_dim = { width: 300, height: 30, top: 0, right: 20, bottom: 0, left: 20 }
document.getElementById('score-color-canvas').width = legend_dim.width;
document.getElementById('score-color-canvas').height = legend_dim.height;
var legend_svg = d3.select('#score-color-d3').append('svg')
.attr('width', legend_dim.width)
.attr('height', legend_dim.height);
function hex_to_rgb(hex) {
var result = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);
return result ? {
r: parseInt(result[1], 16),
g: parseInt(result[2], 16),
b: parseInt(result[3], 16)
} : null;
}
function draw_bilinear(canvas, legend_dim, top_color_list, bottom_color_list, offsetX) {
canvas.width = legend_dim.width;
canvas.height = legend_dim.height;
var ctx = canvas.getContext('2d');
// setup x color interpolators
var top_color_interpolator = chroma.scale(top_color_list).domain([legend_dim.left, legend_dim.width - legend_dim.right]);
var bottom_color_interpolator = chroma.scale(bottom_color_list).domain([legend_dim.left, legend_dim.width - legend_dim.right]);
if (offsetX) {
var g = ctx.createLinearGradient(0, 0, 0, legend_dim.height);
g.addColorStop(0, top_color_interpolator(offsetX).hex());
g.addColorStop(1, bottom_color_interpolator(offsetX).hex());
ctx.fillStyle = g;
ctx.fillRect(0, 0, canvas.width, canvas.height);
} else {
var imageData = ctx.getImageData(0, 0, legend_dim.width, legend_dim.height);
var pixels = imageData.data;
var inner_width = legend_dim.width - legend_dim.left - legend_dim.right;
var y_domain = [0, legend_dim.height];
var x_offset = legend_dim.width * 4;
for (var x = 0; x < legend_dim.width; x++) {
// setup y color interpolator
var y_color_list = [top_color_interpolator(x).hex(), bottom_color_interpolator(x).hex()]
var y_color_interpolator = chroma.scale(y_color_list).domain(y_domain);
for (var y = 0; y < legend_dim.height; y++) {
var color = y_color_interpolator(y).rgb();
pixels[y * x_offset + x * 4] = color[0];
pixels[y * x_offset + x * 4 + 1] = color[1];
pixels[y * x_offset + x * 4 + 2] = color[2];
pixels[y * x_offset + x * 4 + 3] = 255;
}
}
ctx.putImageData(imageData, 0, 0);
}
}
function draw_legend_continuous(color_list, li_text) {
// draw background
var canvas = $('#score-color-canvas')[0];
draw_bilinear(canvas, legend_dim, light_color_list, dark_color_list);
// draw axis
var range_max = legend_svg.attr('width') - legend_dim.left - legend_dim.right;
var x = d3.scale.linear().range([0, range_max]).domain([min_score, max_score]);
var xAxis = d3.svg.axis().scale(x).orient('bottom').tickValues(d3.range(min_score, max_score + 1, (max_score - min_score) / (color_list.length - 1)));
legend_svg.select("g").remove();
legend_svg.append("g").attr("class", "x axis")
.attr("transform", "translate(" + legend_dim.left + "," + legend_dim.top + ")")
.call(xAxis);
}
// mouse over events
$('#score-color-canvas').mousemove(function (e) {
$('#score-color-rule').css('left', e.offsetX);
var x = d3.scale.linear().range([min_score, max_score]).domain([legend_dim.left, legend_dim.width - legend_dim.left]);
$('#score-color-rule-text').text(Math.round(x(e.offsetX)));
// draw background
var canvas = $('#score-color-canvas')[0];
draw_bilinear(canvas, legend_dim, light_color_list, dark_color_list, Math.round(e.offsetX));
});
$('#score-color-rule').hide();
$('#score-color-map').mouseleave(function (e) {
$('#score-color-rule').hide();
// draw background
var canvas = $('#score-color-canvas')[0];
draw_bilinear(canvas, legend_dim, light_color_list, dark_color_list);
});
$('#score-color-map').mouseenter(function (e) {
$('#score-color-rule').show();
//console.log(e.offsetX);
});
$('#score-to-color-checkbox').bootstrapSwitch({
onText: 'Dynamic', offText: 'Static', onInit: function (event, state) {
$('.bootstrap-switch-id-score-to-color-checkbox').popover({
title: 'Dynamic / Static Switch',
content: '<b>Dynamic</b> color keys help visualize <i>relative</i> scores between all BLAST hits.<br><b>Static</b> color keys help visualize the <i>absolute</i> scores of each BLAST hit.',
html: true,
trigger: 'hover',
placement: 'bottom',
});
}, onSwitchChange: function (event, state) {
if (state) {
// dynamic
min_score = dynamic_min_score;
max_score = dynamic_max_score;
// #fc9272, #bcbddc, #a1d99b, #9ecae1, #bdbdbd
light_color_interpolator = chroma.scale(light_color_list).domain([min_score, max_score], 50);
// #7f0000, #4d004b, #004529, #081d58, #000000
dark_color_interpolator = chroma.scale(dark_color_list).domain([min_score, max_score], 50);
// build color lookup tables
score_to_color_light = {};
score_to_color_dark = {};
for (var i = min_score; i <= max_score; i++) {
score_to_color_light[i] = light_color_interpolator(i).hex();
score_to_color_dark[i] = dark_color_interpolator(i).hex();
}
color_scale = d3.scale.quantize().domain([min_score, max_score]).range(_.zip(light_color_list, dark_color_list));
draw_legend_continuous(color_scale.range(), function (c) {
var r = color_scale.invertExtent(c);
return Math.round(r[0]);
});
updateAlignmentGraph();
} else {
// static
min_score = 40;
max_score = 200;
// #fc9272, #bcbddc, #a1d99b, #9ecae1, #bdbdbd
light_color_interpolator = chroma.scale(light_color_list).domain([min_score, max_score], 5);
// #7f0000, #4d004b, #004529, #081d58, #000000
dark_color_interpolator = chroma.scale(dark_color_list).domain([min_score, max_score], 5);
// build color lookup tables
score_to_color_light = {};
score_to_color_dark = {};
for (var i = min_score; i <= max_score; i++) {
score_to_color_light[i] = light_color_interpolator(i).hex();
score_to_color_dark[i] = dark_color_interpolator(i).hex();
}
color_scale = d3.scale.quantize().domain([min_score, max_score]).range(_.zip(light_color_list, dark_color_list));
draw_legend_continuous(color_scale.range(), function (c) {
var r = color_scale.invertExtent(c);
return Math.round(r[0]);
});
//$('.score-to-color-text').text('Static');
updateAlignmentGraph();
}
}
});
function draw_legend(legend_id, color_list, li_text) {
d3.select(legend_id).selectAll('div').remove();
var legend = d3.select(legend_id).selectAll('div').data(color_list).enter().append('div').attr('class', 'color-key')
.style('background', function (c) {
return c[0];
})
.style('background', function (c) {
return '-moz-linear-gradient(top, ' + c[0] + ' 0%, ' + c[1] + ' 100%)';
}) //-moz-linear-gradient(top, #1e5799 0%, #7db9e8 100%);
.style('background', function (c) {
return '-webkit-gradient(linear, left top, left bottom, color-stop(0%,' + c[0] + '), color-stop(100%,' + c[1] + '))';
}) //-webkit-gradient(linear, left top, left bottom, color-stop(0%,#1e5799), color-stop(100%,#7db9e8))
.style('background', function (c) {
return '-webkit-linear-gradient(top, ' + c[0] + ' 0%,' + c[1] + ' 100%)';
}) //-webkit-linear-gradient(top, #1e5799 0%,#7db9e8 100%)
.style('background', function (c) {
return '-o-linear-gradient(top, ' + c[0] + ' 0%,' + c[1] + ' 100%)';
}) //-o-linear-gradient(top, #1e5799 0%,#7db9e8 100%)
.style('background', function (c) {
return '-ms-linear-gradient(top, ' + c[0] + ' 0%,' + c[1] + ' 100%)';
}) //-ms-linear-gradient(top, #1e5799 0%,#7db9e8 100%)
.style('background', function (c) {
return 'linear-gradient(to bottom, ' + c[0] + ' 0%,' + c[1] + ' 100%)';
}) //linear-gradient(to bottom, #1e5799 0%,#7db9e8 100%)
.style('background', function (c) {
return 'progid:DXImageTransform.Microsoft.gradient( startColorstr="' + c[0] + '", endColorstr="' + c[1] + '",GradientType=0 )';
}) //progid:DXImageTransform.Microsoft.gradient( startColorstr='#1e5799', endColorstr='#7db9e8',GradientType=0 )
.text(li_text || String);
}
var color_scale = d3.scale.quantize().domain([min_score, max_score]).range(_.zip(light_color_list, dark_color_list));
draw_legend_continuous(color_scale.range(), function (c) {
var r = color_scale.invertExtent(c);
return Math.round(r[0]);
});
draw_legend('#selected-hsp-color', [selected_color_gradient.slice(1)], function (c) { return ''; });
draw_legend('#mouseover-hsp-color', [hover_color_gradient.slice(1)], function (c) { return ''; });
// ctrl and shift detection
var ctrl_down = false;
var shift_down = false;
$(document).keydown(function (event) {
if (event.which == '17')
ctrl_down = true;
else if (event.which == '16')
shift_down = true;
});
$(document).keyup(function (event) {
if (event.which == '17')
ctrl_down = false;
else if (event.which == '16')
shift_down = false;
});
function renderAlignmentGraph(canvas_name, focus_row_index) {
// Get Canvas and Create Chart
var canvas = document.getElementById(canvas_name);
var canvas_parent = canvas.parentNode;
// Remove all previous events
var canvas_clone = canvas.cloneNode(true);
// Copy jquery data
var $canvas = $(canvas);
var $canvas_clone = $(canvas_clone);
$canvas_clone.data('lane_size', $canvas.data('lane_size'));
//canvas = canvas_clone;
//$canvas = $canvas_clone;
// Clear canvas
var ctx = canvas_clone.getContext('2d');
ctx.clearRect(0, 0, canvas_clone.width, canvas_clone.height);
//var chart = new Scribl(canvas_clone, canvas_clone.width);
var offset = 45; // so scale text won't get cutoff
var chart = new Scribl(canvas_clone, canvas_clone.width - offset * 2);
chart.offset = offset;
chart.scrollable = true;
// Change laneSizes and buffers
chart.laneSizes = 20;
chart.laneBuffer = 0;
chart.trackBuffer = 0;
// Change text color
chart.glyph.text.color = 'white';
var focus_row_data = results_table_api.row(focus_row_index).data();
// Get data indexes
var other_canvas = canvas_name == 'query-canvas' ? 'subject-canvas' : 'query-canvas';
var rseqid = canvas_name == 'query-canvas' ? col_idx['qseqid'] : col_idx['sseqid'];
var rstart = canvas_name == 'query-canvas' ? col_idx['qstart'] : col_idx['sstart'];
var rend = canvas_name == 'query-canvas' ? col_idx['qend'] : col_idx['send'];
var sstart = col_idx['sstart'];
var send = col_idx['send'];
var bitscore = col_idx['bitscore'];
// Get data as ordered and filtered in datatable
var table_data = results_table_api.rows({ search: 'applied' }).data();
// Filter data, only keep rows associated with the reference given by focus_row_data
var hsp_nt_range = 16000;
var center_position = focus_row_data[rend] < focus_row_data[rstart] ? focus_row_data[rend] : focus_row_data[rstart];
var filtered_rows = results_table_api.rows({ search: 'applied' }).eq(0).filter(function (row_index) {
var row_data = results_table_api.row(row_index).data();