@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/dist/shared/index.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.FilterModel = void 0;
-exports.getUniqueTagValues = getUniqueTagValues;
-exports.getUniqueModificationValues = getUniqueModificationValues;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-async function getUniqueTagValues({ self, tag, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const { adapterConfig } = self;
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const values = await rpcManager.call((0, tracks_1.getRpcSessionId)(self), 'PileupGetGlobalValueForTag', {
-        adapterConfig,
-        tag,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}
-async function getUniqueModificationValues({ self, adapterConfig, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
-        adapterConfig,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}
-exports.FilterModel = mobx_state_tree_1.types.model({
-    flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-    flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
-    readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
-        tag: mobx_state_tree_1.types.string,
-        value: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    })),
-});

package/esm/LinearAlignmentsDisplay/models/configSchema.js

@@ -1,33 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
-/**
- * #config LinearAlignmentsDisplay
- * has a "pileup" sub-display, where you can see individual reads and a
- * quantitative "snpcoverage" sub-display track showing SNP frequencies
- */
-export default function configModelFactory(pm) {
-    return ConfigurationSchema('LinearAlignmentsDisplay', {
-        /**
-         * #slot
-         */
-        pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
-        /**
-         * #slot
-         */
-        snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
-            .configSchema,
-        /**
-         * #slot
-         */
-        height: {
-            type: 'number',
-            defaultValue: 250,
-        },
-    }, {
-        /**
-         * #baseConfiguration
-         */
-        baseConfiguration: baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}

package/esm/LinearPileupDisplay/components/ColorByModificationsDialog.d.ts

@@ -1,15 +0,0 @@
-import React from 'react';
-import { ObservableMap } from 'mobx';
-declare const ColorByModificationsDialog: ({ model, handleClose, }: {
-    model: {
-        setColorScheme: (arg: {
-            type: string;
-        }) => void;
-        modificationTagMap: ObservableMap<string, string>;
-        colorBy?: {
-            type: string;
-        };
-    };
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default ColorByModificationsDialog;

package/esm/LinearPileupDisplay/components/ColorByModificationsDialog.js

@@ -1,36 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { Button, CircularProgress, DialogActions, DialogContent, Typography, } from '@mui/material';
-import { Dialog } from '@jbrowse/core/ui';
-import ModificationTable from './ModificationsTable';
-const ColorByModificationsDialog = observer(function ({ model, handleClose, }) {
-    const { colorBy, modificationTagMap } = model;
-    const modifications = [...modificationTagMap.entries()];
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."),
-            React.createElement(Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
-            React.createElement("div", { style: { margin: 20 } },
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? (React.createElement("div", null, modifications.length ? (React.createElement(React.Fragment, null,
-                    "Current modification-type-to-color mapping",
-                    React.createElement(ModificationTable, { modifications: [...modificationTagMap.entries()] }))) : (React.createElement(React.Fragment, null,
-                    React.createElement(Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."),
-                    React.createElement(CircularProgress, { size: 15 }))))) : null,
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (React.createElement(ModificationTable, { modifications: [
-                        ['methylated', 'red'],
-                        ['unmethylated', 'blue'],
-                    ] })) : null),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", onClick: () => {
-                        model.setColorScheme({ type: 'modifications' });
-                        handleClose();
-                    } }, "Modifications"),
-                React.createElement(Button, { variant: "contained", onClick: () => {
-                        model.setColorScheme({ type: 'methylation' });
-                        handleClose();
-                    } }, "Methylation"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
-});
-export default ColorByModificationsDialog;

package/esm/LinearPileupDisplay/components/ModificationsTable.d.ts

@@ -1,4 +0,0 @@
-import React from 'react';
-export default function ModificationTable({ modifications, }: {
-    modifications: [string, string | undefined][];
-}): React.JSX.Element;

package/esm/LinearPileupDisplay/components/ModificationsTable.js

@@ -1,22 +0,0 @@
-import React from 'react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
-    table: {
-        border: '1px solid #888',
-        margin: theme.spacing(4),
-        '& td': {
-            padding: theme.spacing(1),
-        },
-    },
-}));
-export default function ModificationTable({ modifications, }) {
-    const { classes } = useStyles();
-    return (React.createElement("table", { className: classes.table },
-        React.createElement("tbody", null, modifications.map(([key, value]) => (React.createElement("tr", { key: key },
-            React.createElement("td", null, key),
-            React.createElement("td", null, value),
-            React.createElement("td", { style: {
-                    width: '1em',
-                    background: value,
-                } })))))));
-}

package/esm/shared/index.d.ts

@@ -1,49 +0,0 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export declare function getUniqueTagValues({ self, tag, blocks, opts, }: {
-    self: IAnyStateTreeNode & {
-        adapterConfig: AnyConfigurationModel;
-    };
-    tag: string;
-    blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        signal?: AbortSignal;
-        filters: string[];
-    };
-}): Promise<string[]>;
-type Track = IAnyStateTreeNode & {
-    configuration: AnyConfigurationModel;
-};
-export declare function getUniqueModificationValues({ self, adapterConfig, blocks, opts, }: {
-    self: IAnyStateTreeNode & {
-        parentTrack: Track;
-    };
-    adapterConfig: AnyConfigurationModel;
-    blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        signal?: AbortSignal;
-        filters: string[];
-    };
-}): Promise<string[]>;
-export declare const FilterModel: import("mobx-state-tree").IModelType<{
-    flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        tag: import("mobx-state-tree").ISimpleType<string>;
-        value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export interface IFilter {
-    flagExclude: number;
-    flagInclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value?: string;
-    };
-}
-export {};

package/esm/shared/index.js

@@ -1,36 +0,0 @@
-import { types } from 'mobx-state-tree';
-import { getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-export async function getUniqueTagValues({ self, tag, blocks, opts, }) {
-    const { rpcManager } = getSession(self);
-    const { adapterConfig } = self;
-    const sessionId = getRpcSessionId(self);
-    const values = await rpcManager.call(getRpcSessionId(self), 'PileupGetGlobalValueForTag', {
-        adapterConfig,
-        tag,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}
-export async function getUniqueModificationValues({ self, adapterConfig, blocks, opts, }) {
-    const { rpcManager } = getSession(self);
-    const sessionId = getRpcSessionId(self);
-    const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
-        adapterConfig,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}
-export const FilterModel = types.model({
-    flagInclude: types.optional(types.number, 0),
-    flagExclude: types.optional(types.number, 1540),
-    readName: types.maybe(types.string),
-    tagFilter: types.maybe(types.model({
-        tag: types.string,
-        value: types.maybe(types.string),
-    })),
-});