@jbrowse/plugin-sv-inspector 2.17.0 → 3.0.0

package/esm/SvInspectorView/models/adhocFeatureUtils.d.ts

@@ -1,44 +0,0 @@
-export declare function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: any, row: any, loc1: any, loc2: any, rowNumber: any): {
-    uniqueId: string;
-    refName: any;
-    start: any;
-    end: any;
-    mate: {
-        refName: any;
-        start: any;
-        end: any;
-    };
-};
-export declare function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnNumbers: any, row: any, rowNumber: any, isValidRefName: any): {
-    uniqueId: string;
-    refName: any;
-    start: any;
-    end: any;
-    mate: {
-        refName: any;
-        start: any;
-        end: any;
-    };
-};
-export declare function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefColumnNumbers: any, locStartColumnNumbers: any, locEndColumnNumbers: any, row: any, rowNumber: any): {
-    uniqueId: string;
-    refName: any;
-    start: any;
-    end: any;
-    mate: {
-        refName: any;
-        start: any;
-        end: any;
-    };
-};
-export declare function makeAdHocSvFeature(sheet: any, rowNumber: any, row: any, isValidRefName: any): {
-    uniqueId: string;
-    refName: any;
-    start: any;
-    end: any;
-    mate: {
-        refName: any;
-        start: any;
-        end: any;
-    };
-} | undefined;

package/esm/SvInspectorView/models/adhocFeatureUtils.js

@@ -1,90 +0,0 @@
-// @ts-nocheck
-// this file contains the rather verbose functions for
-// creating features from CSV/TSV lines
-import { parseLocString } from '@jbrowse/core/util';
-export function makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc2, rowNumber) {
-    // load all the other data in the row into an `otherData` object
-    const otherData = {};
-    columns.forEach((column, columnNumber) => {
-        if (columnsAlreadyUsedInLocations.includes(columnNumber)) {
-            return;
-        }
-        let { text } = row.cells[columnNumber];
-        if (column.dataType.type === 'Number') {
-            text = Number.parseFloat(text);
-        }
-        otherData[column.name] = text;
-    });
-    // make the final feature data out of otherData + the parsed locations
-    return {
-        ...otherData,
-        uniqueId: `sv-inspector-adhoc-${rowNumber}`,
-        refName: loc1.refName,
-        start: loc1.start,
-        end: loc1.end,
-        mate: {
-            refName: loc2.refName,
-            start: loc2.start,
-            end: loc2.end,
-        },
-    };
-}
-export function makeAdHocSvFeatureFromTwoLocations(columns, locationColumnNumbers, row, rowNumber, isValidRefName) {
-    // use the first two locations we found (first according to *displayed* order)
-    const loc1 = parseLocString(row.cells[locationColumnNumbers[0]].text, isValidRefName);
-    const loc2 = parseLocString(row.cells[locationColumnNumbers[1]].text, isValidRefName);
-    const columnsAlreadyUsedInLocations = [
-        locationColumnNumbers[0],
-        locationColumnNumbers[1],
-    ];
-    return makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc2, rowNumber);
-}
-export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns, locRefColumnNumbers, locStartColumnNumbers, locEndColumnNumbers, row, rowNumber) {
-    const textOf = colno => row.cells[colno].text;
-    const loc1 = {
-        refName: textOf(locRefColumnNumbers[0]),
-        start: Number.parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
-        end: Number.parseInt(textOf(locEndColumnNumbers[0]), 10),
-    };
-    const loc2 = {
-        refName: textOf(locRefColumnNumbers[1]),
-        start: Number.parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
-        end: Number.parseInt(textOf(locEndColumnNumbers[1]), 10),
-    };
-    const columnsAlreadyUsedInLocations = [
-        locRefColumnNumbers[0],
-        locStartColumnNumbers[0],
-        locEndColumnNumbers[0],
-        locRefColumnNumbers[1],
-        locStartColumnNumbers[1],
-        locEndColumnNumbers[1],
-    ];
-    return makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc2, rowNumber);
-}
-// makes a feature data object (passed as `data` to a SimpleFeature constructor)
-// out of table row if the row has 2 location columns. undefined if not
-export function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) {
-    const { columns, columnDisplayOrder } = sheet;
-    const columnTypes = {};
-    columnDisplayOrder.forEach(columnNumber => {
-        const columnDefinition = columns[columnNumber];
-        if (!columnTypes[columnDefinition.dataType.type]) {
-            columnTypes[columnDefinition.dataType.type] = [];
-        }
-        columnTypes[columnDefinition.dataType.type].push(columnNumber);
-    });
-    const locationColumnNumbers = columnTypes.LocString || [];
-    const locStartColumnNumbers = columnTypes.LocStart || [];
-    const locEndColumnNumbers = columnTypes.LocEnd || [];
-    const locRefColumnNumbers = columnTypes.LocRef || [];
-    // if we have 2 or more columns of type location, make a feature from them
-    if (locationColumnNumbers.length >= 2) {
-        return makeAdHocSvFeatureFromTwoLocations(columns, locationColumnNumbers, row, rowNumber, isValidRefName);
-    }
-    if (locRefColumnNumbers.length >= 2 &&
-        locStartColumnNumbers.length >= 2 &&
-        locEndColumnNumbers.length >= 2) {
-        return makeAdHocSvFeatureFromTwoRefStartEndSets(columns, locRefColumnNumbers, locStartColumnNumbers, locEndColumnNumbers, row, rowNumber);
-    }
-    return undefined;
-}

package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.d.ts

@@ -1,4 +0,0 @@
-export declare function getFeatureForRow(session: any, spreadsheetView: any, row: any, rowNumber: any): any;
-export declare function breakpointSplitViewSnapshotFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): any;
-export declare function openBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): void;
-export declare function canOpenBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): boolean;

package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.js

@@ -1,42 +0,0 @@
-// @ts-nocheck
-import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util';
-import { makeAdHocSvFeature } from './adhocFeatureUtils';
-export function getFeatureForRow(session, spreadsheetView, row, rowNumber) {
-    var _a, _b;
-    return (((_a = row.extendedData) === null || _a === void 0 ? void 0 : _a.vcfFeature) ||
-        ((_b = row.extendedData) === null || _b === void 0 ? void 0 : _b.feature) ||
-        makeAdHocSvFeature(spreadsheetView.spreadsheet, rowNumber, row, session.assemblyManager.isValidRefName));
-}
-export function breakpointSplitViewSnapshotFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber) {
-    const { pluginManager } = getEnv(svInspectorView);
-    const session = getSession(spreadsheetView);
-    const featureData = getFeatureForRow(session, spreadsheet, row, rowNumber);
-    if (featureData) {
-        const feature = new SimpleFeature(featureData);
-        session.setSelection(feature);
-        return pluginManager
-            .getViewType('BreakpointSplitView')
-            .snapshotFromBreakendFeature(feature, svInspectorView.circularView);
-    }
-    return undefined;
-}
-export function openBreakpointSplitViewFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber) {
-    const viewSnapshot = breakpointSplitViewSnapshotFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber);
-    if (viewSnapshot) {
-        // try to center the offsetPx
-        const { circularView } = svInspectorView;
-        viewSnapshot.views[0].offsetPx -= circularView.width / 2 + 100;
-        viewSnapshot.views[1].offsetPx -= circularView.width / 2 + 100;
-        const session = getSession(spreadsheetView);
-        session.addView('BreakpointSplitView', viewSnapshot);
-    }
-}
-export function canOpenBreakpointSplitViewFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber) {
-    try {
-        return Boolean(breakpointSplitViewSnapshotFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber));
-    }
-    catch (e) {
-        console.error('Unable to open breakpoint split view from table row', e);
-        return false;
-    }
-}