https://www.cancerhotspots.org/src/js/render/PdbChainsRender.js

1/*
2 * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center.
3 *
4 * This library is distributed in the hope that it will be useful, but WITHOUT
5 * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
6 * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
7 * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
8 * obligations to provide maintenance, support, updates, enhancements or
9 * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
10 * liable to any party for direct, indirect, special, incidental or
11 * consequential damages, including lost profits, arising out of the use of this
12 * software and its documentation, even if Memorial Sloan-Kettering Cancer
13 * Center has been advised of the possibility of such damage.
14 */
15
16/*
17 * This file is part of cBioPortal Cancer Hotspots.
18 *
19 * cBioPortal is free software: you can redistribute it and/or modify
20 * it under the terms of the GNU Affero General Public License as
21 * published by the Free Software Foundation, either version 3 of the
22 * License.
23 *
24 * This program is distributed in the hope that it will be useful,
25 * but WITHOUT ANY WARRANTY; without even the implied warranty of
26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27 * GNU Affero General Public License for more details.
28 *
29 * You should have received a copy of the GNU Affero General Public License
30 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
31 */
32
33/**
34 * @author Selcuk Onur Sumer
35 */
36function PdbChainsRender(options)
37{
38    var _defaultOpts = {
39        templateId: "pdb_chains_column",
40        linkTemplateId: "cluster_pdb_link",
41        threshold: 2,
42        pValueThreshold: 0.0001,
43        dataManager: false,
44        pdbIdData: function(row) {
45            return {
46                pdbId: row["pdbId"],
47                chain: row["chain"]
48            };
49        }
50    };
51
52    // merge options with default options to use defaults for missing values
53    var _options = jQuery.extend(true, {}, _defaultOpts, options);
54
55    function render(data, type)
56    {
57        if (type === 'sort')
58        {
59            return _.size(data);
60        }
61        else
62        {
63            // convert map into an array and sort by count
64            var pdbChains = MutationUtils.convertToPdbList(data);
65
66            // create an array of display values
67            var values = [];
68            var linkTemplateFn = _.template($("#" + _options.linkTemplateId).html());
69
70            _.each(_.first(pdbChains, _options.threshold), function(pdbChain) {
71
72                values.push(linkTemplateFn({
73                    pdbChain: pdbChain.pdbId + ":" + pdbChain.chain
74                }));
75            });
76
77            if (_.size(pdbChains) > _options.threshold)
78            {
79                values.push('and ' + (_.size(pdbChains) - _options.threshold) + ' more');
80            }
81
82            var templateFn = _.template($("#" + _options.templateId).html());
83            return templateFn({pdbChains: values.join(", ")});
84        }
85
86    }
87
88    function postRender(td, cellData, rowData, row, col)
89    {
90        if (_.isEmpty(cellData))
91        {
92            // nothing to render
93            return;
94        }
95
96        var pdbIdRender = new PdbIdRender({
97            dataManager: _options.dataManager
98        });
99
100        var pValueRender = new DecimalValueRender({
101            threshold: _options.pValueThreshold
102        });
103
104        var noWrapRender = new NoWrapRender();
105
106        // convert map into a list
107        var pdbList = MutationUtils.convertToPdbList(cellData);
108
109        var viewOpts = {
110            //templateId: '#pdb_chain_composition',
111            //dataTableTarget: ".pdb-chain-composition",
112            templateId: '#variant_composition',
113            dataTableTarget: ".variant-composition",
114            dom: "t",
115            data: pdbList,
116            order: [[2 , "asc" ], [1, "asc"]],
117            columns: [
118                {title: "PDB Id",
119                    data: _options.pdbIdData,
120                    render: pdbIdRender.render,
121                    createdCell: pdbIdRender.postRender},
122                {title: "Chain",
123                    data: "chain"},
124                {id: "pValue",
125                    title: noWrapRender.render("P-value"),
126                    data: "pValue",
127                    render: pValueRender.render}
128            ]
129        };
130
131        addEventListeners(td);
132
133        cbio.util.addTargetedQTip($(td).find('.qtipped-text'),
134                                  TooltipUtils.tooltipOptions(cellData, viewOpts));
135    }
136
137    function addEventListeners(td)
138    {
139        var pdbElem = $(td).find(".cluster-pdb");
140
141        pdbElem.on('click', function() {
142            // show the 3D vis
143            if (_options.dataManager)
144            {
145                // select the pdb!
146                _options.dataManager.selectPdbChain($(this).text());
147            }
148        });
149    }
150
151    this.render = render;
152    this.postRender = postRender;
153}
154