gramene-search 1.2.39 → 1.2.40

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Files changed (18) hide show
  1. package/.parcel-cache/{8e5f8335bb9561c6 → 05d97b9b7df0959a} +0 -0
  2. package/.parcel-cache/0eebcef07661bc3d +0 -0
  3. package/.parcel-cache/109421cc5334effc +0 -0
  4. package/.parcel-cache/2de2aad73a84c506.txt +2 -2
  5. package/.parcel-cache/475da2e0135128de +0 -0
  6. package/.parcel-cache/{2d46b4d6f4bda0b6 → 4c5c2b22a8963eeb} +0 -0
  7. package/.parcel-cache/data.mdb +0 -0
  8. package/.parcel-cache/{b15edcceffbc7149 → e30d924c1c10119c} +0 -0
  9. package/.parcel-cache/lock.mdb +0 -0
  10. package/dist/index.css +1 -1
  11. package/dist/index.css.map +1 -1
  12. package/dist/index.js +170 -26
  13. package/dist/index.js.map +1 -1
  14. package/package.json +1 -1
  15. package/src/components/results/GeneList.js +23 -7
  16. package/src/components/results/details/Publications.js +145 -0
  17. package/src/components/results/details/Xrefs.js +4 -32
  18. package/src/components/results/genes.css +3 -0
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{\n position: fixed;\n background-color: dimgray;\n padding-left: 8px;\n padding-right: 8px;\n padding-bottom: 8px;\n max-width: 16.67%;\n}\n.gramene-filter-container {\n background-color: #cfb5e6;\n padding-left: 4px;\n}\n.gramene-filter {\n padding-left: 4px;\n padding-right: 4px;\n padding-bottom: 4px;\n background-color: white;\n font-size: small;\n}\n.gramene-filter span:hover {\n font-weight:bolder;\n}\n.gramene-filter-AND {\n background-color: #ffcd82;\n}\n.gramene-filter-OR {\n background-color: #c5eeb9;\n}\n.gramene-filter-NOT {\n border-left-color: #ff5354;\n border-left-style: inset;\n border-left-width: 4px;\n padding-left: 4px;\n}\n.gramene-filter-operation {\n text-align: center;\n font-style: italic;\n}\n.gramene-filter-marked {\n font-weight: bolder;\n /*background-color: #feff96;*/\n}\n.gramene-filter-menu ul {\n border-top-style: solid;\n border-top-width: 2px;\n padding-left: 0;\n}\n.gramene-filter-menu li {\n display: block;\n cursor: pointer;\n padding-left: 15px;\n}\n.gramene-filter-menu li:hover {\n background-color: #feff96;\n}\n\n.gramene-view-container {\n background-color: lightblue;\n padding-left: 10px;\n}\n.gramene-view {\n padding-left: 5px;\n margin: 4px;\n background-color: white;\n}\n.gramene-view li {\n display: block;\n cursor: pointer;\n padding-left: 5px;\n border-left-style: inset;\n border-left-width: 4px;\n margin-bottom: 2px;\n}\n\n.gramene-view-on {\n border-left-color: #40a0ff;\n}\n.gramene-view-off {\n border-left-color: #ff6d68;\n}\n.gramene-view-disabled {\n color: darkgray;\n border-left-color: #efefef;\n}\n#gramene-suggestion button {\n border-radius: .6rem;\n line-height: 1;\n}\n#gramene-suggestion button:focus {\n color: #fff;\n background-color: #6c757d;\n border-color: #6c757d;\n}",".taxogenomic-vis {\n @import 'taxonomy';\n}","@import 'colors';\n\n.gramene-search-vis {\n -webkit-user-select: none;\n cursor: pointer;\n\n canvas {\n position: absolute;\n }\n\n > * {\n display: inline;\n }\n\n text {\n font-family: \"Helvetica Neue\", Helvetica, Arial, sans-serif;\n font-size: 12px;\n fill: gray;\n\n /* since font weight transition is not smooth, emulate\n bold font with text stroke, and transition opacity. */\n stroke: @gramene-darkgreen;\n stroke-opacity: 0;\n stroke-width: 0.5px;\n user-select: none;\n }\n\n text::selection {\n background: none;\n }\n\n .taxonomy * {\n transition: fill 200ms ease-in-out,\n stroke-opacity 200ms ease-in-out; /*,\n transform 200ms ease-in-out;*/\n }\n\n .clade {\n .results-count {\n font-size: 10px;\n }\n\n .node circle {\n stroke: @gramene-darkgreen;\n stroke-width: 1px; // This is referenced in Edge.jsx\n fill: @gramene-offwhite;\n }\n\n .edge rect {\n fill: #cccccc;\n }\n\n //\n //.genome .interaction-helper {\n // stroke-opacity: 0;\n // fill-opacity: 0;\n // stroke: @gramene-darkgreen;\n // stroke-width: 1.5px;\n //}\n\n // color the nodes above the hovered node\n // (the highlight class is added dynamically\n // in code)\n .clade.highlight {\n > .node > circle,\n > .edge > rect {\n fill: @gramene-orange;\n }\n > .node-label text {\n fill: @gramene-darkgreen;\n stroke-opacity: 1;\n }\n\n }\n\n // color the clade underneath the hovered node.\n .node:hover,\n .edge:hover {\n > circle,\n > rect,\n ~ .node > circle,\n ~ .clade .edge > rect,\n ~ .clade .node > circle {\n fill: @gramene-orange;\n }\n }\n\n .node:hover,\n .edge:hover {\n ~ .node-label text,\n ~ .clade text {\n fill: @gramene-darkgreen;\n stroke-opacity: 1;\n }\n }\n\n .node-label:hover text {\n fill: @gramene-darkgreen;\n stroke-opacity: 1;\n }\n\n .bin, .full-region {\n transition: none;\n stroke: @gramene-darkgreen;\n stroke-width: 0;\n shape-rendering: crispEdges;\n }\n\n .bin.selected {\n fill: @gramene-red;\n }\n\n .bin:hover {\n fill: @gramene-darkgreen;\n }\n\n .full-region.selected {\n stroke-width: 1px;\n stroke: @gramene-red;\n }\n\n .full-region:hover {\n stroke-width: 1px;\n stroke: @gramene-darkgreen;\n }\n\n .species-background {\n fill: none;\n }\n\n .node:hover ~ .species-background,\n .edge:hover ~ .species-background,\n .node:hover ~ .clade .species-background,\n .edge:hover ~ .clade .species-background,\n .clade.highlight > .species-background {\n fill: lighten(@gramene-orange, 20%);\n }\n\n }\n}\n","/*\n\n<classNamePrefix>-root\n\nThe outer container\n\n*/\n.tree-view-root {\n}\n\n/*\n\n<classNamePrefix>-root\n\nThe outer container for a single node\n\n*/\n.tree-view-node {\n margin-left: 10px;\n}\n\n\n/*\n\n<classNamePrefix>-node-collapse-toggle.collapse-spacer\n\nUsed to provide spacing when a parent node has no children\n\n*/\n.tree-view-node-collapse-toggle.collapse-spacer {\n width: 14px;\n display: inline-block;\n}\n\n/*\n<classNamePrefix>-node-collapse-toggle.<expandIconClass>\n\nThe class to use for the icon that expands a collapsed parent node\n\n*/\n\n\n/*\n\n<classNamePrefix>-node-collapse-toggle.<collapseIconClass>\n\nThe class to use for the icon that collapses an expanded parent node\n\n*/\n\n.tree-view-node-collapse-toggle {\n margin-right: 3px;\n width: 14px;\n}\n\n/*\n\n<classNamePrefix>-node-label\n\n*/\n.tree-view-node-label {\n font-size: smaller;\n margin-left: 3px;\n padding: 1px;\n border: 1px solid #fff;\n}\n\n/*\n\n<classNamePrefix>-node-label.selected\n\n*/\n.tree-view-node-label.selected {\n border: 1px solid #003f81;\n border-radius: 3px;\n background-color: #808080;\n}\n\n/*\n\n<classNamePrefix>-node-checkbox\n\nThe class for a node checkbox\n\n*/\n\n.tree-view-node-checkbox {}\n\n/*\n\n<classNamePrefix>-node-children\n\nThe class for the element that wraps a nodes children (if any exist)\n\n*/\n\n.tree-view-node-children {}\n\n","@transition_time: 20ms;\n\n/* see src/components/Edge.jsx#HOVER_SCALE_FACTOR (currently line 8) */\n@hover_scale_factor: 2;\n@hover_stroke_width: 2;\n@collapsed_node_stroke_width: 1;\n\n@default_node_fill: #fff;\n@default_node_stroke: #777;\n\n@ortholog_stroke_color: orange;\n@paralog_stroke_color: green;\n@representative_fill_color: @ortholog_stroke_color;\n@self_color: red;\n\n@speciation_color: #000080;\n@duplication_color: #cd0000;\n\n@font_size: 11px;\n@font_weight_highlight: bolder;\n\n@invisible: 0;\n@visible: 1;\n\n.display-mode {\n .btn-toolbar {\n position: absolute;\n padding-left: 10px\n }\n}\n.tooltip-inner {\n max-width : 400px;\n}\n.genetree-vis {\n .node, .edge {\n cursor: pointer;\n }\n\n .tree-wrapper {\n /* transitions for mouse hover, etc, interactions */\n * {\n transition: all @transition_time ease-in-out;\n }\n\n /* transitions for expanding/contracting clades */\n .clade {\n transition: transform @transition_time ease-in-out;\n\n .edge-rect {\n transition: scaleY @transition_time ease-in-out, scaleX @transition_time ease-in-out, transform @transition_time ease-in-out;\n }\n }\n }\n\n .interaction-helper {\n opacity: @invisible;\n }\n\n .node circle {\n stroke: @default_node_stroke;\n fill: @default_node_fill;\n }\n\n .speciation rect {\n fill: @speciation_color;\n }\n\n .duplication rect {\n fill: @duplication_color;\n }\n\n .node:hover, .edge:hover {\n .internal,\n .gene circle,\n ~ .clade .node rect,\n + .node rect {\n transform: scale(@hover_scale_factor);\n }\n\n ~ .clade .interaction-rect {\n opacity: @visible;\n fill-opacity: @visible;\n }\n\n ~ .clade circle,\n + .node circle,\n .collapsed path,\n ~ .clade .collapsed path,\n + .node .collapsed path {\n stroke-width: @hover_stroke_width;\n }\n\n ~ .clade text, text {\n font-weight: @font_weight_highlight;\n }\n }\n\n .node {\n .gene.ortholog_one2one circle,\n .gene.ortholog_one2many circle,\n .gene.ortholog_many2many circle {\n stroke: @ortholog_stroke_color;\n }\n\n .gene.within_species_paralog circle {\n stroke: @paralog_stroke_color;\n }\n\n .gene.self {\n circle {\n stroke: @self_color;\n fill: @self_color;\n }\n text {\n font-weight: @font_weight_highlight;\n }\n }\n\n .gene.representative circle {\n stroke: @ortholog_stroke_color;\n fill: @representative_fill_color;\n }\n\n text {\n font-size: @font_size;\n fill-opacity: @visible;\n text-anchor: start;\n }\n }\n\n .collapsed {\n path {\n stroke-width: @collapsed_node_stroke_width;\n }\n }\n\n .domains rect {\n cursor: pointer;\n stroke-opacity: 0\n }\n\n .domains rect:hover {\n cursor: pointer;\n stroke-opacity: 1.0\n }\n @transition_time: 20ms;\n\n /* see src/components/Edge.jsx#HOVER_SCALE_FACTOR (currently line 8) */\n @hover_scale_factor: 2;\n @hover_stroke_width: 2;\n @collapsed_node_stroke_width: 1;\n\n @default_node_fill: #fff;\n @default_node_stroke: #777;\n\n @ortholog_stroke_color: orange;\n @paralog_stroke_color: green;\n @representative_fill_color: @ortholog_stroke_color;\n @self_color: red;\n\n @speciation_color: #000080;\n @duplication_color: #cd0000;\n\n @font_size: 11px;\n @font_weight_highlight: bolder;\n\n @invisible: 0;\n @visible: 1;\n\n}\n\n.popover-title .tooltip-title-button {\n margin-top: -4px !important;\n margin-right: 4px !important;\n}\n\n.msa-slider {\n position: relative;\n padding-top: 10px;\n padding-bottom: 0px;\n margin-bottom: -10px;\n}\n\n.resize-drag {\n background: rgba(0, 0, 0, 0.0);\n border: 4px solid #7c8383;\n color: red;\n font-size: 1px;\n font-family: sans-serif;\n border-radius: 8px;\n\n /* This makes things *much* easier */\n box-sizing: border-box;\n}\n\n.resize-container {\n width: 100%;\n height: 100%;\n}\n",".MSAlignments-wrapper {\n overflow-x: scroll;\n overflow-y: hidden;\n}\n.clustal {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.clustal .A,\n.clustal .I,\n.clustal .L,\n.clustal .M,\n.clustal .F,\n.clustal .W,\n.clustal .V {\n background-color: #80a0f0;\n}\n.clustal .R,\n.clustal .K {\n background-color: #f01505;\n color: #fcff89;\n}\n.clustal .N,\n.clustal .Q,\n.clustal .S,\n.clustal .T {\n background-color: #00ff00;\n}\n.clustal .D,\n.clustal .E {\n background-color: #c048c0;\n color: #fcff89;\n}\n.clustal .C {\n background-color: #f08080;\n}\n.clustal .G {\n background-color: #f09048;\n}\n.clustal .Y\n.clustal .H {\n background-color: #15a4a4;\n}\n.clustal .P {\n background-color: #ffff00;\n}\n.clustal .B,\n.clustal .X,\n.clustal .Z {\n background-color: #ffffff;\n}\n.clustal .gap {\n color: #ccc;\n}\n.zappo {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.zappo .A,\n.zappo .I,\n.zappo .L,\n.zappo .M,\n.zappo .V {\n background-color: #ffafaf;\n}\n.zappo .R,\n.zappo .H,\n.zappo .K {\n background-color: #6464ff;\n color: #fcff89;\n}\n.zappo .N,\n.zappo .Q,\n.zappo .S,\n.zappo .T {\n background-color: #00ff00;\n}\n.zappo .D,\n.zappo .E {\n background-color: #ff0000;\n}\n.zappo .C {\n background-color: #ffff00;\n}\n.zappo .G,\n.zappo .P {\n background-color: #ff00ff;\n color: #fcff89;\n}\n.zappo .F,\n.zappo .W,\n.zappo .Y {\n background-color: #ffc800;\n}\n.zappo .B,\n.zappo .X,\n.zappo .Z {\n background-color: #ffffff;\n}\n.zappo .gap {\n color: #ccc;\n}\n.taylor {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.taylor .A {\n background-color: #ccff00;\n}\n.taylor .R {\n background-color: #0000ff;\n color: #fcff89;\n}\n.taylor .N {\n background-color: #cc00ff;\n color: #fcff89;\n}\n.taylor .D {\n background-color: #ff0000;\n color: #fcff89;\n}\n.taylor .C {\n background-color: #ffff00;\n}\n.taylor .Q {\n background-color: #ff00cc;\n}\n.taylor .E {\n background-color: #ff0066;\n color: #fcff89;\n}\n.taylor .G {\n background-color: #ff9900;\n}\n.taylor .H {\n background-color: #0066ff;\n color: #fcff89;\n}\n.taylor .I {\n background-color: #66ff00;\n}\n.taylor .L {\n background-color: #33ff00;\n}\n.taylor .K {\n background-color: #6600ff;\n color: #fcff89;\n}\n.taylor .M {\n background-color: #00ff00;\n}\n.taylor .F {\n background-color: #00ff66;\n}\n.taylor .P {\n background-color: #ffcc00;\n}\n.taylor .S {\n background-color: #ff3300;\n color: #fcff89;\n}\n.taylor .T {\n background-color: #ff6600;\n}\n.taylor .W {\n background-color: #00ccff;\n}\n.taylor .Y {\n background-color: #00ffcc;\n}\n.taylor .V {\n background-color: #99ff00;\n}\n.taylor .B,\n.taylor .X,\n.taylor .Z {\n background-color: #ffffff;\n}\n.taylor .gap {\n color: #ccc;\n}\n.hydrophobicity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n color: #fcff89;\n}\n.hydrophobicity .A {\n background-color: #ad0052;\n}\n.hydrophobicity .R,\n.hydrophobicity .K {\n background-color: #0000ff;\n}\n.hydrophobicity .N,\n.hydrophobicity .D,\n.hydrophobicity .Q,\n.hydrophobicity .E,\n.hydrophobicity .B,\n.hydrophobicity .Z {\n background-color: #0c00f3;\n}\n.hydrophobicity .C {\n background-color: #c2003d;\n}\n.hydrophobicity .G {\n background-color: #6a0095;\n}\n.hydrophobicity .H {\n background-color: #1500ea;\n}\n.hydrophobicity .L {\n background-color: #ea0015;\n}\n.hydrophobicity .M {\n background-color: #b0004f;\n}\n.hydrophobicity .F {\n background-color: #cb0034;\n}\n.hydrophobicity .P {\n background-color: #4600b9;\n}\n.hydrophobicity .S {\n background-color: #5e00a1;\n}\n.hydrophobicity .T {\n background-color: #61009e;\n}\n.hydrophobicity .W {\n background-color: #5b00a4;\n}\n.hydrophobicity .Y {\n background-color: #4f00b0;\n}\n.hydrophobicity .V {\n background-color: #f60009;\n}\n.hydrophobicity .X {\n background-color: #680097;\n}\n.hydrophobicity .gap {\n color: #ccc;\n}\n.helix_propensity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.helix_propensity .A {\n background-color: #e718e7;\n}\n.helix_propensity .R {\n background-color: #6f906f;\n}\n.helix_propensity .N {\n background-color: #1be41b;\n}\n.helix_propensity .D {\n background-color: #778877;\n}\n.helix_propensity .C {\n background-color: #23dc23;\n}\n.helix_propensity .Q {\n background-color: #926d92;\n}\n.helix_propensity .E {\n background-color: #ff00ff;\n}\n.helix_propensity .G {\n background-color: #00ff00;\n}\n.helix_propensity .H {\n background-color: #758a75;\n}\n.helix_propensity .I {\n background-color: #8a758a;\n}\n.helix_propensity .L {\n background-color: #ae51ae;\n}\n.helix_propensity .K {\n background-color: #a05fa0;\n}\n.helix_propensity .M {\n background-color: #ef10ef;\n}\n.helix_propensity .F {\n background-color: #986798;\n}\n.helix_propensity .P {\n background-color: #00ff00;\n}\n.helix_propensity .S {\n background-color: #36c936;\n}\n.helix_propensity .T {\n background-color: #47b847;\n}\n.helix_propensity .W {\n background-color: #8a758a;\n}\n.helix_propensity .Y {\n background-color: #21de21;\n}\n.helix_propensity .V {\n background-color: #857a85;\n}\n.helix_propensity .B {\n background-color: #49b649;\n}\n.helix_propensity .X {\n background-color: #758a75;\n}\n.helix_propensity .Z {\n background-color: #c936c9;\n}\n.helix_propensity .gap {\n color: #ccc;\n}\n.strand_propensity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.strand_propensity .A {\n background-color: #5858a7;\n}\n.strand_propensity .R {\n background-color: #6b6b94;\n}\n.strand_propensity .N {\n background-color: #64649b;\n}\n.strand_propensity .D {\n background-color: #2121de;\n}\n.strand_propensity .C {\n background-color: #9d9d62;\n}\n.strand_propensity .Q {\n background-color: #8c8c73;\n}\n.strand_propensity .E {\n background-color: #0000ff;\n}\n.strand_propensity .G {\n background-color: #4949b6;\n}\n.strand_propensity .H {\n background-color: #60609f;\n}\n.strand_propensity .I {\n background-color: #ecec13;\n}\n.strand_propensity .L {\n background-color: #b2b24d;\n}\n.strand_propensity .K {\n background-color: #4747b8;\n}\n.strand_propensity .M {\n background-color: #82827d;\n}\n.strand_propensity .F {\n background-color: #c2c23d;\n}\n.strand_propensity .P {\n background-color: #2323dc;\n}\n.strand_propensity .S {\n background-color: #4949b6;\n}\n.strand_propensity .T {\n background-color: #9d9d62;\n}\n.strand_propensity .W {\n background-color: #c0c03f;\n}\n.strand_propensity .Y {\n background-color: #d3d32c;\n}\n.strand_propensity .V {\n background-color: #ffff00;\n}\n.strand_propensity .B {\n background-color: #4343bc;\n}\n.strand_propensity .X {\n background-color: #797986;\n}\n.strand_propensity .Z {\n background-color: #4747b8;\n}\n.strand_propensity .A,\n.strand_propensity .R,\n.strand_propensity .N,\n.strand_propensity .D,\n.strand_propensity .E,\n.strand_propensity .G,\n.strand_propensity .H,\n.strand_propensity .K,\n.strand_propensity .P,\n.strand_propensity .S,\n.strand_propensity .B,\n.strand_propensity .Z {\n color: #fcff89;\n}\n.strand_propensity .gap {\n color: #ccc;\n}\n.turn_propensity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.turn_propensity .gap {\n color: #ccc;\n}\n.turn_propensity .A {\n background-color: #2cd3d3;\n}\n.turn_propensity .R {\n background-color: #708f8f;\n}\n.turn_propensity .N {\n background-color: #ff0000;\n}\n.turn_propensity .D {\n background-color: #e81717;\n}\n.turn_propensity .C {\n background-color: #a85757;\n}\n.turn_propensity .Q {\n background-color: #3fc0c0;\n}\n.turn_propensity .E {\n background-color: #778888;\n}\n.turn_propensity .G {\n background-color: #ff0000;\n}\n.turn_propensity .H {\n background-color: #708f8f;\n}\n.turn_propensity .I {\n background-color: #00ffff;\n}\n.turn_propensity .L {\n background-color: #1ce3e3;\n}\n.turn_propensity .K {\n background-color: #7e8181;\n}\n.turn_propensity .M {\n background-color: #1ee1e1;\n}\n.turn_propensity .F {\n background-color: #1ee1e1;\n}\n.turn_propensity .P {\n background-color: #f60909;\n}\n.turn_propensity .S {\n background-color: #e11e1e;\n}\n.turn_propensity .T {\n background-color: #738c8c;\n}\n.turn_propensity .W {\n background-color: #738c8c;\n}\n.turn_propensity .Y {\n background-color: #9d6262;\n}\n.turn_propensity .V {\n background-color: #07f8f8;\n}\n.turn_propensity .B {\n background-color: #f30c0c;\n}\n.turn_propensity .X {\n background-color: #7c8383;\n}\n.turn_propensity .Z {\n background-color: #5ba4a4;\n}\n.turn_propensity .N,\n.turn_propensity .D,\n.turn_propensity .G,\n.turn_propensity .P,\n.turn_propensity .S,\n.turn_propensity .B {\n color: #fcff89;\n}\n.buried_index {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.buried_index .gap {\n color: #ccc;\n}\n.buried_index .A {\n background-color: #00a35c;\n}\n.buried_index .R {\n background-color: #00fc03;\n}\n.buried_index .N {\n background-color: #00eb14;\n}\n.buried_index .D {\n background-color: #00eb14;\n}\n.buried_index .C {\n background-color: #0000ff;\n}\n.buried_index .Q {\n background-color: #00f10e;\n}\n.buried_index .E {\n background-color: #00f10e;\n}\n.buried_index .G {\n background-color: #009d62;\n}\n.buried_index .H {\n background-color: #00d52a;\n}\n.buried_index .I {\n background-color: #0054ab;\n}\n.buried_index .L {\n background-color: #007b84;\n}\n.buried_index .K {\n background-color: #00ff00;\n}\n.buried_index .M {\n background-color: #009768;\n}\n.buried_index .F {\n background-color: #008778;\n}\n.buried_index .P {\n background-color: #00e01f;\n}\n.buried_index .S {\n background-color: #00d52a;\n}\n.buried_index .T {\n background-color: #00db24;\n}\n.buried_index .W {\n background-color: #00a857;\n}\n.buried_index .Y {\n background-color: #00e619;\n}\n.buried_index .V {\n background-color: #005fa0;\n}\n.buried_index .B {\n background-color: #00eb14;\n}\n.buried_index .X {\n background-color: #00b649;\n}\n.buried_index .Z {\n background-color: #00f10e;\n}\n.buried_index .C,\n.buried_index .I,\n.buried_index .V {\n color: #fcff89;\n}\n",".visible-detail {\n border: 1px solid #557B74;\n padding: 6px 12px;\n}\n.detail {\n margin-right: auto;\n margin-left: auto;\n padding-left: 15px;\n padding-right: 15px;\n}\n.table {\n width: 100%;\n max-width: 100%;\n}\n.xrefs {\n border-collapse: collapse;\n border-spacing: 0;\n border-color: grey;\n table-layout: fixed;\n}\n.xref-name-col {\n width: 20%;\n}\n.xref-value-col {\n width: 80%;\n}\n.xref-70-col {\n width: 70%;\n}\n.xref-10-col {\n width: 10%;\n}\n.xref-id-list {\n padding-left: 0;\n list-style: none;\n}\n.result-gene {\n padding: 0.2em;\n border: 5px solid white;\n}\n.result-gene:hover {\n border-color: antiquewhite;\n}\n.gene-title {\n padding-top:0.5em;\n}\n.gene-id {\n white-space: nowrap;\n}\n.gene-name {\n color: #557B74;\n}\n.gene-description {\n margin-bottom: 0;\n}\n.gene-species {\n white-space: nowrap;\n font-style: italic;\n padding-left: 1em;\n}\n.gene-synonyms {\n white-space: nowrap;\n font-size: small;\n}\n.gene-extras {\n float: right;\n border: dashed 1px blue;\n}\n.gene-detail-tabs {\n display: flex;\n flex-wrap: wrap;\n width: 80em;\n}\n.gene-detail-tab-closed {\n color: darkgreen;\n cursor: pointer;\n /*background-color: lightgray;*/\n}\n.gene-detail-tab-disabled {\n /*color: white;*/\n /*background-color: lightgray;*/\n color: lightgray;\n cursor: not-allowed;\n}\n.gene-detail-tab-expanded {\n color: white;\n background-color: #557B74;\n cursor: pointer;\n}\n.result-gene-summary {\n display: flex;\n flex-flow: row nowrap;\n justify-content: flex-start;\n}\n.result-gene-summary .species-name {\n white-space: nowrap;\n font-style: italic;\n}\n.result-gene-title-body {\n flex: 1 1 auto;\n width: 1036px;\n}\n.closest-ortholog, .gene-summary-tair {\n cursor: pointer;\n flex: 1 1 auto;\n width: 500px;\n font-size: smaller;\n margin-top: 10px;\n padding: 0 1rem;\n margin-left: 1rem;\n border: 1px solid darkorange;\n}\n\n.closest-ortholog {\n border: 1px dotted darkorange;\n}\n\n.gene-summary-tair {\n border: 1px dotted darkgreen;\n}\n.gene-summary-tair .rest {\n display: none;\n}\n\n.gene-summary-tair:hover .rest {\n display: inline;\n}\n.gene-summary-tair:focus .rest {\n display: inline;\n}\n.gene-summary-tair:hover .ellipsis {\n display: none;\n}\n.gene-summary-tair:focus .ellipsis {\n display: none;\n}\n\n/* this is the \"title\" of the closest ortholog box */\n.closest-ortholog::before,\n.gene-summary-tair::before {\n position: relative;\n float: right;\n margin-top: -12px;\n margin-right: 6px;\n border: dotted 1px;\n padding: 0 1rem;\n background: #fff;\n}\n\n.closest-ortholog::before {\n content: \"Model Species Homolog\";\n color: orange;\n}\n\n/* this is the \"title\" of the closest ortholog box */\n.gene-summary-tair::before {\n content: \"TAIR Curated Description\";\n color: darkgreen;\n}\n\n.gene-search-pic-sugg {\n width: 100%;\n height: 200px;\n background: url(\"../../static/images/suggestions.png\");\n background-size: contain;\n background-repeat: no-repeat;\n}\n.gene-search-pic-results {\n width: 100%;\n height: 200px;\n background: url(\"../../static/images/results.png\");\n background-size: contain;\n background-repeat: no-repeat;\n}\n.gene-search-pic-genetree {\n width: 100%;\n height: 200px;\n background: url(\"../../static/images/genetree.png\");\n background-size: contain;\n background-repeat: no-repeat;\n}"],"names":[],"version":3,"file":"index.css.map"}
1
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{\n position: fixed;\n background-color: dimgray;\n padding-left: 8px;\n padding-right: 8px;\n padding-bottom: 8px;\n max-width: 16.67%;\n}\n.gramene-filter-container {\n background-color: #cfb5e6;\n padding-left: 4px;\n}\n.gramene-filter {\n padding-left: 4px;\n padding-right: 4px;\n padding-bottom: 4px;\n background-color: white;\n font-size: small;\n}\n.gramene-filter span:hover {\n font-weight:bolder;\n}\n.gramene-filter-AND {\n background-color: #ffcd82;\n}\n.gramene-filter-OR {\n background-color: #c5eeb9;\n}\n.gramene-filter-NOT {\n border-left-color: #ff5354;\n border-left-style: inset;\n border-left-width: 4px;\n padding-left: 4px;\n}\n.gramene-filter-operation {\n text-align: center;\n font-style: italic;\n}\n.gramene-filter-marked {\n font-weight: bolder;\n /*background-color: #feff96;*/\n}\n.gramene-filter-menu ul {\n border-top-style: solid;\n border-top-width: 2px;\n padding-left: 0;\n}\n.gramene-filter-menu li {\n display: block;\n cursor: pointer;\n padding-left: 15px;\n}\n.gramene-filter-menu li:hover {\n background-color: #feff96;\n}\n\n.gramene-view-container {\n background-color: lightblue;\n padding-left: 10px;\n}\n.gramene-view {\n padding-left: 5px;\n margin: 4px;\n background-color: white;\n}\n.gramene-view li {\n display: block;\n cursor: pointer;\n padding-left: 5px;\n border-left-style: inset;\n border-left-width: 4px;\n margin-bottom: 2px;\n}\n\n.gramene-view-on {\n border-left-color: #40a0ff;\n}\n.gramene-view-off {\n border-left-color: #ff6d68;\n}\n.gramene-view-disabled {\n color: darkgray;\n border-left-color: #efefef;\n}\n#gramene-suggestion button {\n border-radius: .6rem;\n line-height: 1;\n}\n#gramene-suggestion button:focus {\n color: #fff;\n background-color: #6c757d;\n border-color: #6c757d;\n}",".taxogenomic-vis {\n @import 'taxonomy';\n}","@import 'colors';\n\n.gramene-search-vis {\n -webkit-user-select: none;\n cursor: pointer;\n\n canvas {\n position: absolute;\n }\n\n > * {\n display: inline;\n }\n\n text {\n font-family: \"Helvetica Neue\", Helvetica, Arial, sans-serif;\n font-size: 12px;\n fill: gray;\n\n /* since font weight transition is not smooth, emulate\n bold font with text stroke, and transition opacity. */\n stroke: @gramene-darkgreen;\n stroke-opacity: 0;\n stroke-width: 0.5px;\n user-select: none;\n }\n\n text::selection {\n background: none;\n }\n\n .taxonomy * {\n transition: fill 200ms ease-in-out,\n stroke-opacity 200ms ease-in-out; /*,\n transform 200ms ease-in-out;*/\n }\n\n .clade {\n .results-count {\n font-size: 10px;\n }\n\n .node circle {\n stroke: @gramene-darkgreen;\n stroke-width: 1px; // This is referenced in Edge.jsx\n fill: @gramene-offwhite;\n }\n\n .edge rect {\n fill: #cccccc;\n }\n\n //\n //.genome .interaction-helper {\n // stroke-opacity: 0;\n // fill-opacity: 0;\n // stroke: @gramene-darkgreen;\n // stroke-width: 1.5px;\n //}\n\n // color the nodes above the hovered node\n // (the highlight class is added dynamically\n // in code)\n .clade.highlight {\n > .node > circle,\n > .edge > rect {\n fill: @gramene-orange;\n }\n > .node-label text {\n fill: @gramene-darkgreen;\n stroke-opacity: 1;\n }\n\n }\n\n // color the clade underneath the hovered node.\n .node:hover,\n .edge:hover {\n > circle,\n > rect,\n ~ .node > circle,\n ~ .clade .edge > rect,\n ~ .clade .node > circle {\n fill: @gramene-orange;\n }\n }\n\n .node:hover,\n .edge:hover {\n ~ .node-label text,\n ~ .clade text {\n fill: @gramene-darkgreen;\n stroke-opacity: 1;\n }\n }\n\n .node-label:hover text {\n fill: @gramene-darkgreen;\n stroke-opacity: 1;\n }\n\n .bin, .full-region {\n transition: none;\n stroke: @gramene-darkgreen;\n stroke-width: 0;\n shape-rendering: crispEdges;\n }\n\n .bin.selected {\n fill: @gramene-red;\n }\n\n .bin:hover {\n fill: @gramene-darkgreen;\n }\n\n .full-region.selected {\n stroke-width: 1px;\n stroke: @gramene-red;\n }\n\n .full-region:hover {\n stroke-width: 1px;\n stroke: @gramene-darkgreen;\n }\n\n .species-background {\n fill: none;\n }\n\n .node:hover ~ .species-background,\n .edge:hover ~ .species-background,\n .node:hover ~ .clade .species-background,\n .edge:hover ~ .clade .species-background,\n .clade.highlight > .species-background {\n fill: lighten(@gramene-orange, 20%);\n }\n\n }\n}\n","/*\n\n<classNamePrefix>-root\n\nThe outer container\n\n*/\n.tree-view-root {\n}\n\n/*\n\n<classNamePrefix>-root\n\nThe outer container for a single node\n\n*/\n.tree-view-node {\n margin-left: 10px;\n}\n\n\n/*\n\n<classNamePrefix>-node-collapse-toggle.collapse-spacer\n\nUsed to provide spacing when a parent node has no children\n\n*/\n.tree-view-node-collapse-toggle.collapse-spacer {\n width: 14px;\n display: inline-block;\n}\n\n/*\n<classNamePrefix>-node-collapse-toggle.<expandIconClass>\n\nThe class to use for the icon that expands a collapsed parent node\n\n*/\n\n\n/*\n\n<classNamePrefix>-node-collapse-toggle.<collapseIconClass>\n\nThe class to use for the icon that collapses an expanded parent node\n\n*/\n\n.tree-view-node-collapse-toggle {\n margin-right: 3px;\n width: 14px;\n}\n\n/*\n\n<classNamePrefix>-node-label\n\n*/\n.tree-view-node-label {\n font-size: smaller;\n margin-left: 3px;\n padding: 1px;\n border: 1px solid #fff;\n}\n\n/*\n\n<classNamePrefix>-node-label.selected\n\n*/\n.tree-view-node-label.selected {\n border: 1px solid #003f81;\n border-radius: 3px;\n background-color: #808080;\n}\n\n/*\n\n<classNamePrefix>-node-checkbox\n\nThe class for a node checkbox\n\n*/\n\n.tree-view-node-checkbox {}\n\n/*\n\n<classNamePrefix>-node-children\n\nThe class for the element that wraps a nodes children (if any exist)\n\n*/\n\n.tree-view-node-children {}\n\n","@transition_time: 20ms;\n\n/* see src/components/Edge.jsx#HOVER_SCALE_FACTOR (currently line 8) */\n@hover_scale_factor: 2;\n@hover_stroke_width: 2;\n@collapsed_node_stroke_width: 1;\n\n@default_node_fill: #fff;\n@default_node_stroke: #777;\n\n@ortholog_stroke_color: orange;\n@paralog_stroke_color: green;\n@representative_fill_color: @ortholog_stroke_color;\n@self_color: red;\n\n@speciation_color: #000080;\n@duplication_color: #cd0000;\n\n@font_size: 11px;\n@font_weight_highlight: bolder;\n\n@invisible: 0;\n@visible: 1;\n\n.display-mode {\n .btn-toolbar {\n position: absolute;\n padding-left: 10px\n }\n}\n.tooltip-inner {\n max-width : 400px;\n}\n.genetree-vis {\n .node, .edge {\n cursor: pointer;\n }\n\n .tree-wrapper {\n /* transitions for mouse hover, etc, interactions */\n * {\n transition: all @transition_time ease-in-out;\n }\n\n /* transitions for expanding/contracting clades */\n .clade {\n transition: transform @transition_time ease-in-out;\n\n .edge-rect {\n transition: scaleY @transition_time ease-in-out, scaleX @transition_time ease-in-out, transform @transition_time ease-in-out;\n }\n }\n }\n\n .interaction-helper {\n opacity: @invisible;\n }\n\n .node circle {\n stroke: @default_node_stroke;\n fill: @default_node_fill;\n }\n\n .speciation rect {\n fill: @speciation_color;\n }\n\n .duplication rect {\n fill: @duplication_color;\n }\n\n .node:hover, .edge:hover {\n .internal,\n .gene circle,\n ~ .clade .node rect,\n + .node rect {\n transform: scale(@hover_scale_factor);\n }\n\n ~ .clade .interaction-rect {\n opacity: @visible;\n fill-opacity: @visible;\n }\n\n ~ .clade circle,\n + .node circle,\n .collapsed path,\n ~ .clade .collapsed path,\n + .node .collapsed path {\n stroke-width: @hover_stroke_width;\n }\n\n ~ .clade text, text {\n font-weight: @font_weight_highlight;\n }\n }\n\n .node {\n .gene.ortholog_one2one circle,\n .gene.ortholog_one2many circle,\n .gene.ortholog_many2many circle {\n stroke: @ortholog_stroke_color;\n }\n\n .gene.within_species_paralog circle {\n stroke: @paralog_stroke_color;\n }\n\n .gene.self {\n circle {\n stroke: @self_color;\n fill: @self_color;\n }\n text {\n font-weight: @font_weight_highlight;\n }\n }\n\n .gene.representative circle {\n stroke: @ortholog_stroke_color;\n fill: @representative_fill_color;\n }\n\n text {\n font-size: @font_size;\n fill-opacity: @visible;\n text-anchor: start;\n }\n }\n\n .collapsed {\n path {\n stroke-width: @collapsed_node_stroke_width;\n }\n }\n\n .domains rect {\n cursor: pointer;\n stroke-opacity: 0\n }\n\n .domains rect:hover {\n cursor: pointer;\n stroke-opacity: 1.0\n }\n @transition_time: 20ms;\n\n /* see src/components/Edge.jsx#HOVER_SCALE_FACTOR (currently line 8) */\n @hover_scale_factor: 2;\n @hover_stroke_width: 2;\n @collapsed_node_stroke_width: 1;\n\n @default_node_fill: #fff;\n @default_node_stroke: #777;\n\n @ortholog_stroke_color: orange;\n @paralog_stroke_color: green;\n @representative_fill_color: @ortholog_stroke_color;\n @self_color: red;\n\n @speciation_color: #000080;\n @duplication_color: #cd0000;\n\n @font_size: 11px;\n @font_weight_highlight: bolder;\n\n @invisible: 0;\n @visible: 1;\n\n}\n\n.popover-title .tooltip-title-button {\n margin-top: -4px !important;\n margin-right: 4px !important;\n}\n\n.msa-slider {\n position: relative;\n padding-top: 10px;\n padding-bottom: 0px;\n margin-bottom: -10px;\n}\n\n.resize-drag {\n background: rgba(0, 0, 0, 0.0);\n border: 4px solid #7c8383;\n color: red;\n font-size: 1px;\n font-family: sans-serif;\n border-radius: 8px;\n\n /* This makes things *much* easier */\n box-sizing: border-box;\n}\n\n.resize-container {\n width: 100%;\n height: 100%;\n}\n",".MSAlignments-wrapper {\n overflow-x: scroll;\n overflow-y: hidden;\n}\n.clustal {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.clustal .A,\n.clustal .I,\n.clustal .L,\n.clustal .M,\n.clustal .F,\n.clustal .W,\n.clustal .V {\n background-color: #80a0f0;\n}\n.clustal .R,\n.clustal .K {\n background-color: #f01505;\n color: #fcff89;\n}\n.clustal .N,\n.clustal .Q,\n.clustal .S,\n.clustal .T {\n background-color: #00ff00;\n}\n.clustal .D,\n.clustal .E {\n background-color: #c048c0;\n color: #fcff89;\n}\n.clustal .C {\n background-color: #f08080;\n}\n.clustal .G {\n background-color: #f09048;\n}\n.clustal .Y\n.clustal .H {\n background-color: #15a4a4;\n}\n.clustal .P {\n background-color: #ffff00;\n}\n.clustal .B,\n.clustal .X,\n.clustal .Z {\n background-color: #ffffff;\n}\n.clustal .gap {\n color: #ccc;\n}\n.zappo {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.zappo .A,\n.zappo .I,\n.zappo .L,\n.zappo .M,\n.zappo .V {\n background-color: #ffafaf;\n}\n.zappo .R,\n.zappo .H,\n.zappo .K {\n background-color: #6464ff;\n color: #fcff89;\n}\n.zappo .N,\n.zappo .Q,\n.zappo .S,\n.zappo .T {\n background-color: #00ff00;\n}\n.zappo .D,\n.zappo .E {\n background-color: #ff0000;\n}\n.zappo .C {\n background-color: #ffff00;\n}\n.zappo .G,\n.zappo .P {\n background-color: #ff00ff;\n color: #fcff89;\n}\n.zappo .F,\n.zappo .W,\n.zappo .Y {\n background-color: #ffc800;\n}\n.zappo .B,\n.zappo .X,\n.zappo .Z {\n background-color: #ffffff;\n}\n.zappo .gap {\n color: #ccc;\n}\n.taylor {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.taylor .A {\n background-color: #ccff00;\n}\n.taylor .R {\n background-color: #0000ff;\n color: #fcff89;\n}\n.taylor .N {\n background-color: #cc00ff;\n color: #fcff89;\n}\n.taylor .D {\n background-color: #ff0000;\n color: #fcff89;\n}\n.taylor .C {\n background-color: #ffff00;\n}\n.taylor .Q {\n background-color: #ff00cc;\n}\n.taylor .E {\n background-color: #ff0066;\n color: #fcff89;\n}\n.taylor .G {\n background-color: #ff9900;\n}\n.taylor .H {\n background-color: #0066ff;\n color: #fcff89;\n}\n.taylor .I {\n background-color: #66ff00;\n}\n.taylor .L {\n background-color: #33ff00;\n}\n.taylor .K {\n background-color: #6600ff;\n color: #fcff89;\n}\n.taylor .M {\n background-color: #00ff00;\n}\n.taylor .F {\n background-color: #00ff66;\n}\n.taylor .P {\n background-color: #ffcc00;\n}\n.taylor .S {\n background-color: #ff3300;\n color: #fcff89;\n}\n.taylor .T {\n background-color: #ff6600;\n}\n.taylor .W {\n background-color: #00ccff;\n}\n.taylor .Y {\n background-color: #00ffcc;\n}\n.taylor .V {\n background-color: #99ff00;\n}\n.taylor .B,\n.taylor .X,\n.taylor .Z {\n background-color: #ffffff;\n}\n.taylor .gap {\n color: #ccc;\n}\n.hydrophobicity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n color: #fcff89;\n}\n.hydrophobicity .A {\n background-color: #ad0052;\n}\n.hydrophobicity .R,\n.hydrophobicity .K {\n background-color: #0000ff;\n}\n.hydrophobicity .N,\n.hydrophobicity .D,\n.hydrophobicity .Q,\n.hydrophobicity .E,\n.hydrophobicity .B,\n.hydrophobicity .Z {\n background-color: #0c00f3;\n}\n.hydrophobicity .C {\n background-color: #c2003d;\n}\n.hydrophobicity .G {\n background-color: #6a0095;\n}\n.hydrophobicity .H {\n background-color: #1500ea;\n}\n.hydrophobicity .L {\n background-color: #ea0015;\n}\n.hydrophobicity .M {\n background-color: #b0004f;\n}\n.hydrophobicity .F {\n background-color: #cb0034;\n}\n.hydrophobicity .P {\n background-color: #4600b9;\n}\n.hydrophobicity .S {\n background-color: #5e00a1;\n}\n.hydrophobicity .T {\n background-color: #61009e;\n}\n.hydrophobicity .W {\n background-color: #5b00a4;\n}\n.hydrophobicity .Y {\n background-color: #4f00b0;\n}\n.hydrophobicity .V {\n background-color: #f60009;\n}\n.hydrophobicity .X {\n background-color: #680097;\n}\n.hydrophobicity .gap {\n color: #ccc;\n}\n.helix_propensity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.helix_propensity .A {\n background-color: #e718e7;\n}\n.helix_propensity .R {\n background-color: #6f906f;\n}\n.helix_propensity .N {\n background-color: #1be41b;\n}\n.helix_propensity .D {\n background-color: #778877;\n}\n.helix_propensity .C {\n background-color: #23dc23;\n}\n.helix_propensity .Q {\n background-color: #926d92;\n}\n.helix_propensity .E {\n background-color: #ff00ff;\n}\n.helix_propensity .G {\n background-color: #00ff00;\n}\n.helix_propensity .H {\n background-color: #758a75;\n}\n.helix_propensity .I {\n background-color: #8a758a;\n}\n.helix_propensity .L {\n background-color: #ae51ae;\n}\n.helix_propensity .K {\n background-color: #a05fa0;\n}\n.helix_propensity .M {\n background-color: #ef10ef;\n}\n.helix_propensity .F {\n background-color: #986798;\n}\n.helix_propensity .P {\n background-color: #00ff00;\n}\n.helix_propensity .S {\n background-color: #36c936;\n}\n.helix_propensity .T {\n background-color: #47b847;\n}\n.helix_propensity .W {\n background-color: #8a758a;\n}\n.helix_propensity .Y {\n background-color: #21de21;\n}\n.helix_propensity .V {\n background-color: #857a85;\n}\n.helix_propensity .B {\n background-color: #49b649;\n}\n.helix_propensity .X {\n background-color: #758a75;\n}\n.helix_propensity .Z {\n background-color: #c936c9;\n}\n.helix_propensity .gap {\n color: #ccc;\n}\n.strand_propensity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.strand_propensity .A {\n background-color: #5858a7;\n}\n.strand_propensity .R {\n background-color: #6b6b94;\n}\n.strand_propensity .N {\n background-color: #64649b;\n}\n.strand_propensity .D {\n background-color: #2121de;\n}\n.strand_propensity .C {\n background-color: #9d9d62;\n}\n.strand_propensity .Q {\n background-color: #8c8c73;\n}\n.strand_propensity .E {\n background-color: #0000ff;\n}\n.strand_propensity .G {\n background-color: #4949b6;\n}\n.strand_propensity .H {\n background-color: #60609f;\n}\n.strand_propensity .I {\n background-color: #ecec13;\n}\n.strand_propensity .L {\n background-color: #b2b24d;\n}\n.strand_propensity .K {\n background-color: #4747b8;\n}\n.strand_propensity .M {\n background-color: #82827d;\n}\n.strand_propensity .F {\n background-color: #c2c23d;\n}\n.strand_propensity .P {\n background-color: #2323dc;\n}\n.strand_propensity .S {\n background-color: #4949b6;\n}\n.strand_propensity .T {\n background-color: #9d9d62;\n}\n.strand_propensity .W {\n background-color: #c0c03f;\n}\n.strand_propensity .Y {\n background-color: #d3d32c;\n}\n.strand_propensity .V {\n background-color: #ffff00;\n}\n.strand_propensity .B {\n background-color: #4343bc;\n}\n.strand_propensity .X {\n background-color: #797986;\n}\n.strand_propensity .Z {\n background-color: #4747b8;\n}\n.strand_propensity .A,\n.strand_propensity .R,\n.strand_propensity .N,\n.strand_propensity .D,\n.strand_propensity .E,\n.strand_propensity .G,\n.strand_propensity .H,\n.strand_propensity .K,\n.strand_propensity .P,\n.strand_propensity .S,\n.strand_propensity .B,\n.strand_propensity .Z {\n color: #fcff89;\n}\n.strand_propensity .gap {\n color: #ccc;\n}\n.turn_propensity {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.turn_propensity .gap {\n color: #ccc;\n}\n.turn_propensity .A {\n background-color: #2cd3d3;\n}\n.turn_propensity .R {\n background-color: #708f8f;\n}\n.turn_propensity .N {\n background-color: #ff0000;\n}\n.turn_propensity .D {\n background-color: #e81717;\n}\n.turn_propensity .C {\n background-color: #a85757;\n}\n.turn_propensity .Q {\n background-color: #3fc0c0;\n}\n.turn_propensity .E {\n background-color: #778888;\n}\n.turn_propensity .G {\n background-color: #ff0000;\n}\n.turn_propensity .H {\n background-color: #708f8f;\n}\n.turn_propensity .I {\n background-color: #00ffff;\n}\n.turn_propensity .L {\n background-color: #1ce3e3;\n}\n.turn_propensity .K {\n background-color: #7e8181;\n}\n.turn_propensity .M {\n background-color: #1ee1e1;\n}\n.turn_propensity .F {\n background-color: #1ee1e1;\n}\n.turn_propensity .P {\n background-color: #f60909;\n}\n.turn_propensity .S {\n background-color: #e11e1e;\n}\n.turn_propensity .T {\n background-color: #738c8c;\n}\n.turn_propensity .W {\n background-color: #738c8c;\n}\n.turn_propensity .Y {\n background-color: #9d6262;\n}\n.turn_propensity .V {\n background-color: #07f8f8;\n}\n.turn_propensity .B {\n background-color: #f30c0c;\n}\n.turn_propensity .X {\n background-color: #7c8383;\n}\n.turn_propensity .Z {\n background-color: #5ba4a4;\n}\n.turn_propensity .N,\n.turn_propensity .D,\n.turn_propensity .G,\n.turn_propensity .P,\n.turn_propensity .S,\n.turn_propensity .B {\n color: #fcff89;\n}\n.buried_index {\n white-space: nowrap;\n font-family: monospace;\n height: 18px;\n font-size: 12px;\n}\n.buried_index .gap {\n color: #ccc;\n}\n.buried_index .A {\n background-color: #00a35c;\n}\n.buried_index .R {\n background-color: #00fc03;\n}\n.buried_index .N {\n background-color: #00eb14;\n}\n.buried_index .D {\n background-color: #00eb14;\n}\n.buried_index .C {\n background-color: #0000ff;\n}\n.buried_index .Q {\n background-color: #00f10e;\n}\n.buried_index .E {\n background-color: #00f10e;\n}\n.buried_index .G {\n background-color: #009d62;\n}\n.buried_index .H {\n background-color: #00d52a;\n}\n.buried_index .I {\n background-color: #0054ab;\n}\n.buried_index .L {\n background-color: #007b84;\n}\n.buried_index .K {\n background-color: #00ff00;\n}\n.buried_index .M {\n background-color: #009768;\n}\n.buried_index .F {\n background-color: #008778;\n}\n.buried_index .P {\n background-color: #00e01f;\n}\n.buried_index .S {\n background-color: #00d52a;\n}\n.buried_index .T {\n background-color: #00db24;\n}\n.buried_index .W {\n background-color: #00a857;\n}\n.buried_index .Y {\n background-color: #00e619;\n}\n.buried_index .V {\n background-color: #005fa0;\n}\n.buried_index .B {\n background-color: #00eb14;\n}\n.buried_index .X {\n background-color: #00b649;\n}\n.buried_index .Z {\n background-color: #00f10e;\n}\n.buried_index .C,\n.buried_index .I,\n.buried_index .V {\n color: #fcff89;\n}\n",".visible-detail {\n border: 1px solid #557B74;\n padding: 6px 12px;\n}\n.detail {\n margin-right: auto;\n margin-left: auto;\n padding-left: 15px;\n padding-right: 15px;\n}\n.table {\n width: 100%;\n max-width: 100%;\n}\n.xrefs {\n border-collapse: collapse;\n border-spacing: 0;\n border-color: grey;\n table-layout: fixed;\n}\n.xref-name-col {\n width: 20%;\n}\n.xref-value-col {\n width: 80%;\n}\n.xref-80-col {\n width: 80%;\n}\n.xref-70-col {\n width: 70%;\n}\n.xref-10-col {\n width: 10%;\n}\n.xref-id-list {\n padding-left: 0;\n list-style: none;\n}\n.result-gene {\n padding: 0.2em;\n border: 5px solid white;\n}\n.result-gene:hover {\n border-color: antiquewhite;\n}\n.gene-title {\n padding-top:0.5em;\n}\n.gene-id {\n white-space: nowrap;\n}\n.gene-name {\n color: #557B74;\n}\n.gene-description {\n margin-bottom: 0;\n}\n.gene-species {\n white-space: nowrap;\n font-style: italic;\n padding-left: 1em;\n}\n.gene-synonyms {\n white-space: nowrap;\n font-size: small;\n}\n.gene-extras {\n float: right;\n border: dashed 1px blue;\n}\n.gene-detail-tabs {\n display: flex;\n flex-wrap: wrap;\n width: 80em;\n}\n.gene-detail-tab-closed {\n color: darkgreen;\n cursor: pointer;\n /*background-color: lightgray;*/\n}\n.gene-detail-tab-disabled {\n /*color: white;*/\n /*background-color: lightgray;*/\n color: lightgray;\n cursor: not-allowed;\n}\n.gene-detail-tab-expanded {\n color: white;\n background-color: #557B74;\n cursor: pointer;\n}\n.result-gene-summary {\n display: flex;\n flex-flow: row nowrap;\n justify-content: flex-start;\n}\n.result-gene-summary .species-name {\n white-space: nowrap;\n font-style: italic;\n}\n.result-gene-title-body {\n flex: 1 1 auto;\n width: 1036px;\n}\n.closest-ortholog, .gene-summary-tair {\n cursor: pointer;\n flex: 1 1 auto;\n width: 500px;\n font-size: smaller;\n margin-top: 10px;\n padding: 0 1rem;\n margin-left: 1rem;\n border: 1px solid darkorange;\n}\n\n.closest-ortholog {\n border: 1px dotted darkorange;\n}\n\n.gene-summary-tair {\n border: 1px dotted darkgreen;\n}\n.gene-summary-tair .rest {\n display: none;\n}\n\n.gene-summary-tair:hover .rest {\n display: inline;\n}\n.gene-summary-tair:focus .rest {\n display: inline;\n}\n.gene-summary-tair:hover .ellipsis {\n display: none;\n}\n.gene-summary-tair:focus .ellipsis {\n display: none;\n}\n\n/* this is the \"title\" of the closest ortholog box */\n.closest-ortholog::before,\n.gene-summary-tair::before {\n position: relative;\n float: right;\n margin-top: -12px;\n margin-right: 6px;\n border: dotted 1px;\n padding: 0 1rem;\n background: #fff;\n}\n\n.closest-ortholog::before {\n content: \"Model Species Homolog\";\n color: orange;\n}\n\n/* this is the \"title\" of the closest ortholog box */\n.gene-summary-tair::before {\n content: \"TAIR Curated Description\";\n color: darkgreen;\n}\n\n.gene-search-pic-sugg {\n width: 100%;\n height: 200px;\n background: url(\"../../static/images/suggestions.png\");\n background-size: contain;\n background-repeat: no-repeat;\n}\n.gene-search-pic-results {\n width: 100%;\n height: 200px;\n background: url(\"../../static/images/results.png\");\n background-size: contain;\n background-repeat: no-repeat;\n}\n.gene-search-pic-genetree {\n width: 100%;\n height: 200px;\n background: url(\"../../static/images/genetree.png\");\n background-size: contain;\n background-repeat: no-repeat;\n}"],"names":[],"version":3,"file":"index.css.map"}
package/dist/index.js CHANGED
@@ -2646,6 +2646,139 @@ class $b7cae39a716ca5a8$var$Xref extends (0, ($parcel$interopDefault($gXNCa$reac
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2646
  className: "xref-name-col",
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  children: db
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  }),
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
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+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("ol", {
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+ className: "xref-id-list",
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+ })
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+ })
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+ ]
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+ });
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+ }
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+ }
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+ function $b7cae39a716ca5a8$var$formatXrefsForGene(gene) {
2661
+ if (!gene || !(0, ($parcel$interopDefault($gXNCa$lodash))).isArray(gene.xrefs)) throw new Error("No xrefs for " + (0, ($parcel$interopDefault($gXNCa$lodash))).get(gene._id));
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+ return gene.xrefs.filter((xr)=>(0, ($parcel$interopDefault($gXNCa$gramenedbxrefs))).isKnown(xr.db) && xr.db !== "PUBMED").sort().map((xr, idx)=>{
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+ var xref = (0, ($parcel$interopDefault($gXNCa$gramenedbxrefs))).fetch(xr.db);
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+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($b7cae39a716ca5a8$var$Xref, {
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+ xref: xref,
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+ members: xr.ids,
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+ source: xr.source,
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+ text: xr.text
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+ }, idx);
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+ });
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+ }
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+ const $b7cae39a716ca5a8$var$Xrefs = ({ searchResult: searchResult , geneDocs: geneDocs })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $5c2c79352d3d7b81$export$47eb42ff093406d4), {
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+ children: [
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$f99233281efd08a0), {
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+ children: "Cross-references"
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+ }, "title"),
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$393edc798c47379d), {
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+ children: "References to this gene in other databases:"
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+ }, "description"),
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$7c6e2c02157bb7d2), {
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+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("table", {
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+ className: "xrefs table",
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+ children: [
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
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+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
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+ children: [
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
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+ className: "xref-name-col",
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+ children: "Database"
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+ }),
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
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+ className: "xref-value-col",
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+ children: "IDs and links"
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+ })
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+ ]
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+ })
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+ }),
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
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+ children: $b7cae39a716ca5a8$var$formatXrefsForGene(geneDocs[searchResult.id])
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+ })
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+ ]
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+ })
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+ }, "content")
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+ ]
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+ });
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+ var $b7cae39a716ca5a8$export$2e2bcd8739ae039 = $b7cae39a716ca5a8$var$Xrefs;
2707
+
2708
+
2709
+
2710
+
2711
+
2712
+
2713
+
2714
+
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+ const $830f925242a0b007$var$HOW_MANY_TO_SHOW_BY_DEFAULT = 10;
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+ class $830f925242a0b007$var$Xref extends (0, ($parcel$interopDefault($gXNCa$react))).Component {
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+ constructor(props){
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+ super(props);
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+ this.state = {
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+ showAll: false
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+ };
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+ }
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+ toggleShowAll() {
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+ this.setState({
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+ showAll: !this.state.showAll
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+ });
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+ }
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+ possiblyTruncateList(vals) {
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+ var ellipsis, ellipsisChar, ellipsisTitle;
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+ if (vals.length > $830f925242a0b007$var$HOW_MANY_TO_SHOW_BY_DEFAULT) {
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+ if (this.state.showAll) {
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+ ellipsisChar = "^ show first " + $830f925242a0b007$var$HOW_MANY_TO_SHOW_BY_DEFAULT;
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+ ellipsisTitle = "Show less";
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+ } else {
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+ ellipsisChar = "… show all (" + (vals.length - $830f925242a0b007$var$HOW_MANY_TO_SHOW_BY_DEFAULT) + " more)";
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+ ellipsisTitle = "Show more";
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+ vals = vals.slice(0, $830f925242a0b007$var$HOW_MANY_TO_SHOW_BY_DEFAULT);
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+ }
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+ ellipsis = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
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+ className: "showAll",
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+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
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+ title: ellipsisTitle,
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+ onClick: this.toggleShowAll.bind(this),
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+ children: ellipsisChar
2745
+ })
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+ }, "showMore");
2747
+ vals.push(ellipsis);
2748
+ }
2749
+ return vals;
2750
+ }
2751
+ render() {
2752
+ var db = this.props.xref.label;
2753
+ var urlfcn = this.props.xref.url;
2754
+ var members = this.props.members.sort();
2755
+ var vals = members.map(function(item, idx) {
2756
+ var url = urlfcn(item), liClass = idx < $830f925242a0b007$var$HOW_MANY_TO_SHOW_BY_DEFAULT ? "default" : "extra";
2757
+ let external = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("small", {
2758
+ title: "This link opens a page from an external site",
2759
+ children: [
2760
+ " ",
2761
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("i", {
2762
+ className: "fa fa-external-link"
2763
+ })
2764
+ ]
2765
+ });
2766
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
2767
+ className: liClass,
2768
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, ($parcel$interopDefault($gXNCa$reactga))).OutboundLink, {
2769
+ eventLabel: db,
2770
+ to: url,
2771
+ target: "_blank",
2772
+ children: [
2773
+ item,
2774
+ external
2775
+ ]
2776
+ })
2777
+ }, idx);
2778
+ });
2779
+ vals = this.possiblyTruncateList(vals);
2780
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
2781
+ children: [
2649
2782
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
2650
2783
  className: "xref-value-col",
2651
2784
  children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("ol", {
@@ -2665,9 +2798,10 @@ class $b7cae39a716ca5a8$var$Xref extends (0, ($parcel$interopDefault($gXNCa$reac
2665
2798
  });
2666
2799
  }
2667
2800
  }
2668
- function $b7cae39a716ca5a8$var$formatXrefsForGene(gene) {
2801
+ function $830f925242a0b007$var$formatPubsForGene(gene) {
2669
2802
  if (!gene || !(0, ($parcel$interopDefault($gXNCa$lodash))).isArray(gene.xrefs)) throw new Error("No xrefs for " + (0, ($parcel$interopDefault($gXNCa$lodash))).get(gene._id));
2670
- return gene.xrefs.filter((xr)=>(0, ($parcel$interopDefault($gXNCa$gramenedbxrefs))).isKnown(xr.db)).sort((a, b)=>{
2803
+ return gene.xrefs.filter((xr)=>xr.db === "PUBMED") //dbxrefs.isKnown(xr.db))
2804
+ .sort((a, b)=>{
2671
2805
  if (a.source) {
2672
2806
  if (b.source) {
2673
2807
  if (a.source < b.source) return -1;
@@ -2679,7 +2813,7 @@ function $b7cae39a716ca5a8$var$formatXrefsForGene(gene) {
2679
2813
  return 0;
2680
2814
  }).map((xr, idx)=>{
2681
2815
  var xref = (0, ($parcel$interopDefault($gXNCa$gramenedbxrefs))).fetch(xr.db);
2682
- return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($b7cae39a716ca5a8$var$Xref, {
2816
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($830f925242a0b007$var$Xref, {
2683
2817
  xref: xref,
2684
2818
  members: xr.ids,
2685
2819
  source: xr.source,
@@ -2687,13 +2821,13 @@ function $b7cae39a716ca5a8$var$formatXrefsForGene(gene) {
2687
2821
  }, idx);
2688
2822
  });
2689
2823
  }
2690
- const $b7cae39a716ca5a8$var$Xrefs = ({ searchResult: searchResult , geneDocs: geneDocs })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $5c2c79352d3d7b81$export$47eb42ff093406d4), {
2824
+ const $830f925242a0b007$var$Publications = ({ searchResult: searchResult , geneDocs: geneDocs })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $5c2c79352d3d7b81$export$47eb42ff093406d4), {
2691
2825
  children: [
2692
2826
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$f99233281efd08a0), {
2693
- children: "Cross-references"
2827
+ children: "Curated publications"
2694
2828
  }, "title"),
2695
2829
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$393edc798c47379d), {
2696
- children: "References to this gene in other databases:"
2830
+ children: "This gene has been described in the literature:"
2697
2831
  }, "description"),
2698
2832
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$7c6e2c02157bb7d2), {
2699
2833
  children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("table", {
@@ -2704,32 +2838,28 @@ const $b7cae39a716ca5a8$var$Xrefs = ({ searchResult: searchResult , geneDocs: ge
2704
2838
  children: [
2705
2839
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
2706
2840
  className: "xref-10-col",
2707
- children: "Database"
2708
- }),
2709
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
2710
- className: "xref-10-col",
2711
- children: "IDs and links"
2841
+ children: "PubMed link"
2712
2842
  }),
2713
2843
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
2714
2844
  className: "xref-10-col",
2715
- children: "Source"
2845
+ children: "Curation source"
2716
2846
  }),
2717
2847
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
2718
- className: "xref-70-col",
2719
- children: "Text"
2848
+ className: "xref-80-col",
2849
+ children: "Title/Description"
2720
2850
  })
2721
2851
  ]
2722
2852
  })
2723
2853
  }),
2724
2854
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
2725
- children: $b7cae39a716ca5a8$var$formatXrefsForGene(geneDocs[searchResult.id])
2855
+ children: $830f925242a0b007$var$formatPubsForGene(geneDocs[searchResult.id])
2726
2856
  })
2727
2857
  ]
2728
2858
  })
2729
2859
  }, "content")
2730
2860
  ]
2731
2861
  });
2732
- var $b7cae39a716ca5a8$export$2e2bcd8739ae039 = $b7cae39a716ca5a8$var$Xrefs;
2862
+ var $830f925242a0b007$export$2e2bcd8739ae039 = $830f925242a0b007$var$Publications;
2733
2863
 
2734
2864
 
2735
2865
 
@@ -2748,7 +2878,8 @@ let $6c5c4f90059875bf$var$inventory = {
2748
2878
  expression: (0, $9e29a4f60318db7a$export$2e2bcd8739ae039),
2749
2879
  homology: (0, $64fad37f770d2bfe$export$2e2bcd8739ae039),
2750
2880
  pathways: (0, $54c74a4689d5a778$export$2e2bcd8739ae039),
2751
- xrefs: (0, $b7cae39a716ca5a8$export$2e2bcd8739ae039)
2881
+ xrefs: (0, $b7cae39a716ca5a8$export$2e2bcd8739ae039),
2882
+ pubs: (0, $830f925242a0b007$export$2e2bcd8739ae039)
2752
2883
  };
2753
2884
  function $6c5c4f90059875bf$var$renderTairSummary(searchResult) {
2754
2885
  const summary = searchResult.summary;
@@ -2835,31 +2966,37 @@ class $6c5c4f90059875bf$var$Gene extends (0, ($parcel$interopDefault($gXNCa$reac
2835
2966
  {
2836
2967
  id: "location",
2837
2968
  label: "Location",
2969
+ popup: "Genome Browser",
2838
2970
  available: false
2839
2971
  },
2840
2972
  {
2841
2973
  id: "expression",
2842
2974
  label: "Expression",
2975
+ popup: "Gene Expression Atlas",
2843
2976
  available: false
2844
2977
  },
2845
2978
  {
2846
2979
  id: "homology",
2847
2980
  label: "Homology",
2981
+ popup: "Gene Family Tree",
2848
2982
  available: false
2849
2983
  },
2850
2984
  {
2851
2985
  id: "pathways",
2852
2986
  label: "Pathways",
2987
+ popup: "Plant Reactome Pathways",
2988
+ available: false
2989
+ },
2990
+ {
2991
+ id: "pubs",
2992
+ label: "Papers",
2993
+ popup: "Curated Publications",
2853
2994
  available: false
2854
2995
  },
2855
- // {
2856
- // id: 'pubs',
2857
- // label: 'Publications',
2858
- // available: false
2859
- // },
2860
2996
  {
2861
2997
  id: "xrefs",
2862
2998
  label: "Xrefs",
2999
+ popup: "Database Cross-references",
2863
3000
  available: false
2864
3001
  }
2865
3002
  ],
@@ -2958,10 +3095,17 @@ class $6c5c4f90059875bf$var$Gene extends (0, ($parcel$interopDefault($gXNCa$reac
2958
3095
  }),
2959
3096
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
2960
3097
  className: "gene-detail-tabs",
2961
- children: this.state.details.map((d, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
2962
- className: `col-md-1 text-center gene-detail-tab-${this.getDetailStatus(d)}`,
2963
- onClick: ()=>this.setExpanded(d),
2964
- children: d.label
3098
+ children: this.state.details.map((d, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.OverlayTrigger), {
3099
+ placement: "bottom",
3100
+ overlay: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tooltip), {
3101
+ id: `tooltip`,
3102
+ children: d.popup
3103
+ }),
3104
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
3105
+ className: `col-md-1 text-center gene-detail-tab-${this.getDetailStatus(d)}`,
3106
+ onClick: ()=>this.setExpanded(d),
3107
+ children: d.label
3108
+ }, idx)
2965
3109
  }, idx))
2966
3110
  }),
2967
3111
  this.state.expandedDetail && this.ensureGene(searchResult.id) && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {