├── .eslintrc.json ├── .gitignore ├── .npmignore ├── LICENSE ├── README.md ├── debug.webpack.config.js ├── debug ├── data.js ├── debug.html ├── images │ ├── ajax-loader.gif │ ├── help.png │ └── warning.gif └── main.js ├── legacy ├── 3Dmol-nojquery-min.js ├── FileSaver.min.js ├── backbone-min.js ├── cbio-util.js ├── css │ ├── dataTables.tableTools.min.css │ ├── data_table.css │ ├── data_table_ColVis.css │ ├── data_table_jui.css │ ├── jquery.qtip.min.css │ ├── smoothness │ │ ├── images │ │ │ ├── animated-overlay.gif │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ ├── ui-bg_flat_75_ffffff_40x100.png │ │ │ ├── ui-bg_glass_55_fbf9ee_1x400.png │ │ │ ├── ui-bg_glass_65_ffffff_1x400.png │ │ │ ├── ui-bg_glass_75_dadada_1x400.png │ │ │ ├── ui-bg_glass_75_e6e6e6_1x400.png │ │ │ ├── ui-bg_glass_95_fef1ec_1x400.png │ │ │ ├── ui-bg_highlight-soft_75_cccccc_1x100.png │ │ │ ├── ui-icons_222222_256x240.png │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ ├── ui-icons_454545_256x240.png │ │ │ ├── ui-icons_888888_256x240.png │ │ │ └── ui-icons_cd0a0a_256x240.png │ │ └── jquery-ui-1.10.3.custom.css │ └── tipTip.css ├── d3.min.js ├── download-util.js ├── igv_webstart.js ├── jquery-migrate.js ├── jquery-ui.min.js ├── jquery.dataTables.ColVis.min.js ├── jquery.dataTables.columnFilter.js ├── jquery.dataTables.fnSetFilteringDelay.js ├── jquery.dataTables.js ├── jquery.dataTables.min.js ├── jquery.dataTables.tableTools.min.js ├── jquery.expander.min.js ├── jquery.min.js ├── jquery.qtip.min.js ├── jquery.scrollTo.min.js ├── jquery.tipTip.min.js ├── mutation-file-example.txt ├── rainbowvis.js ├── ui.tabs.paging.js └── underscore-min.js ├── package.json ├── src ├── css │ ├── mutation_3d.css │ ├── mutation_details.css │ ├── mutation_diagram.css │ ├── mutation_info_panel.css │ ├── mutation_pdb_panel.css │ ├── mutation_pdb_table.css │ └── mutation_table.css ├── images │ ├── ajax-loader.gif │ ├── help.png │ ├── ma.png │ └── warning.gif ├── js │ ├── MutationMapper.js │ ├── api.js │ ├── component │ │ ├── AdvancedDataTable.js │ │ ├── Mutation3dVis.js │ │ ├── MutationDetailsTable.js │ │ ├── MutationDiagram.js │ │ ├── MutationPdbPanel.js │ │ ├── MutationPdbTable.js │ │ └── PancanMutationHistogram.js │ ├── controller │ │ ├── MainMutationController.js │ │ ├── Mutation3dController.js │ │ ├── MutationDataFilterController.js │ │ ├── MutationDetailsController.js │ │ ├── MutationDetailsEvents.js │ │ ├── MutationDetailsTableController.js │ │ ├── MutationDiagramController.js │ │ └── MutationInfoController.js │ ├── data │ │ ├── AbstractDataProxy.js │ │ ├── ClinicalDataProxy.js │ │ ├── MutationAlignerDataProxy.js │ │ ├── MutationData.js │ │ ├── MutationDataManager.js │ │ ├── MutationDataProxy.js │ │ ├── PancanMutationDataProxy.js │ │ ├── PdbDataProxy.js │ │ ├── PfamDataProxy.js │ │ ├── PortalDataProxy.js │ │ └── VariantAnnotationDataProxy.js │ ├── helper │ │ └── datatables.js │ ├── legacy │ │ ├── igv_webstart.js │ │ ├── jquery.dataTables.fnSetFilteringDelay.js │ │ └── ui.tabs.paging.js │ ├── model │ │ ├── MutationCollection.js │ │ ├── MutationModel.js │ │ ├── PdbAlignmentCollection.js │ │ ├── PdbAlignmentModel.js │ │ ├── PdbChainCollection.js │ │ ├── PdbChainModel.js │ │ ├── PdbCollection.js │ │ ├── PdbModel.js │ │ └── Pileup.js │ ├── util │ │ ├── BackboneTemplateCache.js │ │ ├── DataProxyUtil.js │ │ ├── DataTableUtil.js │ │ ├── JSmolWrapper.js │ │ ├── JmolScriptGenerator.js │ │ ├── JmolWrapper.js │ │ ├── MergedAlignmentSegmentor.js │ │ ├── Mol3DScriptGenerator.js │ │ ├── Mol3DWrapper.js │ │ ├── MolScriptGenerator.js │ │ ├── MutationDataConverter.js │ │ ├── MutationDetailsTableFormatter.js │ │ ├── MutationDetailsUtil.js │ │ ├── MutationInputParser.js │ │ ├── MutationViewsUtil.js │ │ ├── PancanMutationDataUtil.js │ │ ├── PdbDataUtil.js │ │ ├── PileupUtil.js │ │ ├── PymolScriptGenerator.js │ │ ├── RequestQueue.js │ │ ├── VariantAnnotationUtil.js │ │ ├── VepParser.js │ │ ├── cbio-util.js │ │ └── download-util.js │ └── view │ │ ├── CosmicTipView.js │ │ ├── LollipopTipStatsView.js │ │ ├── LollipopTipView.js │ │ ├── MainMutationView.js │ │ ├── Mutation3dView.js │ │ ├── Mutation3dVisInfoView.js │ │ ├── Mutation3dVisView.js │ │ ├── MutationCustomizePanelView.js │ │ ├── MutationDetailsTableView.js │ │ ├── MutationDetailsView.js │ │ ├── MutationDiagramView.js │ │ ├── MutationHelpPanelView.js │ │ ├── MutationInfoPanelView.js │ │ ├── MutationSummaryView.js │ │ ├── PancanMutationHistTipView.js │ │ ├── PdbChainTipView.js │ │ ├── PdbPanelView.js │ │ ├── PdbTableView.js │ │ ├── PredictedImpactTipView.js │ │ └── RegionTipView.js └── template │ ├── 3d │ ├── 3Dmol_basic_interaction.html │ ├── jsmol_basic_interaction.html │ ├── mutation_3d_view.html │ ├── mutation_3d_vis.html │ ├── mutation_3d_vis_info.html │ ├── non_protein_tip.html │ ├── side_chain_tip.html │ ├── structure_color_tip.html │ └── type_color_tip.html │ ├── info_panel │ ├── info_panel.html │ └── info_panel_type.html │ ├── mutation_details │ ├── gene_info.html │ ├── info.html │ ├── list_content.html │ ├── main_content.html │ ├── mutation_details.html │ ├── mutation_summary_view.html │ └── mutation_view.html │ ├── mutation_diagram │ ├── lollipop_tip.html │ ├── lollipop_tip_stats.html │ ├── mutation_aligner_info.html │ ├── mutation_customize_panel.html │ ├── mutation_diagram_view.html │ ├── mutation_help_panel.html │ └── region_tip.html │ ├── mutation_table │ ├── cancer_study.html │ ├── case_id.html │ ├── cbio_portal.html │ ├── cna.html │ ├── cosmic.html │ ├── cosmic_tip.html │ ├── end_position.html │ ├── fis_tip.html │ ├── igv_link.html │ ├── mutation_assessor.html │ ├── mutation_count.html │ ├── mutation_status.html │ ├── mutation_table.html │ ├── mutation_table_placeholder.html │ ├── mutation_type.html │ ├── normal_alt_count.html │ ├── normal_freq.html │ ├── normal_ref_count.html │ ├── pancan_mutation_hist_tip.html │ ├── protein_change.html │ ├── start_position.html │ ├── tumor_alt_count.html │ ├── tumor_freq.html │ ├── tumor_ref_count.html │ ├── tumor_type.html │ └── validation_status.html │ ├── pdb_panel │ ├── pdb_chain_tip.html │ ├── pdb_help_tip.html │ └── pdb_panel_view.html │ └── pdb_table │ ├── chain_cell.html │ ├── pdb_cell.html │ ├── pdb_table_view.html │ └── summary_cell.html └── webpack.config.js /.eslintrc.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cBioPortal/mutation-mapper/HEAD/.eslintrc.json -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.iml 2 | .idea 3 | node_modules 4 | *.log 5 | .eslintcache -------------------------------------------------------------------------------- /.npmignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cBioPortal/mutation-mapper/HEAD/.npmignore -------------------------------------------------------------------------------- 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