jbrowse-plugin-gwas 2.1.2 → 2.1.3

package/dist/GWASAdapter/index.js

@@ -1,5 +1,5 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 export default function GWASAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         const res = pluginManager.getAdapterType('BedTabixAdapter');

package/dist/GWASAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAGzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,aAA4B;IAC/D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,aAAa,CAAC,cAAc,CAAC,iBAAiB,CAAE,CAAA;QAC5D,MAAM,YAAY,GAAG,mBAAmB,CACtC,aAAa,EACb,EAAE,EACF,EAAE,iBAAiB,EAAE,GAAG,CAAC,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC/D,CAAA;QACD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,WAAW,EAAE,cAAc;YAC3B,YAAY;YACZ,eAAe,EAAE,GAAG,CAAC,eAAe;SACrC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAIzE,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,aAA4B;IAC/D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,aAAa,CAAC,cAAc,CAAC,iBAAiB,CAAE,CAAA;QAC5D,MAAM,YAAY,GAAG,mBAAmB,CACtC,aAAa,EACb,EAAE,EACF,EAAE,iBAAiB,EAAE,GAAG,CAAC,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC/D,CAAA;QACD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,WAAW,EAAE,cAAc;YAC3B,YAAY;YACZ,eAAe,EAAE,GAAG,CAAC,eAAe;SACrC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/GWASAddTrackComponent/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASAddTrackComponent/index.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAI5B,MAAM,qBAAqB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,yBAAyB,CAAC,CAAC,CAAA;AAE3E,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAC5C,aAA4B;IAE5B,aAAa,CAAC,mBAAmB,CAC/B,wBAAwB;IACxB,mBAAmB;IACnB,CAAC,IAAI,EAAE,EAAE,KAAK,EAAgC,EAAE,EAAE;QAChD,OAAO,KAAK,CAAC,gBAAgB,KAAK,aAAa;YAC7C,CAAC,CAAC,qBAAqB;YACvB,CAAC,CAAC,IAAI,CAAA;IACV,CAAC,CACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASAddTrackComponent/index.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAI5B,MAAM,qBAAqB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,yBAAyB,CAAC,CAAC,CAAA;AAE3E,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,aAA4B;IACzE,aAAa,CAAC,mBAAmB,CAC/B,wBAAwB;IACxB,mBAAmB;IACnB,CAAC,IAAI,EAAE,EAAE,KAAK,EAAgC,EAAE,EAAE;QAChD,OAAO,KAAK,CAAC,gBAAgB,KAAK,aAAa;YAC7C,CAAC,CAAC,qBAAqB;YACvB,CAAC,CAAC,IAAI,CAAA;IACV,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/GuessAdapter/index.js

@@ -5,19 +5,16 @@ export default function GuessAdapterF(pluginManager) {
         return (file, index, adapterHint) => {
             const fileName = getFileName(file);
             const indexName = index && getFileName(index);
-            if (testAdapter(fileName, /\.txt\.gz$/i, adapterHint, 'GWASAdapter')) {
-                return {
+            return testAdapter(fileName, /\.txt\.gz$/i, adapterHint, 'GWASAdapter')
+                ? {
                     type: 'GWASAdapter',
                     bedGzLocation: file,
                     index: {
                         location: index || makeIndex(file, '.tbi'),
                         indexType: makeIndexType(indexName, 'CSI', 'TBI'),
                     },
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
+                }
+                : adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {

package/dist/GuessAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAChD,OAAO,EACL,WAAW,EACX,SAAS,EACT,aAAa,GACd,MAAM,2BAA2B,CAAA;AASlC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;YAC7C,IACE,WAAW,CAAC,QAAQ,EAAE,aAAa,EAAE,WAAW,EAAE,aAAa,CAAC,EAChE,CAAC;gBACD,OAAO;oBACL,IAAI,EAAE,aAAa;oBACnB,aAAa,EAAE,IAAI;oBACnB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;YACH,CAAC;iBAAM,CAAC;gBACN,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC;QACH,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;QACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;YAC7B,OAAO,WAAW,KAAK,aAAa;gBAClC,CAAC,CAAC,WAAW;gBACb,CAAC,CAAC,gBAAgB,CAAC,WAAW,CAAC,CAAA;QACnC,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAChD,OAAO,EACL,WAAW,EACX,SAAS,EACT,aAAa,GACd,MAAM,2BAA2B,CAAA;AASlC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;YAC7C,OAAO,WAAW,CAAC,QAAQ,EAAE,aAAa,EAAE,WAAW,EAAE,aAAa,CAAC;gBACrE,CAAC,CAAC;oBACE,IAAI,EAAE,aAAa;oBACnB,aAAa,EAAE,IAAI;oBACnB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF;gBACH,CAAC,CAAC,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QAC9C,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;QACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;YAC7B,OAAO,WAAW,KAAK,aAAa;gBAClC,CAAC,CAAC,WAAW;gBACb,CAAC,CAAC,gBAAgB,CAAC,WAAW,CAAC,CAAA;QACnC,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/LinearManhattanDisplay/components/AddFiltersDialog.js

@@ -16,9 +16,6 @@ const useStyles = makeStyles()({
         fontSize: '0.8em',
     },
 });
-function checkJexl(code) {
-    stringToJexlExpression(code);
-}
 const AddFiltersDialog = observer(function ({ model, handleClose, }) {
     const { classes } = useStyles();
     const { activeFilters } = model;
@@ -26,13 +23,12 @@ const AddFiltersDialog = observer(function ({ model, handleClose, }) {
     const [error, setError] = useState();
     useEffect(() => {
         try {
-            data
-                .split('\n')
-                .map(line => line.trim())
-                .filter(line => !!line)
-                .map(line => {
-                checkJexl(line.trim());
-            });
+            for (const line of data.split('\n')) {
+                const trimmed = line.trim();
+                if (trimmed) {
+                    stringToJexlExpression(trimmed);
+                }
+            }
             setError(undefined);
         }
         catch (e) {

package/dist/LinearManhattanDisplay/components/AddFiltersDialog.js.map

@@ -1 +1 @@
-{"version":3,"file":"AddFiltersDialog.js","sourceRoot":"","sources":["../../../src/LinearManhattanDisplay/components/AddFiltersDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,sBAAsB,EAAE,MAAM,gCAAgC,CAAA;AACvE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC/E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IAED,KAAK,EAAE;QACL,KAAK,EAAE,KAAK;QACZ,QAAQ,EAAE,OAAO;KAClB;CACF,CAAC,CAAA;AAEF,SAAS,SAAS,CAAC,IAAY;IAC7B,sBAAsB,CAAC,IAAI,CAAC,CAAA;AAC9B,CAAC;AAED,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,EACL,WAAW,GAQZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC;YACH,IAAI;iBACD,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;iBACxB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;iBACtB,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAA;YACxB,CAAC,CAAC,CAAA;YACJ,QAAQ,CAAC,SAAS,CAAC,CAAA;QACrB,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAA;IAEV,OAAO,CACL,oBAAC,MAAM,IAAC,QAAQ,EAAC,IAAI,EAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,mBAAmB;QACxE,oBAAC,aAAa;YACZ;;gBAEmB,GAAG;gBACpB;oBACE;wBACE,sEAA8C;iFAE3C;oBACL;wBACE,qEAA6C;qGAE1C;oBACL;wBACE,oEAA+C;mFAE5C,CACF,CACD;YAEL,KAAK,CAAC,CAAC,CAAC,2BAAG,SAAS,EAAE,OAAO,CAAC,KAAK,IAAG,GAAG,KAAK,EAAE,CAAK,CAAC,CAAC,CAAC,IAAI;YAC7D,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,SAAS,QACT,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC7B,CAAC,EACD,SAAS,EAAE;oBACT,KAAK,EAAE;wBACL,OAAO,EAAE;4BACP,KAAK,EAAE,OAAO,CAAC,YAAY;yBAC5B;qBACF;iBACF,GACD,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,CAAC,KAAK,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAA;oBACtC,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}
+{"version":3,"file":"AddFiltersDialog.js","sourceRoot":"","sources":["../../../src/LinearManhattanDisplay/components/AddFiltersDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,sBAAsB,EAAE,MAAM,gCAAgC,CAAA;AACvE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC/E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IAED,KAAK,EAAE;QACL,KAAK,EAAE,KAAK;QACZ,QAAQ,EAAE,OAAO;KAClB;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,EACL,WAAW,GAQZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC;YACH,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;gBACpC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;gBAC3B,IAAI,OAAO,EAAE,CAAC;oBACZ,sBAAsB,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,SAAS,CAAC,CAAA;QACrB,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAA;IAEV,OAAO,CACL,oBAAC,MAAM,IAAC,QAAQ,EAAC,IAAI,EAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,mBAAmB;QACxE,oBAAC,aAAa;YACZ;;gBAEmB,GAAG;gBACpB;oBACE;wBACE,sEAA8C;iFAE3C;oBACL;wBACE,qEAA6C;qGAE1C;oBACL;wBACE,oEAA+C;mFAE5C,CACF,CACD;YAEL,KAAK,CAAC,CAAC,CAAC,2BAAG,SAAS,EAAE,OAAO,CAAC,KAAK,IAAG,GAAG,KAAK,EAAE,CAAK,CAAC,CAAC,CAAC,IAAI;YAC7D,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,SAAS,QACT,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC7B,CAAC,EACD,SAAS,EAAE;oBACT,KAAK,EAAE;wBACL,OAAO,EAAE;4BACP,KAAK,EAAE,OAAO,CAAC,YAAY;yBAC5B;qBACF;iBACF,GACD,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,CAAC,KAAK,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAA;oBACtC,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/LinearManhattanDisplay/components/TooltipComponent.d.ts

@@ -1,7 +1,6 @@
 import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
-import type { TooltipContentsComponent } from '@jbrowse/plugin-wiggle';
 export interface Props {
     feature: Feature;
     model: Model;
@@ -10,13 +9,11 @@ export interface Model {
     configuration: AnyConfigurationModel;
     featureUnderMouse?: Feature;
 }
-type Coord = [number, number];
 declare const TooltipComponent: (props: {
     model: Model;
     height: number;
-    offsetMouseCoord: Coord;
-    clientMouseCoord: Coord;
+    offsetMouseCoord: [number, number];
+    clientMouseCoord: [number, number];
     clientRect?: DOMRect;
-    TooltipContents?: TooltipContentsComponent;
 }) => React.JSX.Element;
 export default TooltipComponent;

package/dist/LinearManhattanDisplay/components/TooltipComponent.js.map

@@ -1 +1 @@
-{"version":3,"file":"TooltipComponent.js","sourceRoot":"","sources":["../../../src/LinearManhattanDisplay/components/TooltipComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAerC,MAAM,eAAe,GAAG,KAAK,CAAC,UAAU,CACtC,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,GAAG;IAC/C,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG;QACX,oBAAC,aAAa,IAAC,IAAI,EAAE,OAAO,CAAC,KAAK,EAAE,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,GAAI,CAC7D,CACP,CAAA;AACH,CAAC,CACF,CAAA;AAID,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,KAO3C;IACC,OAAO,oBAAC,OAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CAAA;AACjE,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}
+{"version":3,"file":"TooltipComponent.js","sourceRoot":"","sources":["../../../src/LinearManhattanDisplay/components/TooltipComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAcrC,MAAM,eAAe,GAAG,KAAK,CAAC,UAAU,CACtC,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,GAAG;IAC/C,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG;QACX,oBAAC,aAAa,IAAC,IAAI,EAAE,OAAO,CAAC,KAAK,EAAE,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,GAAI,CAC7D,CACP,CAAA;AACH,CAAC,CACF,CAAA;AAED,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,KAM3C;IACC,OAAO,oBAAC,OAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CAAA;AACjE,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/LinearManhattanDisplay/configSchemaFactory.d.ts

@@ -37,11 +37,6 @@ export declare function configSchemaFactory(pluginManager: PluginManager): impor
         description: string;
         defaultValue: boolean;
     };
-    defaultRendering: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        defaultValue: string;
-    };
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         LinearManhattanRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/LinearManhattanDisplay/configSchemaFactory.js

@@ -48,11 +48,6 @@ export function configSchemaFactory(pluginManager) {
             description: 'draw upside down',
             defaultValue: false,
         },
-        defaultRendering: {
-            type: 'stringEnum',
-            model: types.enumeration('Rendering', ['density', 'xyplot', 'line']),
-            defaultValue: 'xyplot',
-        },
         renderers: ConfigurationSchema('RenderersConfiguration', {
             LinearManhattanRenderer: LinearManhattanRendererConfigSchema,
         }),

package/dist/LinearManhattanDisplay/configSchemaFactory.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchemaFactory.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/configSchemaFactory.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAKvC,MAAM,UAAU,mBAAmB,CAAC,aAA4B;IAC9D,MAAM,SAAS,GAAG,aAAa,CAAC,SAAS,CACvC,wBAAwB,CACZ,CAAA;IACd,MAAM,EAAE,6BAA6B,EAAE,GAAG,SAAS,CAAC,OAAO,CAAA;IAE3D,MAAM,mCAAmC,GAAG,aAAa,CAAC,eAAe,CACvE,yBAAyB,CACzB,CAAC,YAAY,CAAA;IAEf,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,0BAA0B;YACxC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,OAAO;YACrB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,gBAAgB,EAAE;gBACzC,QAAQ;gBACR,OAAO;gBACP,UAAU;gBACV,SAAS;gBACT,QAAQ;aACT,CAAC;YACF,WAAW,EACT,sFAAsF;SACzF;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,MAAM,CAAC,SAAS;YAC9B,WAAW,EAAE,+BAA+B;SAC7C;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,+BAA+B;YAC5C,YAAY,EAAE,MAAM,CAAC,SAAS;SAC/B;QACD,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EACT,8EAA8E;YAChF,YAAY,EAAE,CAAC;SAChB;QACD,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC,EAAE,cAAc;YACzE,WAAW,EAAE,0BAA0B;YACvC,YAAY,EAAE,QAAQ;SACvB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,kBAAkB;YAC/B,YAAY,EAAE,KAAK;SACpB;QACD,SAAS,EAAE,mBAAmB,CAAC,wBAAwB,EAAE;YACvD,uBAAuB,EAAE,mCAAmC;SAC7D,CAAC;KACH,EACD;QACE,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}

package/dist/LinearManhattanDisplay/jexlMouseover.js

@@ -1,5 +1,5 @@
 function toP(s = 0) {
-    return +(+s).toPrecision(6);
+    return +s.toPrecision(6);
 }
 const en = (n) => n.toLocaleString('en-US');
 function getTooltip(feature) {

package/dist/LinearManhattanDisplay/jexlMouseover.js.map

@@ -1 +1 @@
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+{"version":3,"file":"jexlMouseover.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/jexlMouseover.ts"],"names":[],"mappings":"AAGA,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC;IAChB,OAAO,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AAEnD,SAAS,UAAU,CAAC,OAAgB;IAClC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IACtC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACtC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,MAAM,GAAG,GAAG,CAAC,OAAO,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SAC1E,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,GAAG,GAAG,QAAQ,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,QAAQ,IAAI,IAAI,IAAI,EAAE,CAAA;AACtE,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,aAA4B;IACjE,aAAa,CAAC,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,OAAgB,EAAE,EAAE,CAChE,UAAU,CAAC,OAAO,CAAC,CACpB,CAAA;AACH,CAAC"}

package/dist/LinearManhattanDisplay/stateModelFactory.d.ts

@@ -1,4 +1,3 @@
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
@@ -447,7 +446,6 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];
         clientRect?: DOMRect;
-        TooltipContents?: import("@jbrowse/plugin-wiggle").TooltipContentsComponent;
     }) => import("react").JSX.Element;
     /**
      * #getter
@@ -455,17 +453,10 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     readonly rendererTypeName: string;
     /**
      * #getter
-     * older way of showing y-scalebar
      */
     readonly needsScalebar: boolean;
     /**
      * #getter
-     * newer way of showing y-scalebar
-     */
-    readonly graphType: boolean;
-    /**
-     * #getter
-     * never too large!
      */
     readonly regionTooLarge: boolean;
     /**
@@ -490,20 +481,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     /**
      * #method
      */
-    renderProps(): {
-        config: {
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-        filters: SerializableFilterChain;
-    };
+    renderProps(): any;
     /**
      * #method
      */

package/dist/LinearManhattanDisplay/stateModelFactory.js

@@ -36,21 +36,12 @@ export function stateModelFactory(pluginManager, configSchema) {
         },
         /**
          * #getter
-         * older way of showing y-scalebar
          */
         get needsScalebar() {
             return true;
         },
         /**
          * #getter
-         * newer way of showing y-scalebar
-         */
-        get graphType() {
-            return true;
-        },
-        /**
-         * #getter
-         * never too large!
          */
         get regionTooLarge() {
             return false;
@@ -100,9 +91,8 @@ export function stateModelFactory(pluginManager, configSchema) {
              * #method
              */
             renderProps() {
-                const superProps = superRenderProps();
                 return {
-                    ...superProps,
+                    ...superRenderProps(),
                     config: self.rendererConfig,
                     filters: new SerializableFilterChain({
                         filters: self.activeFilters,
@@ -120,10 +110,7 @@ export function stateModelFactory(pluginManager, configSchema) {
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 AddFiltersDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
+                                { model: self, handleClose },
                             ]);
                         },
                     },

package/dist/LinearManhattanDisplay/stateModelFactory.js.map

@@ -1 +1 @@
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package/dist/LinearManhattanRenderer/LinearManhattanRenderer.d.ts

@@ -1,82 +1,89 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature, Region } from '@jbrowse/core/util';
-import type PluginManager from '@jbrowse/core/PluginManager';
-interface ManhattanProps {
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature, Region } from '@jbrowse/core/util';
+interface ManhattanRenderProps extends RenderArgsDeserialized {
     features: Map<string, Feature>;
     regions: Region[];
     bpPerPx: number;
     statusCallback?: (arg: string) => void;
     config: AnyConfigurationModel;
-    scaleOpts: any;
+    scaleOpts: {
+        domain: number[];
+        scaleType: string;
+        pivotValue?: number;
+        inverted?: boolean;
+    };
     height: number;
     displayCrossHatches: boolean;
     ticks: {
         values: number[];
     };
-    stopToken?: string;
+    highResolutionScaling?: number;
+}
+interface ClickMapItem {
+    minX: number;
+    minY: number;
+    maxX: number;
+    maxY: number;
+    feature: ReturnType<Feature['toJSON']>;
 }
-export default function rendererFactory(pluginManager: PluginManager): {
-    new (stuff: {
-        name: string;
-        ReactComponent: import("@jbrowse/core/util").AnyReactComponentType;
-        displayName?: string;
-        configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        pluginManager: PluginManager;
+export default class ManhattanPlotRenderer extends FeatureRendererType {
+    supportsSVG: boolean;
+    render(renderProps: ManhattanRenderProps): Promise<{
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        clickMap: {
+            index: ArrayBufferLike;
+            items: ClickMapItem[];
+        };
+        canvasRecordedData: Record<string, unknown>;
+        reactElement?: React.ReactElement;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        clickMap: {
+            index: ArrayBufferLike;
+            items: ClickMapItem[];
+        };
+        imageData: any;
+        reactElement?: React.ReactElement;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        clickMap: {
+            index: ArrayBufferLike;
+            items: ClickMapItem[];
+        };
+        reactElement: React.ReactElement;
+        html?: string;
+    }>;
+    draw(ctx: CanvasRenderingContext2D, props: ManhattanRenderProps & {
+        features: Map<string, Feature>;
     }): {
-        draw(ctx: CanvasRenderingContext2D, props: ManhattanProps): Promise<{
-            clickMap: {
-                index: ArrayBufferLike;
-                items: {
-                    minX: number;
-                    minY: number;
-                    maxX: number;
-                    maxY: number;
-                    feature: any;
-                }[];
-            };
-        }>;
-        supportsSVG: boolean;
-        render(renderProps: import("@jbrowse/plugin-wiggle/dist/WiggleBaseRenderer").RenderArgsDeserialized): Promise<{
-            features: Map<string, Feature>;
-            height: number;
-            width: number;
-            containsNoTransferables: boolean;
-            canvasRecordedData: Record<string, unknown>;
-            reactElement?: React.ReactElement;
-            html?: string;
-        } | {
-            features: Map<string, Feature>;
-            height: number;
-            width: number;
-            containsNoTransferables: boolean;
-            imageData: any;
-            reactElement?: React.ReactElement;
-            html?: string;
-        } | {
-            features: Map<string, Feature>;
-            height: number;
-            width: number;
-            containsNoTransferables: boolean;
-            reactElement: React.ReactElement;
-            html?: string;
-        }>;
-        serializeArgsInClient(args: import("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType").RenderArgs): import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized;
-        deserializeResultsInClient(result: import("@jbrowse/plugin-wiggle/dist/WiggleBaseRenderer").ResultsSerialized, args: import("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType").RenderArgs): import("@jbrowse/plugin-wiggle/dist/WiggleBaseRenderer").ResultsDeserialized;
-        serializeResultsInWorker(result: import("@jbrowse/plugin-wiggle/dist/WiggleBaseRenderer").RenderResults, args: import("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType").RenderArgsDeserialized): import("@jbrowse/plugin-wiggle/dist/WiggleBaseRenderer").ResultsSerialized;
-        getExpandedRegion(region: import("@jbrowse/core/util").AugmentedRegion, _renderArgs: import("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType").RenderArgsDeserialized): import("@jbrowse/core/util").AugmentedRegion;
-        getFeatures(renderArgs: import("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType").RenderArgsDeserialized): Promise<Map<string, Feature>>;
-        featurePassesFilters(renderArgs: import("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType").RenderArgsDeserialized, feature: Feature): boolean;
-        deserializeArgsInWorker(args: import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized): import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsDeserialized;
-        renderInClient(rpcManager: import("@jbrowse/core/rpc/RpcManager").default, args: import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgs): Promise<import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
-        renderInWorker(args: import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized): Promise<import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
-        freeResourcesInClient(rpcManager: import("@jbrowse/core/rpc/RpcManager").default, args: import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgs): Promise<void>;
-        ReactComponent: import("@jbrowse/core/util").AnyReactComponentType;
-        configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        pluginManager: PluginManager;
-        freeResources(_args: any): void;
-        name: string;
-        maybeDisplayName?: string;
-        get displayName(): string;
+        clickMap: {
+            index: ArrayBufferLike;
+            items: ClickMapItem[];
+        };
     };
-};
+    drawPoints(ctx: CanvasRenderingContext2D, opts: {
+        features: Map<string, Feature>;
+        regionStart: number;
+        pxPerBp: number;
+        toY: (n: number) => number;
+        config: AnyConfigurationModel;
+        colorValue: string;
+        colorCallback: boolean;
+        canBatch: boolean;
+        stopToken?: string;
+    }): ClickMapItem[];
+}
 export {};