diff --git a/taxonium_component/src/components/TreenomeBrowser.jsx b/taxonium_component/src/components/TreenomeBrowser.jsx
new file mode 100644
index 00000000..1c1bafe8
--- /dev/null
+++ b/taxonium_component/src/components/TreenomeBrowser.jsx
@@ -0,0 +1,10 @@
+import JBrowsePanel from "./JBrowsePanel";
+import { JBrowseErrorBoundary } from "./JBrowseErrorBoundary";
+
+export default function TreenomeBrowser({ state, settings }) {
+ return (
+
+
+
+ );
+}
diff --git a/taxonium_component/src/countries.json b/taxonium_component/src/countries.json
new file mode 100644
index 00000000..1764c172
--- /dev/null
+++ b/taxonium_component/src/countries.json
@@ -0,0 +1,1472 @@
+[
+ {
+ "country": "AD",
+ "latitude": 42.546245,
+ "longitude": 1.601554,
+ "name": "Andorra"
+ },
+ {
+ "country": "AE",
+ "latitude": 23.424076,
+ "longitude": 53.847818,
+ "name": "United Arab Emirates"
+ },
+ {
+ "country": "AF",
+ "latitude": 33.93911,
+ "longitude": 67.709953,
+ "name": "Afghanistan"
+ },
+ {
+ "country": "AG",
+ "latitude": 17.060816,
+ "longitude": -61.796428,
+ "name": "Antigua and Barbuda"
+ },
+ {
+ "country": "AI",
+ "latitude": 18.220554,
+ "longitude": -63.068615,
+ "name": "Anguilla"
+ },
+ {
+ "country": "AL",
+ "latitude": 41.153332,
+ "longitude": 20.168331,
+ "name": "Albania"
+ },
+ {
+ "country": "AM",
+ "latitude": 40.069099,
+ "longitude": 45.038189,
+ "name": "Armenia"
+ },
+ {
+ "country": "AN",
+ "latitude": 12.226079,
+ "longitude": -69.060087,
+ "name": "Netherlands Antilles"
+ },
+ {
+ "country": "AO",
+ "latitude": -11.202692,
+ "longitude": 17.873887,
+ "name": "Angola"
+ },
+ {
+ "country": "AQ",
+ "latitude": -75.250973,
+ "longitude": -0.071389,
+ "name": "Antarctica"
+ },
+ {
+ "country": "AR",
+ "latitude": -38.416097,
+ "longitude": -63.616672,
+ "name": "Argentina"
+ },
+ {
+ "country": "AS",
+ "latitude": -14.270972,
+ "longitude": -170.132217,
+ "name": "American Samoa"
+ },
+ {
+ "country": "AT",
+ "latitude": 47.516231,
+ "longitude": 14.550072,
+ "name": "Austria"
+ },
+ {
+ "country": "AU",
+ "latitude": -25.274398,
+ "longitude": 133.775136,
+ "name": "Australia"
+ },
+ {
+ "country": "AW",
+ "latitude": 12.52111,
+ "longitude": -69.968338,
+ "name": "Aruba"
+ },
+ {
+ "country": "AZ",
+ "latitude": 40.143105,
+ "longitude": 47.576927,
+ "name": "Azerbaijan"
+ },
+ {
+ "country": "BA",
+ "latitude": 43.915886,
+ "longitude": 17.679076,
+ "name": "Bosnia and Herzegovina"
+ },
+ {
+ "country": "BB",
+ "latitude": 13.193887,
+ "longitude": -59.543198,
+ "name": "Barbados"
+ },
+ {
+ "country": "BD",
+ "latitude": 23.684994,
+ "longitude": 90.356331,
+ "name": "Bangladesh"
+ },
+ {
+ "country": "BE",
+ "latitude": 50.503887,
+ "longitude": 4.469936,
+ "name": "Belgium"
+ },
+ {
+ "country": "BF",
+ "latitude": 12.238333,
+ "longitude": -1.561593,
+ "name": "Burkina Faso"
+ },
+ {
+ "country": "BG",
+ "latitude": 42.733883,
+ "longitude": 25.48583,
+ "name": "Bulgaria"
+ },
+ {
+ "country": "BH",
+ "latitude": 25.930414,
+ "longitude": 50.637772,
+ "name": "Bahrain"
+ },
+ {
+ "country": "BI",
+ "latitude": -3.373056,
+ "longitude": 29.918886,
+ "name": "Burundi"
+ },
+ {
+ "country": "BJ",
+ "latitude": 9.30769,
+ "longitude": 2.315834,
+ "name": "Benin"
+ },
+ {
+ "country": "BM",
+ "latitude": 32.321384,
+ "longitude": -64.75737,
+ "name": "Bermuda"
+ },
+ {
+ "country": "BN",
+ "latitude": 4.535277,
+ "longitude": 114.727669,
+ "name": "Brunei"
+ },
+ {
+ "country": "BO",
+ "latitude": -16.290154,
+ "longitude": -63.588653,
+ "name": "Bolivia"
+ },
+ {
+ "country": "BR",
+ "latitude": -14.235004,
+ "longitude": -51.92528,
+ "name": "Brazil"
+ },
+ {
+ "country": "BS",
+ "latitude": 25.03428,
+ "longitude": -77.39628,
+ "name": "Bahamas"
+ },
+ {
+ "country": "BT",
+ "latitude": 27.514162,
+ "longitude": 90.433601,
+ "name": "Bhutan"
+ },
+ {
+ "country": "BV",
+ "latitude": -54.423199,
+ "longitude": 3.413194,
+ "name": "Bouvet Island"
+ },
+ {
+ "country": "BW",
+ "latitude": -22.328474,
+ "longitude": 24.684866,
+ "name": "Botswana"
+ },
+ {
+ "country": "BY",
+ "latitude": 53.709807,
+ "longitude": 27.953389,
+ "name": "Belarus"
+ },
+ {
+ "country": "BZ",
+ "latitude": 17.189877,
+ "longitude": -88.49765,
+ "name": "Belize"
+ },
+ {
+ "country": "CA",
+ "latitude": 56.130366,
+ "longitude": -106.346771,
+ "name": "Canada"
+ },
+ {
+ "country": "CC",
+ "latitude": -12.164165,
+ "longitude": 96.870956,
+ "name": "Cocos [Keeling] Islands"
+ },
+ {
+ "country": "CD",
+ "latitude": -4.038333,
+ "longitude": 21.758664,
+ "name": "Congo [DRC]"
+ },
+ {
+ "country": "CF",
+ "latitude": 6.611111,
+ "longitude": 20.939444,
+ "name": "Central African Republic"
+ },
+ {
+ "country": "CG",
+ "latitude": -0.228021,
+ "longitude": 15.827659,
+ "name": "Congo [Republic]"
+ },
+ {
+ "country": "CH",
+ "latitude": 46.818188,
+ "longitude": 8.227512,
+ "name": "Switzerland"
+ },
+ {
+ "country": "CI",
+ "latitude": 7.539989,
+ "longitude": -5.54708,
+ "name": "Côte d'Ivoire"
+ },
+ {
+ "country": "CK",
+ "latitude": -21.236736,
+ "longitude": -159.777671,
+ "name": "Cook Islands"
+ },
+ {
+ "country": "CL",
+ "latitude": -35.675147,
+ "longitude": -71.542969,
+ "name": "Chile"
+ },
+ {
+ "country": "CM",
+ "latitude": 7.369722,
+ "longitude": 12.354722,
+ "name": "Cameroon"
+ },
+ {
+ "country": "CN",
+ "latitude": 35.86166,
+ "longitude": 104.195397,
+ "name": "China"
+ },
+ {
+ "country": "CO",
+ "latitude": 4.570868,
+ "longitude": -74.297333,
+ "name": "Colombia"
+ },
+ {
+ "country": "CR",
+ "latitude": 9.748917,
+ "longitude": -83.753428,
+ "name": "Costa Rica"
+ },
+ {
+ "country": "CU",
+ "latitude": 21.521757,
+ "longitude": -77.781167,
+ "name": "Cuba"
+ },
+ {
+ "country": "CV",
+ "latitude": 16.002082,
+ "longitude": -24.013197,
+ "name": "Cape Verde"
+ },
+ {
+ "country": "CX",
+ "latitude": -10.447525,
+ "longitude": 105.690449,
+ "name": "Christmas Island"
+ },
+ {
+ "country": "CY",
+ "latitude": 35.126413,
+ "longitude": 33.429859,
+ "name": "Cyprus"
+ },
+ {
+ "country": "CZ",
+ "latitude": 49.817492,
+ "longitude": 15.472962,
+ "name": "Czech Republic"
+ },
+ {
+ "country": "DE",
+ "latitude": 51.165691,
+ "longitude": 10.451526,
+ "name": "Germany"
+ },
+ {
+ "country": "DJ",
+ "latitude": 11.825138,
+ "longitude": 42.590275,
+ "name": "Djibouti"
+ },
+ {
+ "country": "DK",
+ "latitude": 56.26392,
+ "longitude": 9.501785,
+ "name": "Denmark"
+ },
+ {
+ "country": "DM",
+ "latitude": 15.414999,
+ "longitude": -61.370976,
+ "name": "Dominica"
+ },
+ {
+ "country": "DO",
+ "latitude": 18.735693,
+ "longitude": -70.162651,
+ "name": "Dominican Republic"
+ },
+ {
+ "country": "DZ",
+ "latitude": 28.033886,
+ "longitude": 1.659626,
+ "name": "Algeria"
+ },
+ {
+ "country": "EC",
+ "latitude": -1.831239,
+ "longitude": -78.183406,
+ "name": "Ecuador"
+ },
+ {
+ "country": "EE",
+ "latitude": 58.595272,
+ "longitude": 25.013607,
+ "name": "Estonia"
+ },
+ {
+ "country": "EG",
+ "latitude": 26.820553,
+ "longitude": 30.802498,
+ "name": "Egypt"
+ },
+ {
+ "country": "EH",
+ "latitude": 24.215527,
+ "longitude": -12.885834,
+ "name": "Western Sahara"
+ },
+ {
+ "country": "ER",
+ "latitude": 15.179384,
+ "longitude": 39.782334,
+ "name": "Eritrea"
+ },
+ {
+ "country": "ES",
+ "latitude": 40.463667,
+ "longitude": -3.74922,
+ "name": "Spain"
+ },
+ {
+ "country": "ET",
+ "latitude": 9.145,
+ "longitude": 40.489673,
+ "name": "Ethiopia"
+ },
+ {
+ "country": "FI",
+ "latitude": 61.92411,
+ "longitude": 25.748151,
+ "name": "Finland"
+ },
+ {
+ "country": "FJ",
+ "latitude": -16.578193,
+ "longitude": 179.414413,
+ "name": "Fiji"
+ },
+ {
+ "country": "FK",
+ "latitude": -51.796253,
+ "longitude": -59.523613,
+ "name": "Falkland Islands [Islas Malvinas]"
+ },
+ {
+ "country": "FM",
+ "latitude": 7.425554,
+ "longitude": 150.550812,
+ "name": "Micronesia"
+ },
+ {
+ "country": "FO",
+ "latitude": 61.892635,
+ "longitude": -6.911806,
+ "name": "Faroe Islands"
+ },
+ {
+ "country": "FR",
+ "latitude": 46.227638,
+ "longitude": 2.213749,
+ "name": "France"
+ },
+ {
+ "country": "GA",
+ "latitude": -0.803689,
+ "longitude": 11.609444,
+ "name": "Gabon"
+ },
+ {
+ "country": "GB",
+ "latitude": 55.378051,
+ "longitude": -3.435973,
+ "name": "United Kingdom"
+ },
+ {
+ "country": "GD",
+ "latitude": 12.262776,
+ "longitude": -61.604171,
+ "name": "Grenada"
+ },
+ {
+ "country": "GE",
+ "latitude": 42.315407,
+ "longitude": 43.356892,
+ "name": "Georgia"
+ },
+ {
+ "country": "GF",
+ "latitude": 3.933889,
+ "longitude": -53.125782,
+ "name": "French Guiana"
+ },
+ {
+ "country": "GG",
+ "latitude": 49.465691,
+ "longitude": -2.585278,
+ "name": "Guernsey"
+ },
+ {
+ "country": "GH",
+ "latitude": 7.946527,
+ "longitude": -1.023194,
+ "name": "Ghana"
+ },
+ {
+ "country": "GI",
+ "latitude": 36.137741,
+ "longitude": -5.345374,
+ "name": "Gibraltar"
+ },
+ {
+ "country": "GL",
+ "latitude": 71.706936,
+ "longitude": -42.604303,
+ "name": "Greenland"
+ },
+ {
+ "country": "GM",
+ "latitude": 13.443182,
+ "longitude": -15.310139,
+ "name": "Gambia"
+ },
+ {
+ "country": "GN",
+ "latitude": 9.945587,
+ "longitude": -9.696645,
+ "name": "Guinea"
+ },
+ {
+ "country": "GP",
+ "latitude": 16.995971,
+ "longitude": -62.067641,
+ "name": "Guadeloupe"
+ },
+ {
+ "country": "GQ",
+ "latitude": 1.650801,
+ "longitude": 10.267895,
+ "name": "Equatorial Guinea"
+ },
+ {
+ "country": "GR",
+ "latitude": 39.074208,
+ "longitude": 21.824312,
+ "name": "Greece"
+ },
+ {
+ "country": "GS",
+ "latitude": -54.429579,
+ "longitude": -36.587909,
+ "name": "South Georgia and the South Sandwich Islands"
+ },
+ {
+ "country": "GT",
+ "latitude": 15.783471,
+ "longitude": -90.230759,
+ "name": "Guatemala"
+ },
+ {
+ "country": "GU",
+ "latitude": 13.444304,
+ "longitude": 144.793731,
+ "name": "Guam"
+ },
+ {
+ "country": "GW",
+ "latitude": 11.803749,
+ "longitude": -15.180413,
+ "name": "Guinea-Bissau"
+ },
+ {
+ "country": "GY",
+ "latitude": 4.860416,
+ "longitude": -58.93018,
+ "name": "Guyana"
+ },
+ {
+ "country": "GZ",
+ "latitude": 31.354676,
+ "longitude": 34.308825,
+ "name": "Gaza Strip"
+ },
+ {
+ "country": "HK",
+ "latitude": 22.396428,
+ "longitude": 114.109497,
+ "name": "Hong Kong"
+ },
+ {
+ "country": "HM",
+ "latitude": -53.08181,
+ "longitude": 73.504158,
+ "name": "Heard Island and McDonald Islands"
+ },
+ {
+ "country": "HN",
+ "latitude": 15.199999,
+ "longitude": -86.241905,
+ "name": "Honduras"
+ },
+ {
+ "country": "HR",
+ "latitude": 45.1,
+ "longitude": 15.2,
+ "name": "Croatia"
+ },
+ {
+ "country": "HT",
+ "latitude": 18.971187,
+ "longitude": -72.285215,
+ "name": "Haiti"
+ },
+ {
+ "country": "HU",
+ "latitude": 47.162494,
+ "longitude": 19.503304,
+ "name": "Hungary"
+ },
+ {
+ "country": "ID",
+ "latitude": -0.789275,
+ "longitude": 113.921327,
+ "name": "Indonesia"
+ },
+ {
+ "country": "IE",
+ "latitude": 53.41291,
+ "longitude": -8.24389,
+ "name": "Ireland"
+ },
+ {
+ "country": "IL",
+ "latitude": 31.046051,
+ "longitude": 34.851612,
+ "name": "Israel"
+ },
+ {
+ "country": "IM",
+ "latitude": 54.236107,
+ "longitude": -4.548056,
+ "name": "Isle of Man"
+ },
+ {
+ "country": "IN",
+ "latitude": 20.593684,
+ "longitude": 78.96288,
+ "name": "India"
+ },
+ {
+ "country": "IO",
+ "latitude": -6.343194,
+ "longitude": 71.876519,
+ "name": "British Indian Ocean Territory"
+ },
+ {
+ "country": "IQ",
+ "latitude": 33.223191,
+ "longitude": 43.679291,
+ "name": "Iraq"
+ },
+ {
+ "country": "IR",
+ "latitude": 32.427908,
+ "longitude": 53.688046,
+ "name": "Iran"
+ },
+ {
+ "country": "IS",
+ "latitude": 64.963051,
+ "longitude": -19.020835,
+ "name": "Iceland"
+ },
+ {
+ "country": "IT",
+ "latitude": 41.87194,
+ "longitude": 12.56738,
+ "name": "Italy"
+ },
+ {
+ "country": "JE",
+ "latitude": 49.214439,
+ "longitude": -2.13125,
+ "name": "Jersey"
+ },
+ {
+ "country": "JM",
+ "latitude": 18.109581,
+ "longitude": -77.297508,
+ "name": "Jamaica"
+ },
+ {
+ "country": "JO",
+ "latitude": 30.585164,
+ "longitude": 36.238414,
+ "name": "Jordan"
+ },
+ {
+ "country": "JP",
+ "latitude": 36.204824,
+ "longitude": 138.252924,
+ "name": "Japan"
+ },
+ {
+ "country": "KE",
+ "latitude": -0.023559,
+ "longitude": 37.906193,
+ "name": "Kenya"
+ },
+ {
+ "country": "KG",
+ "latitude": 41.20438,
+ "longitude": 74.766098,
+ "name": "Kyrgyzstan"
+ },
+ {
+ "country": "KH",
+ "latitude": 12.565679,
+ "longitude": 104.990963,
+ "name": "Cambodia"
+ },
+ {
+ "country": "KI",
+ "latitude": -3.370417,
+ "longitude": -168.734039,
+ "name": "Kiribati"
+ },
+ {
+ "country": "KM",
+ "latitude": -11.875001,
+ "longitude": 43.872219,
+ "name": "Comoros"
+ },
+ {
+ "country": "KN",
+ "latitude": 17.357822,
+ "longitude": -62.782998,
+ "name": "Saint Kitts and Nevis"
+ },
+ {
+ "country": "KP",
+ "latitude": 40.339852,
+ "longitude": 127.510093,
+ "name": "North Korea"
+ },
+ {
+ "country": "KR",
+ "latitude": 35.907757,
+ "longitude": 127.766922,
+ "name": "South Korea"
+ },
+ {
+ "country": "KW",
+ "latitude": 29.31166,
+ "longitude": 47.481766,
+ "name": "Kuwait"
+ },
+ {
+ "country": "KY",
+ "latitude": 19.513469,
+ "longitude": -80.566956,
+ "name": "Cayman Islands"
+ },
+ {
+ "country": "KZ",
+ "latitude": 48.019573,
+ "longitude": 66.923684,
+ "name": "Kazakhstan"
+ },
+ {
+ "country": "LA",
+ "latitude": 19.85627,
+ "longitude": 102.495496,
+ "name": "Laos"
+ },
+ {
+ "country": "LB",
+ "latitude": 33.854721,
+ "longitude": 35.862285,
+ "name": "Lebanon"
+ },
+ {
+ "country": "LC",
+ "latitude": 13.909444,
+ "longitude": -60.978893,
+ "name": "Saint Lucia"
+ },
+ {
+ "country": "LI",
+ "latitude": 47.166,
+ "longitude": 9.555373,
+ "name": "Liechtenstein"
+ },
+ {
+ "country": "LK",
+ "latitude": 7.873054,
+ "longitude": 80.771797,
+ "name": "Sri Lanka"
+ },
+ {
+ "country": "LR",
+ "latitude": 6.428055,
+ "longitude": -9.429499,
+ "name": "Liberia"
+ },
+ {
+ "country": "LS",
+ "latitude": -29.609988,
+ "longitude": 28.233608,
+ "name": "Lesotho"
+ },
+ {
+ "country": "LT",
+ "latitude": 55.169438,
+ "longitude": 23.881275,
+ "name": "Lithuania"
+ },
+ {
+ "country": "LU",
+ "latitude": 49.815273,
+ "longitude": 6.129583,
+ "name": "Luxembourg"
+ },
+ {
+ "country": "LV",
+ "latitude": 56.879635,
+ "longitude": 24.603189,
+ "name": "Latvia"
+ },
+ {
+ "country": "LY",
+ "latitude": 26.3351,
+ "longitude": 17.228331,
+ "name": "Libya"
+ },
+ {
+ "country": "MA",
+ "latitude": 31.791702,
+ "longitude": -7.09262,
+ "name": "Morocco"
+ },
+ {
+ "country": "MC",
+ "latitude": 43.750298,
+ "longitude": 7.412841,
+ "name": "Monaco"
+ },
+ {
+ "country": "MD",
+ "latitude": 47.411631,
+ "longitude": 28.369885,
+ "name": "Moldova"
+ },
+ {
+ "country": "ME",
+ "latitude": 42.708678,
+ "longitude": 19.37439,
+ "name": "Montenegro"
+ },
+ {
+ "country": "MG",
+ "latitude": -18.766947,
+ "longitude": 46.869107,
+ "name": "Madagascar"
+ },
+ {
+ "country": "MH",
+ "latitude": 7.131474,
+ "longitude": 171.184478,
+ "name": "Marshall Islands"
+ },
+ {
+ "country": "MK",
+ "latitude": 41.608635,
+ "longitude": 21.745275,
+ "name": "Macedonia"
+ },
+ {
+ "country": "ML",
+ "latitude": 17.570692,
+ "longitude": -3.996166,
+ "name": "Mali"
+ },
+ {
+ "country": "MM",
+ "latitude": 21.913965,
+ "longitude": 95.956223,
+ "name": "Myanmar"
+ },
+ {
+ "country": "MN",
+ "latitude": 46.862496,
+ "longitude": 103.846656,
+ "name": "Mongolia"
+ },
+ {
+ "country": "MO",
+ "latitude": 22.198745,
+ "longitude": 113.543873,
+ "name": "Macau"
+ },
+ {
+ "country": "MP",
+ "latitude": 17.33083,
+ "longitude": 145.38469,
+ "name": "Northern Mariana Islands"
+ },
+ {
+ "country": "MQ",
+ "latitude": 14.641528,
+ "longitude": -61.024174,
+ "name": "Martinique"
+ },
+ {
+ "country": "MR",
+ "latitude": 21.00789,
+ "longitude": -10.940835,
+ "name": "Mauritania"
+ },
+ {
+ "country": "MS",
+ "latitude": 16.742498,
+ "longitude": -62.187366,
+ "name": "Montserrat"
+ },
+ {
+ "country": "MT",
+ "latitude": 35.937496,
+ "longitude": 14.375416,
+ "name": "Malta"
+ },
+ {
+ "country": "MU",
+ "latitude": -20.348404,
+ "longitude": 57.552152,
+ "name": "Mauritius"
+ },
+ {
+ "country": "MV",
+ "latitude": 3.202778,
+ "longitude": 73.22068,
+ "name": "Maldives"
+ },
+ {
+ "country": "MW",
+ "latitude": -13.254308,
+ "longitude": 34.301525,
+ "name": "Malawi"
+ },
+ {
+ "country": "MX",
+ "latitude": 23.634501,
+ "longitude": -102.552784,
+ "name": "Mexico"
+ },
+ {
+ "country": "MY",
+ "latitude": 4.210484,
+ "longitude": 101.975766,
+ "name": "Malaysia"
+ },
+ {
+ "country": "MZ",
+ "latitude": -18.665695,
+ "longitude": 35.529562,
+ "name": "Mozambique"
+ },
+ {
+ "country": "NA",
+ "latitude": -22.95764,
+ "longitude": 18.49041,
+ "name": "Namibia"
+ },
+ {
+ "country": "NC",
+ "latitude": -20.904305,
+ "longitude": 165.618042,
+ "name": "New Caledonia"
+ },
+ {
+ "country": "NE",
+ "latitude": 17.607789,
+ "longitude": 8.081666,
+ "name": "Niger"
+ },
+ {
+ "country": "NF",
+ "latitude": -29.040835,
+ "longitude": 167.954712,
+ "name": "Norfolk Island"
+ },
+ {
+ "country": "NG",
+ "latitude": 9.081999,
+ "longitude": 8.675277,
+ "name": "Nigeria"
+ },
+ {
+ "country": "NI",
+ "latitude": 12.865416,
+ "longitude": -85.207229,
+ "name": "Nicaragua"
+ },
+ {
+ "country": "NL",
+ "latitude": 52.132633,
+ "longitude": 5.291266,
+ "name": "Netherlands"
+ },
+ {
+ "country": "NO",
+ "latitude": 60.472024,
+ "longitude": 8.468946,
+ "name": "Norway"
+ },
+ {
+ "country": "NP",
+ "latitude": 28.394857,
+ "longitude": 84.124008,
+ "name": "Nepal"
+ },
+ {
+ "country": "NR",
+ "latitude": -0.522778,
+ "longitude": 166.931503,
+ "name": "Nauru"
+ },
+ {
+ "country": "NU",
+ "latitude": -19.054445,
+ "longitude": -169.867233,
+ "name": "Niue"
+ },
+ {
+ "country": "NZ",
+ "latitude": -40.900557,
+ "longitude": 174.885971,
+ "name": "New Zealand"
+ },
+ {
+ "country": "OM",
+ "latitude": 21.512583,
+ "longitude": 55.923255,
+ "name": "Oman"
+ },
+ {
+ "country": "PA",
+ "latitude": 8.537981,
+ "longitude": -80.782127,
+ "name": "Panama"
+ },
+ {
+ "country": "PE",
+ "latitude": -9.189967,
+ "longitude": -75.015152,
+ "name": "Peru"
+ },
+ {
+ "country": "PF",
+ "latitude": -17.679742,
+ "longitude": -149.406843,
+ "name": "French Polynesia"
+ },
+ {
+ "country": "PG",
+ "latitude": -6.314993,
+ "longitude": 143.95555,
+ "name": "Papua New Guinea"
+ },
+ {
+ "country": "PH",
+ "latitude": 12.879721,
+ "longitude": 121.774017,
+ "name": "Philippines"
+ },
+ {
+ "country": "PK",
+ "latitude": 30.375321,
+ "longitude": 69.345116,
+ "name": "Pakistan"
+ },
+ {
+ "country": "PL",
+ "latitude": 51.919438,
+ "longitude": 19.145136,
+ "name": "Poland"
+ },
+ {
+ "country": "PM",
+ "latitude": 46.941936,
+ "longitude": -56.27111,
+ "name": "Saint Pierre and Miquelon"
+ },
+ {
+ "country": "PN",
+ "latitude": -24.703615,
+ "longitude": -127.439308,
+ "name": "Pitcairn Islands"
+ },
+ {
+ "country": "PR",
+ "latitude": 18.220833,
+ "longitude": -66.590149,
+ "name": "Puerto Rico"
+ },
+ {
+ "country": "PS",
+ "latitude": 31.952162,
+ "longitude": 35.233154,
+ "name": "Palestinian Territories"
+ },
+ {
+ "country": "PT",
+ "latitude": 39.399872,
+ "longitude": -8.224454,
+ "name": "Portugal"
+ },
+ {
+ "country": "PW",
+ "latitude": 7.51498,
+ "longitude": 134.58252,
+ "name": "Palau"
+ },
+ {
+ "country": "PY",
+ "latitude": -23.442503,
+ "longitude": -58.443832,
+ "name": "Paraguay"
+ },
+ {
+ "country": "QA",
+ "latitude": 25.354826,
+ "longitude": 51.183884,
+ "name": "Qatar"
+ },
+ {
+ "country": "RE",
+ "latitude": -21.115141,
+ "longitude": 55.536384,
+ "name": "Réunion"
+ },
+ {
+ "country": "RO",
+ "latitude": 45.943161,
+ "longitude": 24.96676,
+ "name": "Romania"
+ },
+ {
+ "country": "RS",
+ "latitude": 44.016521,
+ "longitude": 21.005859,
+ "name": "Serbia"
+ },
+ {
+ "country": "RU",
+ "latitude": 61.52401,
+ "longitude": 105.318756,
+ "name": "Russia"
+ },
+ {
+ "country": "RW",
+ "latitude": -1.940278,
+ "longitude": 29.873888,
+ "name": "Rwanda"
+ },
+ {
+ "country": "SA",
+ "latitude": 23.885942,
+ "longitude": 45.079162,
+ "name": "Saudi Arabia"
+ },
+ {
+ "country": "SB",
+ "latitude": -9.64571,
+ "longitude": 160.156194,
+ "name": "Solomon Islands"
+ },
+ {
+ "country": "SC",
+ "latitude": -4.679574,
+ "longitude": 55.491977,
+ "name": "Seychelles"
+ },
+ {
+ "country": "SD",
+ "latitude": 12.862807,
+ "longitude": 30.217636,
+ "name": "Sudan"
+ },
+ {
+ "country": "SE",
+ "latitude": 60.128161,
+ "longitude": 18.643501,
+ "name": "Sweden"
+ },
+ {
+ "country": "SG",
+ "latitude": 1.352083,
+ "longitude": 103.819836,
+ "name": "Singapore"
+ },
+ {
+ "country": "SH",
+ "latitude": -24.143474,
+ "longitude": -10.030696,
+ "name": "Saint Helena"
+ },
+ {
+ "country": "SI",
+ "latitude": 46.151241,
+ "longitude": 14.995463,
+ "name": "Slovenia"
+ },
+ {
+ "country": "SJ",
+ "latitude": 77.553604,
+ "longitude": 23.670272,
+ "name": "Svalbard and Jan Mayen"
+ },
+ {
+ "country": "SK",
+ "latitude": 48.669026,
+ "longitude": 19.699024,
+ "name": "Slovakia"
+ },
+ {
+ "country": "SL",
+ "latitude": 8.460555,
+ "longitude": -11.779889,
+ "name": "Sierra Leone"
+ },
+ {
+ "country": "SM",
+ "latitude": 43.94236,
+ "longitude": 12.457777,
+ "name": "San Marino"
+ },
+ {
+ "country": "SN",
+ "latitude": 14.497401,
+ "longitude": -14.452362,
+ "name": "Senegal"
+ },
+ {
+ "country": "SO",
+ "latitude": 5.152149,
+ "longitude": 46.199616,
+ "name": "Somalia"
+ },
+ {
+ "country": "SR",
+ "latitude": 3.919305,
+ "longitude": -56.027783,
+ "name": "Suriname"
+ },
+ {
+ "country": "ST",
+ "latitude": 0.18636,
+ "longitude": 6.613081,
+ "name": "São Tomé and Príncipe"
+ },
+ {
+ "country": "SV",
+ "latitude": 13.794185,
+ "longitude": -88.89653,
+ "name": "El Salvador"
+ },
+ {
+ "country": "SY",
+ "latitude": 34.802075,
+ "longitude": 38.996815,
+ "name": "Syria"
+ },
+ {
+ "country": "SZ",
+ "latitude": -26.522503,
+ "longitude": 31.465866,
+ "name": "Swaziland"
+ },
+ {
+ "country": "TC",
+ "latitude": 21.694025,
+ "longitude": -71.797928,
+ "name": "Turks and Caicos Islands"
+ },
+ {
+ "country": "TD",
+ "latitude": 15.454166,
+ "longitude": 18.732207,
+ "name": "Chad"
+ },
+ {
+ "country": "TF",
+ "latitude": -49.280366,
+ "longitude": 69.348557,
+ "name": "French Southern Territories"
+ },
+ {
+ "country": "TG",
+ "latitude": 8.619543,
+ "longitude": 0.824782,
+ "name": "Togo"
+ },
+ {
+ "country": "TH",
+ "latitude": 15.870032,
+ "longitude": 100.992541,
+ "name": "Thailand"
+ },
+ {
+ "country": "TJ",
+ "latitude": 38.861034,
+ "longitude": 71.276093,
+ "name": "Tajikistan"
+ },
+ {
+ "country": "TK",
+ "latitude": -8.967363,
+ "longitude": -171.855881,
+ "name": "Tokelau"
+ },
+ {
+ "country": "TL",
+ "latitude": -8.874217,
+ "longitude": 125.727539,
+ "name": "Timor-Leste"
+ },
+ {
+ "country": "TM",
+ "latitude": 38.969719,
+ "longitude": 59.556278,
+ "name": "Turkmenistan"
+ },
+ {
+ "country": "TN",
+ "latitude": 33.886917,
+ "longitude": 9.537499,
+ "name": "Tunisia"
+ },
+ {
+ "country": "TO",
+ "latitude": -21.178986,
+ "longitude": -175.198242,
+ "name": "Tonga"
+ },
+ {
+ "country": "TR",
+ "latitude": 38.963745,
+ "longitude": 35.243322,
+ "name": "Turkey"
+ },
+ {
+ "country": "TT",
+ "latitude": 10.691803,
+ "longitude": -61.222503,
+ "name": "Trinidad and Tobago"
+ },
+ {
+ "country": "TV",
+ "latitude": -7.109535,
+ "longitude": 177.64933,
+ "name": "Tuvalu"
+ },
+ {
+ "country": "TW",
+ "latitude": 23.69781,
+ "longitude": 120.960515,
+ "name": "Taiwan"
+ },
+ {
+ "country": "TZ",
+ "latitude": -6.369028,
+ "longitude": 34.888822,
+ "name": "Tanzania"
+ },
+ {
+ "country": "UA",
+ "latitude": 48.379433,
+ "longitude": 31.16558,
+ "name": "Ukraine"
+ },
+ {
+ "country": "UG",
+ "latitude": 1.373333,
+ "longitude": 32.290275,
+ "name": "Uganda"
+ },
+ {
+ "country": "UM",
+ "latitude": "",
+ "longitude": "",
+ "name": "U.S. Minor Outlying Islands"
+ },
+ {
+ "country": "US",
+ "latitude": 37.09024,
+ "longitude": -95.712891,
+ "name": "United States"
+ },
+ {
+ "country": "UY",
+ "latitude": -32.522779,
+ "longitude": -55.765835,
+ "name": "Uruguay"
+ },
+ {
+ "country": "UZ",
+ "latitude": 41.377491,
+ "longitude": 64.585262,
+ "name": "Uzbekistan"
+ },
+ {
+ "country": "VA",
+ "latitude": 41.902916,
+ "longitude": 12.453389,
+ "name": "Vatican City"
+ },
+ {
+ "country": "VC",
+ "latitude": 12.984305,
+ "longitude": -61.287228,
+ "name": "Saint Vincent and the Grenadines"
+ },
+ {
+ "country": "VE",
+ "latitude": 6.42375,
+ "longitude": -66.58973,
+ "name": "Venezuela"
+ },
+ {
+ "country": "VG",
+ "latitude": 18.420695,
+ "longitude": -64.639968,
+ "name": "British Virgin Islands"
+ },
+ {
+ "country": "VI",
+ "latitude": 18.335765,
+ "longitude": -64.896335,
+ "name": "U.S. Virgin Islands"
+ },
+ {
+ "country": "VN",
+ "latitude": 14.058324,
+ "longitude": 108.277199,
+ "name": "Vietnam"
+ },
+ {
+ "country": "VU",
+ "latitude": -15.376706,
+ "longitude": 166.959158,
+ "name": "Vanuatu"
+ },
+ {
+ "country": "WF",
+ "latitude": -13.768752,
+ "longitude": -177.156097,
+ "name": "Wallis and Futuna"
+ },
+ {
+ "country": "WS",
+ "latitude": -13.759029,
+ "longitude": -172.104629,
+ "name": "Samoa"
+ },
+ {
+ "country": "XK",
+ "latitude": 42.602636,
+ "longitude": 20.902977,
+ "name": "Kosovo"
+ },
+ {
+ "country": "YE",
+ "latitude": 15.552727,
+ "longitude": 48.516388,
+ "name": "Yemen"
+ },
+ {
+ "country": "YT",
+ "latitude": -12.8275,
+ "longitude": 45.166244,
+ "name": "Mayotte"
+ },
+ {
+ "country": "ZA",
+ "latitude": -30.559482,
+ "longitude": 22.937506,
+ "name": "South Africa"
+ },
+ {
+ "country": "ZM",
+ "latitude": -13.133897,
+ "longitude": 27.849332,
+ "name": "Zambia"
+ },
+ {
+ "country": "ZW",
+ "latitude": -19.015438,
+ "longitude": 29.154857,
+ "name": "Zimbabwe"
+ }
+]
diff --git a/taxonium_component/src/hooks/useColor.jsx b/taxonium_component/src/hooks/useColor.jsx
index d5fcb755..9575cc48 100644
--- a/taxonium_component/src/hooks/useColor.jsx
+++ b/taxonium_component/src/hooks/useColor.jsx
@@ -76,7 +76,7 @@ const useColor = (colorMapping) => {
return [180, 180, 180];
}
- if (string === "USA") {
+ if (string === "USA" || string === "United States of America") {
return [95, 158, 245]; //This is just because the default is ugly
}
diff --git a/taxonium_component/src/hooks/useLayers.jsx b/taxonium_component/src/hooks/useLayers.jsx
index a4746237..a005e014 100644
--- a/taxonium_component/src/hooks/useLayers.jsx
+++ b/taxonium_component/src/hooks/useLayers.jsx
@@ -4,12 +4,17 @@ import {
PolygonLayer,
TextLayer,
SolidPolygonLayer,
+ GeoJsonLayer,
} from "@deck.gl/layers";
-import { useMemo, useCallback } from "react";
+import { useMemo, useCallback, useEffect } from "react";
import useTreenomeLayers from "./useTreenomeLayers";
import getSVGfunction from "../utils/deckglToSvg";
+// source: https://datahub.io/core/geo-countries
+import geojson from "../worldMap.geo.json";
+import { getCountryCounts } from "../utils/coordinates";
+
const getKeyStuff = (getNodeColorField, colorByField, dataset, toRGB) => {
const counts = {};
for (const node of dataset.nodes) {
@@ -540,6 +545,21 @@ const useLayers = ({
layers.push(minimap_line_horiz, minimap_line_vert, minimap_scatter);
layers.push(minimap_bound_polygon);
+ let lineWidth = 100;
+ if (viewState["map"]) lineWidth = (1 / viewState["map"].zoom) * 9000;
+
+ layers.push({
+ id: "map",
+ data: geojson.features,
+ stroked: true,
+ layerType: "GeoJsonLayer",
+ filled: true,
+ getLineColor: [255, 255, 255],
+ getLineWidth: lineWidth,
+ getFillColor: [169, 169, 169],
+ opacity: 0.8,
+ });
+
const layerFilter = useCallback(
({ layer, viewport, renderPass }) => {
const first_bit =
@@ -552,7 +572,8 @@ const useLayers = ({
viewport.id === "browser-main") ||
(layer.id.startsWith("browser-fillin") &&
viewport.id === "browser-main" &&
- isCurrentlyOutsideBounds);
+ isCurrentlyOutsideBounds) ||
+ (layer.id.startsWith("map") && viewport.id === "map");
return first_bit;
},
@@ -577,6 +598,9 @@ const useLayers = ({
if (layer.layerType === "SolidPolygonLayer") {
return new SolidPolygonLayer(layer);
}
+ if (layer.layerType === "GeoJsonLayer") {
+ return new GeoJsonLayer(layer);
+ }
console.log("could not map layer spec for ", layer);
});
diff --git a/taxonium_component/src/hooks/useSettings.jsx b/taxonium_component/src/hooks/useSettings.jsx
index cb19a119..41f7cc4d 100644
--- a/taxonium_component/src/hooks/useSettings.jsx
+++ b/taxonium_component/src/hooks/useSettings.jsx
@@ -123,6 +123,15 @@ export const useSettings = ({ query, updateQuery }) => {
}
}, []);
+ const [mapViewOpen, setMapViewOpen] = useState(false);
+
+ const setMapOpenAndToast = useCallback((value) => {
+ setMapViewOpen(value);
+ toast(`Map View is now ${value ? "enabled" : "disabled"}`, {
+ position: "bottom-center",
+ });
+ }, []);
+
return {
minimapEnabled,
treenomeEnabled,
@@ -143,6 +152,9 @@ export const useSettings = ({ query, updateQuery }) => {
isCov2Tree,
chromosomeName,
setChromosomeName,
+ mapViewOpen,
+ setMapViewOpen,
+ setMapOpenAndToast,
displaySearchesAsPoints,
setDisplaySearchesAsPoints,
searchPointSize,
diff --git a/taxonium_component/src/hooks/useView.jsx b/taxonium_component/src/hooks/useView.jsx
index a9d3db4c..5ecbad16 100644
--- a/taxonium_component/src/hooks/useView.jsx
+++ b/taxonium_component/src/hooks/useView.jsx
@@ -2,19 +2,24 @@ import { useState, useMemo, useCallback, useEffect } from "react";
import {
OrthographicView,
OrthographicController,
- //OrthographicViewport,
+ MapView,
+ MapController,
} from "@deck.gl/core";
let globalSetZoomAxis = () => {};
const defaultViewState = {
zoom: -2,
target: [window.screen.width < 600 ? 500 : 1400, 1000],
-
pitch: 0,
bearing: 0,
minimap: { zoom: -3, target: [250, 1000] },
"browser-main": { zoom: -2, target: [0, 1000] },
"browser-axis": { zoom: -2, target: [0, 1000] },
+ map: {
+ latitude: 0,
+ longitude: 0,
+ zoom: 0.55,
+ },
};
class MyOrthographicController extends OrthographicController {
@@ -138,12 +143,19 @@ const useView = ({
...viewState,
"browser-main": { zoom: 0, target: [0, 0] },
"browser-axis": { zoom: 0, target: [0, 0] },
+ map: {
+ latitude: 0,
+ longitude: 0,
+ zoom: 0.55,
+ },
};
}, [viewState]);
const views = useMemo(() => {
return [
- ...(settings.minimapEnabled && !settings.treenomeEnabled
+ ...(settings.minimapEnabled &&
+ !settings.treenomeEnabled &&
+ !settings.mapViewOpen
? [
new OrthographicView({
id: "minimap",
@@ -181,7 +193,8 @@ const useView = ({
type: MyOrthographicController,
scrollZoom: { smooth: true, zoomAxis: zoomAxis, xzoom: xzoom },
},
- width: settings.treenomeEnabled ? "40%" : "100%",
+ width:
+ settings.treenomeEnabled || settings.mapViewOpen ? "40%" : "100%",
initialViewState: viewState,
}),
],
@@ -198,12 +211,24 @@ const useView = ({
}),
]
: []),
+ ...(settings.mapViewOpen
+ ? [
+ new MapView({
+ id: "map",
+ width: "60%",
+ initialViewState: viewState,
+ x: "40%",
+ controller: MapController,
+ }),
+ ]
+ : []),
];
}, [
viewState,
zoomAxis,
settings.minimapEnabled,
settings.treenomeEnabled,
+ settings.mapViewOpen,
xzoom,
]);
@@ -250,90 +275,116 @@ const useView = ({
return;
}
- //const temp_viewport = new OrthographicViewport(viewS
- const oldScaleY = 2 ** oldViewState.zoom;
- const newScaleY = 2 ** newViewState.zoom;
- // eslint-disable-line no-unused-vars
-
- if (mouseDownIsMinimap && !specialMinimap && oldScaleY === newScaleY) {
- return;
- }
+ if (viewId === "main" || interactionState === "isZooming") {
+ setViewState((currentViewState) => {
+ //const temp_viewport = new OrthographicViewport(viewS
+ const oldScaleY = 2 ** oldViewState.zoom;
+ const newScaleY = 2 ** newViewState.zoom;
+ // eslint-disable-line no-unused-vars
+
+ if (
+ mouseDownIsMinimap &&
+ !specialMinimap &&
+ oldScaleY === newScaleY
+ ) {
+ return { ...currentViewState, ...newViewState };
+ }
- let newScaleX = 2 ** xzoom;
- if (basicTarget) {
- newViewState.target[0] =
- (newViewState.target[0] / newScaleY) * newScaleX;
- } else {
- if (oldScaleY !== newScaleY) {
- if (localZoomAxis === "Y") {
+ let newScaleX = 2 ** xzoom;
+ if (basicTarget) {
newViewState.target[0] =
- (oldViewState.target[0] / newScaleY) * oldScaleY;
+ (newViewState.target[0] / newScaleY) * newScaleX;
} else {
- const difference = newViewState.zoom - oldViewState.zoom;
-
- setXzoom((old) => old + difference);
-
- newScaleX = 2 ** (xzoom + difference);
-
- newViewState.zoom = oldViewState.zoom;
- newViewState.target[0] =
- (oldViewState.target[0] / oldScaleY) * newScaleY;
+ if (oldScaleY !== newScaleY) {
+ if (localZoomAxis === "Y") {
+ newViewState.target[0] =
+ (oldViewState.target[0] / newScaleY) * oldScaleY;
+ } else {
+ const difference = newViewState.zoom - oldViewState.zoom;
+
+ setXzoom((old) => old + difference);
+
+ newScaleX = 2 ** (xzoom + difference);
+
+ newViewState.zoom = oldViewState.zoom;
+ newViewState.target[0] =
+ (oldViewState.target[0] / oldScaleY) * newScaleY;
+ }
+ }
}
- }
- }
-
- newViewState.target = [...newViewState.target];
-
- newViewState.real_height = deckSize.height / newScaleY;
- newViewState.real_width = deckSize.width / newScaleX;
-
- newViewState.real_target = [...newViewState.target];
- newViewState.real_target[0] =
- (newViewState.real_target[0] * newScaleY) / newScaleX;
-
- const nw = [
- newViewState.real_target[0] - newViewState.real_width / 2,
- newViewState.real_target[1] - newViewState.real_height / 2,
- ];
- const se = [
- newViewState.real_target[0] + newViewState.real_width / 2,
- newViewState.real_target[1] + newViewState.real_height / 2,
- ];
- newViewState.min_x = nw[0];
- newViewState.max_x = se[0];
- newViewState.min_y = nw[1];
- newViewState.max_y = se[1];
-
- newViewState["minimap"] = { zoom: -3, target: [250, 1000] };
-
- if (jbrowseRef.current) {
- const yBound = jbrowseRef.current.children[0].children[0].clientHeight;
- const xBound =
- jbrowseRef.current.children[0].children[0].offsetParent.offsetParent
- .offsetLeft;
- if (
- (mouseXY[0] > xBound && mouseXY[1] < yBound) ||
- mouseXY[0] < 0 ||
- mouseXY[1] < 0
- ) {
- if (!basicTarget && viewId) {
- return;
+ newViewState.target = [...newViewState.target];
+
+ newViewState.real_height = deckSize.height / newScaleY;
+ newViewState.real_width = deckSize.width / newScaleX;
+
+ newViewState.real_target = [...newViewState.target];
+ newViewState.real_target[0] =
+ (newViewState.real_target[0] * newScaleY) / newScaleX;
+
+ const nw = [
+ newViewState.real_target[0] - newViewState.real_width / 2,
+ newViewState.real_target[1] - newViewState.real_height / 2,
+ ];
+ const se = [
+ newViewState.real_target[0] + newViewState.real_width / 2,
+ newViewState.real_target[1] + newViewState.real_height / 2,
+ ];
+
+ newViewState.min_x = nw[0];
+ newViewState.max_x = se[0];
+ newViewState.min_y = nw[1];
+ newViewState.max_y = se[1];
+
+ newViewState["minimap"] = { zoom: -3, target: [250, 1000] };
+
+ if (jbrowseRef.current) {
+ const yBound =
+ jbrowseRef.current.children[0].children[0].clientHeight;
+ const xBound =
+ jbrowseRef.current.children[0].children[0].offsetParent
+ .offsetParent.offsetLeft;
+ if (
+ (mouseXY[0] > xBound && mouseXY[1] < yBound) ||
+ mouseXY[0] < 0 ||
+ mouseXY[1] < 0
+ ) {
+ if (!basicTarget && viewId) {
+ return { ...currentViewState, ...newViewState };
+ }
+ }
}
- }
- }
- // Treenome view state
- if (viewId === "main" || viewId === "main-overlay" || !viewId) {
- newViewState["browser-main"] = {
- ...viewState["browser-main"],
- zoom: newViewState.zoom,
- target: [viewState["browser-main"].target[0], newViewState.target[1]],
- };
+ const combinedViewState = { ...currentViewState, ...newViewState };
+ return combinedViewState;
+ });
+ } else if (viewId === "map") {
+ setViewState((currentViewState) => {
+ const newState = {
+ ...currentViewState,
+ map: {
+ latitude: newViewState.latitude,
+ longitude: newViewState.longitude,
+ zoom: newViewState.zoom,
+ },
+ };
+ return newState;
+ });
+ } else if (!viewId || viewId === "main-overlay" || viewId === "main") {
+ setViewState((currentViewState) => {
+ newViewState["browser-main"] = {
+ ...viewState["browser-main"],
+ zoom: newViewState.zoom,
+ target: [
+ viewState["browser-main"].target[0],
+ newViewState.target[1],
+ ],
+ };
+ const combinedViewState = { ...currentViewState, ...newViewState };
+ return combinedViewState;
+ });
}
-
- setViewState(newViewState);
- return newViewState;
+ return;
},
[zoomAxis, xzoom, deckSize, viewState, jbrowseRef, mouseXY]
);
diff --git a/taxonium_component/src/utils/coordinates.js b/taxonium_component/src/utils/coordinates.js
new file mode 100644
index 00000000..15ebe416
--- /dev/null
+++ b/taxonium_component/src/utils/coordinates.js
@@ -0,0 +1,99 @@
+import countries from "../countries.json";
+
+const newCountryMap = {};
+for (const country of countries) {
+ newCountryMap[country.name] = {
+ latitude: country.latitude,
+ longitude: country.longitude,
+ };
+}
+
+newCountryMap["England"] = newCountryMap["United Kingdom"];
+newCountryMap["Wales"] = newCountryMap["United Kingdom"];
+newCountryMap["Scotland"] = newCountryMap["United Kingdom"];
+newCountryMap["Northern Ireland"] = newCountryMap["United Kingdom"];
+newCountryMap["Northern_Ireland"] = newCountryMap["United Kingdom"];
+newCountryMap["USA"] = newCountryMap["United States"];
+newCountryMap["Viet Nam"] = newCountryMap["Vietnam"];
+newCountryMap["West Bank"] = newCountryMap["Palestinian Territories"];
+
+export const getUniqueCoordinates = (nodes) => {
+ const countryNodes = nodes
+ .filter((node) => node.meta_country)
+ .map((node) => {
+ return node.meta_country;
+ });
+
+ const uniqueCountries = new Set(countryNodes);
+
+ const coords = [];
+ for (const country of uniqueCountries) {
+ if (getCoordinateFromCountry(country)) {
+ coords.push(getCoordinateFromCountry(country));
+ } else {
+ console.log("not found: ", country);
+ }
+ }
+
+ return coords;
+};
+
+export const getCoordinateFromCountry = (countryName) => {
+ return newCountryMap[countryName];
+};
+
+export const getCountryCounts = (nodes) => {
+ const countryNodes = nodes
+ .filter((node) => node.meta_country)
+ .map((node) => {
+ return node.meta_country;
+ });
+
+ const counts = {};
+
+ for (const country of countryNodes) {
+ counts[country] ? counts[country]++ : (counts[country] = 1);
+ }
+
+ const consolidateCounts = (counts, correct_name, wrong_names) => {
+ if (!counts[correct_name]) {
+ counts[correct_name] = 0;
+ }
+ for (const wrong of wrong_names) {
+ if (counts[wrong]) {
+ counts[correct_name] += counts[wrong];
+ delete counts[wrong];
+ }
+ }
+ };
+
+ consolidateCounts(counts, "Vietnam", ["Viet Nam"]);
+
+ consolidateCounts(counts, "United Kingdom", [
+ "England",
+ "Wales",
+ "Scotland",
+ "Northern_Ireland",
+ "Northern Ireland",
+ ]);
+
+ consolidateCounts(counts, "United States of America", ["USA"]);
+
+ return counts;
+};
+
+export const calculateBoundingBox = (coords) => {
+ let min_lat = 90;
+ let min_lon = 180;
+ let max_lat = -90;
+ let max_lon = -180;
+ for (const coord of coords) {
+ const lat = coord.latitude;
+ const lon = coord.longitude;
+ if (lat > max_lat) max_lat = lat;
+ if (lat < min_lat) min_lat = lat;
+ if (lon > max_lon) max_lon = lon;
+ if (lon < min_lon) min_lon = lon;
+ }
+ return [min_lat, max_lat, min_lon, max_lon];
+};
diff --git a/taxonium_component/src/utils/mathFunctions.js b/taxonium_component/src/utils/mathFunctions.js
new file mode 100644
index 00000000..a26e43c1
--- /dev/null
+++ b/taxonium_component/src/utils/mathFunctions.js
@@ -0,0 +1,34 @@
+export const linear_normalization = (
+ enteredValue,
+ minEntry,
+ maxEntry,
+ normalizedMin,
+ normalizedMax
+) => {
+ if (maxEntry === minEntry) {
+ return normalizedMin + (normalizedMax - normalizedMin) / 2;
+ }
+
+ // ensure all input values are positive
+ enteredValue = Math.abs(enteredValue);
+ minEntry = Math.abs(minEntry);
+ maxEntry = Math.abs(maxEntry);
+ normalizedMin = Math.abs(normalizedMin);
+ normalizedMax = Math.abs(normalizedMax);
+
+ // calculate the normalized value
+ let mx =
+ (Math.log(enteredValue) - Math.log(minEntry)) /
+ (Math.log(maxEntry) - Math.log(minEntry));
+ let preshiftNormalized = mx * (normalizedMax - normalizedMin);
+ let shiftedNormalized = preshiftNormalized + normalizedMin;
+
+ // ensure the normalized value is within the specified range
+ if (shiftedNormalized <