@jbrowse/plugin-dotplot-view 2.11.0 → 2.11.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/DotplotDisplay/index.d.ts +1 -2
- package/dist/DotplotDisplay/index.js +3 -2
- package/dist/DotplotRenderer/index.d.ts +1 -2
- package/dist/DotplotRenderer/index.js +3 -2
- package/dist/DotplotView/components/Axes.js +8 -8
- package/dist/DotplotView/components/DotplotTooltip.js +1 -0
- package/dist/DotplotView/components/Grid.js +6 -5
- package/dist/DotplotView/index.d.ts +1 -1
- package/dist/DotplotView/index.js +2 -2
- package/esm/DotplotDisplay/index.d.ts +1 -2
- package/esm/DotplotDisplay/index.js +2 -2
- package/esm/DotplotRenderer/index.d.ts +1 -2
- package/esm/DotplotRenderer/index.js +2 -2
- package/esm/DotplotView/components/Axes.js +9 -9
- package/esm/DotplotView/components/DotplotTooltip.js +1 -0
- package/esm/DotplotView/components/Grid.js +6 -5
- package/esm/DotplotView/index.d.ts +1 -1
- package/esm/DotplotView/index.js +1 -1
- package/package.json +2 -2
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@@ -11,7 +11,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
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// locals
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const stateModelFactory_1 = require("./stateModelFactory");
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const DotplotDisplay_1 = __importDefault(require("./components/DotplotDisplay"));
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function DotplotDisplayF(pm) {
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pm.addDisplayType(() => {
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const configSchema = configSchemaFactory(pm);
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return new DisplayType_1.default({
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@@ -24,7 +24,8 @@ exports.default = (pm) => {
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ReactComponent: DotplotDisplay_1.default,
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});
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});
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}
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}
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exports.default = DotplotDisplayF;
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/**
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* #config DotplotDisplay
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*/
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@@ -6,11 +6,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
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const DotplotRendering_1 = __importDefault(require("./components/DotplotRendering"));
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const DotplotRenderer_1 = __importDefault(require("./DotplotRenderer"));
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const configSchema_1 = __importDefault(require("./configSchema"));
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function DotplotRendererF(pluginManager) {
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pluginManager.addRendererType(() => new DotplotRenderer_1.default({
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name: 'DotplotRenderer',
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configSchema: configSchema_1.default,
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ReactComponent: DotplotRendering_1.default,
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pluginManager,
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}));
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}
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}
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exports.default = DotplotRendererF;
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@@ -65,13 +65,13 @@ exports.HorizontalAxisRaw = (0, mobx_react_1.observer)(function ({ model, }) {
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const x = region.offsetPx;
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const y = 0;
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const xoff = Math.floor(x - hview.offsetPx);
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return (react_1.default.createElement("text", { transform: `rotate(${htextRotation},${xoff},${y})`, key: JSON.stringify(region), x: xoff, y: y + 1,
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return (react_1.default.createElement("text", { transform: `rotate(${htextRotation},${xoff},${y})`, key: JSON.stringify(region), x: xoff, y: y + 1, fontSize: 11, dominantBaseline: "hanging", textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, region.refName));
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}),
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ticks.map(([tick, x]) => x > 0 && x < width ? (react_1.default.createElement("line", { key: `line-${JSON.stringify(tick)}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1,
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ticks.map(([tick, x]) => x > 0 && x < width ? (react_1.default.createElement("line", { key: `line-${JSON.stringify(tick)}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, ...(0, util_1.getFillProps)(theme.palette.text.primary) })) : null),
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ticks
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.filter(t => t[0].type === 'major')
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.map(([tick, x]) => x > 10 && x < width ? (react_1.default.createElement("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},${0})`, key: `text-${JSON.stringify(tick)}`,
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react_1.default.createElement("text", { y: borderY - 12, x: (viewWidth - borderX) / 2,
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.map(([tick, x]) => x > 10 && x < width ? (react_1.default.createElement("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},${0})`, key: `text-${JSON.stringify(tick)}`, fontSize: 11, dominantBaseline: "middle", textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx))) : null),
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react_1.default.createElement("text", { y: borderY - 12, x: (viewWidth - borderX) / 2, textAnchor: "middle", fontSize: 11, dominantBaseline: "hanging", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, hview.assemblyNames.join(','))));
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});
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exports.VerticalAxis = (0, mobx_react_1.observer)(function ({ model, }) {
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const { borderX, viewHeight } = model;
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@@ -111,11 +111,11 @@ exports.VerticalAxisRaw = (0, mobx_react_1.observer)(function ({ model, }) {
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const y = region.offsetPx;
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const x = borderX;
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const yoff = Math.floor(viewHeight - y + offsetPx);
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return (react_1.default.createElement("text", { transform: `rotate(${vtextRotation},${x},${y})`, key: JSON.stringify(region), x: x, y: yoff,
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return (react_1.default.createElement("text", { transform: `rotate(${vtextRotation},${x},${y})`, key: JSON.stringify(region), x: x, y: yoff, fontSize: 11, textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, region.refName));
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}),
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ticks.map(([tick, y]) => y > 0 ? (react_1.default.createElement("line", { key: `line-${JSON.stringify(tick)}`, y1: viewHeight - y, y2: viewHeight - y, x1: borderX, x2: borderX - (tick.type === 'major' ? 6 : 4), strokeWidth: 1,
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ticks.map(([tick, y]) => y > 0 ? (react_1.default.createElement("line", { key: `line-${JSON.stringify(tick)}`, y1: viewHeight - y, y2: viewHeight - y, x1: borderX, x2: borderX - (tick.type === 'major' ? 6 : 4), strokeWidth: 1, ...(0, util_1.getStrokeProps)(theme.palette.grey[400]) })) : null),
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ticks
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.filter(t => t[0].type === 'major')
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.map(([tick, y]) => y > 10 && y < viewHeight ? (react_1.default.createElement("text", { y: viewHeight - y - 3, x: borderX - 7, key: `text-${JSON.stringify(tick)}`, textAnchor: "end",
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react_1.default.createElement("text", { y: (viewHeight - borderY) / 2, x: 12,
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.map(([tick, y]) => y > 10 && y < viewHeight ? (react_1.default.createElement("text", { y: viewHeight - y - 3, x: borderX - 7, key: `text-${JSON.stringify(tick)}`, textAnchor: "end", dominantBaseline: "hanging", fontSize: 11, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx))) : null),
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react_1.default.createElement("text", { y: (viewHeight - borderY) / 2, x: 12, transform: `rotate(-90,12,${(viewHeight - borderY) / 2})`, textAnchor: "middle", fontSize: 11, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, vview.assemblyNames.join(','))));
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});
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@@ -37,6 +37,7 @@ exports.TooltipWhereMouseovered = (0, mobx_react_1.observer)(function ({ model,
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const theme = (0, material_1.useTheme)();
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const { refs, floatingStyles, context } = (0, react_2.useFloating)({
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placement: xdistance < 0 ? 'left' : 'right',
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strategy: 'fixed',
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});
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const clientPoint = (0, react_2.useClientPoint)(context, mouserectClient
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? {
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@@ -7,6 +7,7 @@ exports.GridRaw = void 0;
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const react_1 = __importDefault(require("react"));
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const mobx_react_1 = require("mobx-react");
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const material_1 = require("@mui/material");
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const util_1 = require("@jbrowse/core/util");
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exports.GridRaw = (0, mobx_react_1.observer)(function ({ model, children, }) {
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const { viewWidth, viewHeight, hview, vview } = model;
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const hblocks = hview.dynamicBlocks.contentBlocks;
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let lastx = Infinity;
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let lasty = Infinity;
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return (react_1.default.createElement(react_1.default.Fragment, null,
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react_1.default.createElement("rect", { x: rx, y: ry, width: w, height: h,
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react_1.default.createElement("rect", { x: rx, y: ry, width: w, height: h, ...(0, util_1.getFillProps)(theme.palette.background.default) }),
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react_1.default.createElement("g", null,
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hblocks.map(region => {
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const x = region.offsetPx - hview.offsetPx;
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if (render) {
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lastx = x;
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}
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return render ? (react_1.default.createElement("line", { key: JSON.stringify(region), x1: x, y1: 0, x2: x, y2: viewHeight,
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return render ? (react_1.default.createElement("line", { key: JSON.stringify(region), x1: x, y1: 0, x2: x, y2: viewHeight, ...(0, util_1.getStrokeProps)(stroke) })) : null;
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}),
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vblocks.map(region => {
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const y = viewHeight - (region.offsetPx - vview.offsetPx);
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if (render) {
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lasty = y;
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}
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return render ? (react_1.default.createElement("line", { key: JSON.stringify(region), x1: 0, y1: y, x2: viewWidth, y2: y,
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return render ? (react_1.default.createElement("line", { key: JSON.stringify(region), x1: 0, y1: y, x2: viewWidth, y2: y, ...(0, util_1.getStrokeProps)(stroke) })) : null;
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}),
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react_1.default.createElement("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight,
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react_1.default.createElement("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop,
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react_1.default.createElement("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight, ...(0, util_1.getStrokeProps)(stroke) }),
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react_1.default.createElement("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop, ...(0, util_1.getStrokeProps)(stroke) })),
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children));
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});
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function Grid({ model, children, }) {
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import PluginManager from '@jbrowse/core/PluginManager';
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export default function (pluginManager: PluginManager): void;
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export default function DotplotViewF(pluginManager: PluginManager): void;
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const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
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// locals
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const model_1 = __importDefault(require("./model"));
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function
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function DotplotViewF(pluginManager) {
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pluginManager.addViewType(() => {
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return new ViewType_1.default({
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name: 'DotplotView',
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});
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});
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}
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exports.default =
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exports.default = DotplotViewF;
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// locals
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import { stateModelFactory } from './stateModelFactory';
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import ReactComponent from './components/DotplotDisplay';
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export default (pm)
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export default function DotplotDisplayF(pm) {
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pm.addDisplayType(() => {
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const configSchema = configSchemaFactory(pm);
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return new DisplayType({
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});
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});
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}
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}
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/**
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* #config DotplotDisplay
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import DotplotRenderer from './DotplotRenderer';
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export default (pluginManager)
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export default function DotplotRendererF(pluginManager) {
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pluginManager.addRendererType(() => new DotplotRenderer({
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name: 'DotplotRenderer',
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}
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}
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import { observer } from 'mobx-react';
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import { getSnapshot } from 'mobx-state-tree';
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import { getTickDisplayStr } from '@jbrowse/core/util';
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import { getFillProps, getStrokeProps, getTickDisplayStr, } from '@jbrowse/core/util';
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import { bpToPx } from '@jbrowse/core/util/Base1DUtils';
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// locals
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return (React.createElement("text", { transform: `rotate(${htextRotation},${xoff},${y})`, key: JSON.stringify(region), x: xoff, y: y + 1,
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return (React.createElement("text", { transform: `rotate(${htextRotation},${xoff},${y})`, key: JSON.stringify(region), x: xoff, y: y + 1, fontSize: 11, dominantBaseline: "hanging", textAnchor: "end", ...getFillProps(theme.palette.text.primary) }, region.refName));
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ticks.map(([tick, x]) => x > 0 && x < width ? (React.createElement("line", { key: `line-${JSON.stringify(tick)}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1,
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ticks.map(([tick, x]) => x > 0 && x < width ? (React.createElement("line", { key: `line-${JSON.stringify(tick)}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, ...getFillProps(theme.palette.text.primary) })) : null),
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.map(([tick, x]) => x > 10 && x < width ? (React.createElement("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},${0})`, key: `text-${JSON.stringify(tick)}`,
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.map(([tick, x]) => x > 10 && x < width ? (React.createElement("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},${0})`, key: `text-${JSON.stringify(tick)}`, fontSize: 11, dominantBaseline: "middle", textAnchor: "end", ...getFillProps(theme.palette.text.primary) }, getTickDisplayStr(tick.base + 1, bpPerPx))) : null),
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React.createElement("text", { y: borderY - 12, x: (viewWidth - borderX) / 2, textAnchor: "middle", fontSize: 11, dominantBaseline: "hanging", ...getFillProps(theme.palette.text.primary) }, hview.assemblyNames.join(','))));
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export const VerticalAxis = observer(function ({ model, }) {
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return (React.createElement("text", { transform: `rotate(${vtextRotation},${x},${y})`, key: JSON.stringify(region), x: x, y: yoff,
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return (React.createElement("text", { transform: `rotate(${vtextRotation},${x},${y})`, key: JSON.stringify(region), x: x, y: yoff, fontSize: 11, textAnchor: "end", ...getFillProps(theme.palette.text.primary) }, region.refName));
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ticks.map(([tick, y]) => y > 0 ? (React.createElement("line", { key: `line-${JSON.stringify(tick)}`, y1: viewHeight - y, y2: viewHeight - y, x1: borderX, x2: borderX - (tick.type === 'major' ? 6 : 4), strokeWidth: 1,
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ticks.map(([tick, y]) => y > 0 ? (React.createElement("line", { key: `line-${JSON.stringify(tick)}`, y1: viewHeight - y, y2: viewHeight - y, x1: borderX, x2: borderX - (tick.type === 'major' ? 6 : 4), strokeWidth: 1, ...getStrokeProps(theme.palette.grey[400]) })) : null),
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|
-
.map(([tick, y]) => y > 10 && y < viewHeight ? (React.createElement("text", { y: viewHeight - y - 3, x: borderX - 7, key: `text-${JSON.stringify(tick)}`, textAnchor: "end",
|
|
114
|
-
React.createElement("text", { y: (viewHeight - borderY) / 2, x: 12,
|
|
113
|
+
.map(([tick, y]) => y > 10 && y < viewHeight ? (React.createElement("text", { y: viewHeight - y - 3, x: borderX - 7, key: `text-${JSON.stringify(tick)}`, textAnchor: "end", dominantBaseline: "hanging", fontSize: 11, ...getFillProps(theme.palette.text.primary) }, getTickDisplayStr(tick.base + 1, bpPerPx))) : null),
|
|
114
|
+
React.createElement("text", { y: (viewHeight - borderY) / 2, x: 12, transform: `rotate(-90,12,${(viewHeight - borderY) / 2})`, textAnchor: "middle", fontSize: 11, ...getFillProps(theme.palette.text.primary) }, vview.assemblyNames.join(','))));
|
|
115
115
|
});
|
|
@@ -31,6 +31,7 @@ export const TooltipWhereMouseovered = observer(function ({ model, mouserect, mo
|
|
|
31
31
|
const theme = useTheme();
|
|
32
32
|
const { refs, floatingStyles, context } = useFloating({
|
|
33
33
|
placement: xdistance < 0 ? 'left' : 'right',
|
|
34
|
+
strategy: 'fixed',
|
|
34
35
|
});
|
|
35
36
|
const clientPoint = useClientPoint(context, mouserectClient
|
|
36
37
|
? {
|
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
2
|
import { observer } from 'mobx-react';
|
|
3
3
|
import { useTheme } from '@mui/material';
|
|
4
|
+
import { getFillProps, getStrokeProps } from '@jbrowse/core/util';
|
|
4
5
|
export const GridRaw = observer(function ({ model, children, }) {
|
|
5
6
|
const { viewWidth, viewHeight, hview, vview } = model;
|
|
6
7
|
const hblocks = hview.dynamicBlocks.contentBlocks;
|
|
@@ -23,7 +24,7 @@ export const GridRaw = observer(function ({ model, children, }) {
|
|
|
23
24
|
let lastx = Infinity;
|
|
24
25
|
let lasty = Infinity;
|
|
25
26
|
return (React.createElement(React.Fragment, null,
|
|
26
|
-
React.createElement("rect", { x: rx, y: ry, width: w, height: h,
|
|
27
|
+
React.createElement("rect", { x: rx, y: ry, width: w, height: h, ...getFillProps(theme.palette.background.default) }),
|
|
27
28
|
React.createElement("g", null,
|
|
28
29
|
hblocks.map(region => {
|
|
29
30
|
const x = region.offsetPx - hview.offsetPx;
|
|
@@ -31,7 +32,7 @@ export const GridRaw = observer(function ({ model, children, }) {
|
|
|
31
32
|
if (render) {
|
|
32
33
|
lastx = x;
|
|
33
34
|
}
|
|
34
|
-
return render ? (React.createElement("line", { key: JSON.stringify(region), x1: x, y1: 0, x2: x, y2: viewHeight, stroke
|
|
35
|
+
return render ? (React.createElement("line", { key: JSON.stringify(region), x1: x, y1: 0, x2: x, y2: viewHeight, ...getStrokeProps(stroke) })) : null;
|
|
35
36
|
}),
|
|
36
37
|
vblocks.map(region => {
|
|
37
38
|
const y = viewHeight - (region.offsetPx - vview.offsetPx);
|
|
@@ -39,10 +40,10 @@ export const GridRaw = observer(function ({ model, children, }) {
|
|
|
39
40
|
if (render) {
|
|
40
41
|
lasty = y;
|
|
41
42
|
}
|
|
42
|
-
return render ? (React.createElement("line", { key: JSON.stringify(region), x1: 0, y1: y, x2: viewWidth, y2: y, stroke
|
|
43
|
+
return render ? (React.createElement("line", { key: JSON.stringify(region), x1: 0, y1: y, x2: viewWidth, y2: y, ...getStrokeProps(stroke) })) : null;
|
|
43
44
|
}),
|
|
44
|
-
React.createElement("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight, stroke
|
|
45
|
-
React.createElement("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop, stroke
|
|
45
|
+
React.createElement("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight, ...getStrokeProps(stroke) }),
|
|
46
|
+
React.createElement("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop, ...getStrokeProps(stroke) })),
|
|
46
47
|
children));
|
|
47
48
|
});
|
|
48
49
|
export default function Grid({ model, children, }) {
|
|
@@ -1,2 +1,2 @@
|
|
|
1
1
|
import PluginManager from '@jbrowse/core/PluginManager';
|
|
2
|
-
export default function (pluginManager: PluginManager): void;
|
|
2
|
+
export default function DotplotViewF(pluginManager: PluginManager): void;
|
package/esm/DotplotView/index.js
CHANGED
|
@@ -2,7 +2,7 @@ import { lazy } from 'react';
|
|
|
2
2
|
import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
|
|
3
3
|
// locals
|
|
4
4
|
import stateModelFactory from './model';
|
|
5
|
-
export default function (pluginManager) {
|
|
5
|
+
export default function DotplotViewF(pluginManager) {
|
|
6
6
|
pluginManager.addViewType(() => {
|
|
7
7
|
return new ViewType({
|
|
8
8
|
name: 'DotplotView',
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-dotplot-view",
|
|
3
|
-
"version": "2.11.
|
|
3
|
+
"version": "2.11.1",
|
|
4
4
|
"description": "JBrowse 2 dotplot view",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -63,5 +63,5 @@
|
|
|
63
63
|
"publishConfig": {
|
|
64
64
|
"access": "public"
|
|
65
65
|
},
|
|
66
|
-
"gitHead": "
|
|
66
|
+
"gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
|
|
67
67
|
}
|