init

.gitignore

+node_modules
+dist
+playground/data
+
+
+# Add if you are working with new file types
+*.pdb
+*.csv
+*.gff
+*.bed
+*.txt

.gitlab-ci.yml

+image: node:latest
+
+pages:
+  stage: deploy
+  tags:
+    - shared-fi
+  script:
+    - mkdir public
+    - cd app
+    - npm ci
+    - npm run build
+    - cp -r ./dist/* ../public
+  artifacts:
+    paths:
+    - public
+  only:
+  - main

README.md

+## Chromazoom
+
+Chromatin visualisation app + library
+
+### Development
+
+
+#### Supported browsers:
+ - Google Chrome Canary
+
+#### Project initialization
+
+Windows 10 (Creator's update and later): 
+ - Enable 'Developer mode'
+ - Clone with symlinks enabled
+  
+    `git clone -c core.symlinks=true`
+
+
+Run dev server
+- `cd app`
+- `npm run serve`
+
+
+
+### Pages
+Pushing to `main` branch triggers publish on https://visitlab.pages.fi.muni.cz/chromatin/chromazoom/

app/.eslintrc.json

+{
+    "env": {
+        "browser": true,
+        "es2021": true
+    },
+    "extends": [
+        "eslint:recommended",
+        "plugin:react/recommended",
+        "plugin:@typescript-eslint/recommended",
+        "plugin:react-hooks/recommended"
+    ],
+    "parser": "@typescript-eslint/parser",
+    "parserOptions": {
+        "ecmaFeatures": {
+            "jsx": true
+        },
+        "ecmaVersion": 12,
+        "sourceType": "module"
+    },
+    "plugins": [
+        "react",
+        "@typescript-eslint"
+    ],
+    "rules": {
+    }
+}

app/.gitignore

+node_modules
+dist
\ No newline at end of file

app/.gitlab-ci.yml

+image: node:latest
+
+pages:
+  stage: deploy
+  tags:
+    - shared-fi
+  script:
+    - mkdir public
+    - cd app
+    - npm install
+    - npm run build
+    - cp -r ./dist/* ../public
+  artifacts:
+    paths:
+    - public
+  only:
+  - main

app/.vs/ProjectSettings.json

+{
+  "CurrentProjectSetting": null
+}
\ No newline at end of file

app/.vs/VSWorkspaceState.json

+{
+  "ExpandedNodes": [
+    "",
+    "\\src",
+    "\\src\\RightPanel"
+  ],
+  "SelectedNode": "\\src\\RightPanel\\ChromatinViewportConfiguration.tsx",
+  "PreviewInSolutionExplorer": false
+}
\ No newline at end of file

app/.vs/app/project-colors.json

+{
+  "Version": 1,
+  "ProjectMap": {
+    "a2fe74e1-b743-11d0-ae1a-00a0c90fffc3": {
+      "ProjectGuid": "a2fe74e1-b743-11d0-ae1a-00a0c90fffc3",
+      "DisplayName": "Miscellaneous Files",
+      "ColorIndex": -1
+    }
+  },
+  "NextColorIndex": 0
+}
\ No newline at end of file

app/package.json

+{
+  "name": "chromazoom",
+  "version": "1.0.0",
+  "type": "module",
+  "main": "./dist/main.js",
+  "typings": "./dist/index.d.ts",
+  "repository": "https://gitlab.fi.muni.cz/visitlab/chromatin/chromazoom.git",
+  "author": "Kiraa Corsac <kiraa@mail.muni.cz>",
+  "license": "MIT",
+  "scripts": {
+    "serve": "webpack serve --hot --config webpack.development.mjs",
+    "serve-production": "webpack serve --config webpack.production.mjs",
+    "build": "webpack --config webpack.production.mjs"
+  },
+  "dependencies": {
+    "@gmod/gff": "^1.1.2",
+    "@types/chroma-js": "^2.1.3",
+    "chroma-js": "^2.4.2",
+    "d3": "^7.2.1",
+    "file-saver": "^2.0.5",
+    "flexlayout-react": "^0.6",
+    "gl-matrix": "^3.3.0",
+    "graphology": "^0.23.2",
+    "graphology-layout-forceatlas2": "^0.8.1",
+    "graphology-types": "^0.23.0",
+    "idb-keyval": "^6.0.3",
+    "image-js": "^0.33.1",
+    "immer": "^9.0.6",
+    "lodash": "^4.17.21",
+    "newtype-ts": "^0.3.5",
+    "papaparse": "^5.3.1",
+    "parse-pdb": "^1.0.0",
+    "randomcolor": "^0.6.2",
+    "react": "^17.0.2",
+    "react-complex-tree": "^1.1.1",
+    "react-dom": "^17.0.2",
+    "react-fast-compare": "^3.2.0",
+    "react-hot-keys": "^2.7.1",
+    "react-redux": "^7.2.4",
+    "react-sigma-v2": "^1.3.0",
+    "react-use": "^17.3.1",
+    "rooks": "^5.7.3",
+    "sigma": "^2.2.0",
+    "simple-statistics": "^7.7.0",
+    "stream": "^0.0.2",
+    "use-deep-compare-effect": "^1.8.1"
+  },
+  "devDependencies": {
+    "@fluentui/react": "^8.30.3",
+    "@fluentui/react-icons": "^1.1.145",
+    "@fluentui/svg-icons": "^1.1.139",
+    "@minoru/react-dnd-treeview": "^1.5.3",
+    "@pmmmwh/react-refresh-webpack-plugin": "^0.5.1",
+    "@react-hook/mouse-position": "^4.1.1",
+    "@reduxjs/toolkit": "^1.6.1",
+    "@thi.ng/color": "^3.2.7",
+    "@types/d3": "^7.1.0",
+    "@types/file-saver": "^2.0.4",
+    "@types/lodash": "^4.14.172",
+    "@types/papaparse": "^5.2.6",
+    "@types/randomcolor": "^0.5.6",
+    "@types/react": "^17.0.19",
+    "@types/react-dom": "^17.0.9",
+    "@types/react-redux": "^7.1.18",
+    "@types/resize-observer-browser": "^0.1.6",
+    "@typescript-eslint/eslint-plugin": "^4.30.0",
+    "@typescript-eslint/parser": "^4.30.0",
+    "@webgpu/types": "^0.1.13",
+    "css-loader": "^6.2.0",
+    "eslint": "^7.32.0",
+    "eslint-plugin-react": "^7.25.1",
+    "eslint-plugin-react-hooks": "^4.3.0",
+    "fork-ts-checker-webpack-plugin": "^6.4.0",
+    "html-webpack-plugin": "^5.3.2",
+    "react-refresh": "^0.10.0",
+    "react-refresh-typescript": "^2.0.2",
+    "sass": "^1.39.0",
+    "sass-loader": "^12.1.0",
+    "style-loader": "^3.2.1",
+    "svg-inline-loader": "^0.8.2",
+    "ts-loader": "^9.2.5",
+    "type-fest": "^2.5.1",
+    "typescript": "^4.4.2",
+    "webpack": "^5.52.0",
+    "webpack-cli": "^4.8.0",
+    "webpack-dev-server": "^4.1.0",
+    "webpack-merge": "^5.8.0"
+  }
+}

app/public/index.html

+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="UTF-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
+    <link rel="stylesheet" href="https://unpkg.com/higlass@1.11.3/dist/hglib.css">
+
+    <title>Webpack</title>
+
+    <script defer src="main.js"></script>
+</head>
+
+<body>
+    <div id="root"></div>
+</body>
+
+</html>
\ No newline at end of file

app/src/App.scss

+@import '@fluentui/react/dist/sass/References';
+
+ul, li {
+  list-style-type: none;
+}
+
+.App {
+    display: flex;
+    flex-direction: column;
+}
+
+.topPanel {
+    flex-grow: 0;
+    flex-basis: 44px;
+    border-bottom: 1px solid $ms-color-gray140;
+}
+
+.mainArea {
+    flex: 1;
+    display: flex;
+    flex-direction: row;
+    overflow: hidden;
+}
+
+.flexlayout__layout {
+    flex: 1;
+    position: relative;
+    overflow: hidden;
+  }
+
+  .flexlayout__splitter {
+    background-color: #1a1a1a;
+  }
+  @media (hover: hover) {
+    .flexlayout__splitter:hover {
+      background-color: #333333;
+    }
+  }
+  .flexlayout__splitter_border {
+    z-index: 10;
+  }
+  .flexlayout__splitter_drag {
+    z-index: 1000;
+    border-radius: 5px;
+    background-color: #404040;
+  }
+  .flexlayout__outline_rect {
+    position: absolute;
+    cursor: move;
+    box-sizing: border-box;
+    border: 2px solid #cfe8ff;
+    box-shadow: inset 0 0 60px rgba(0, 0, 0, 0.2);
+    border-radius: 5px;
+    z-index: 1000;
+  }
+  .flexlayout__outline_rect_edge {
+    cursor: move;
+    border: 2px solid #b7d1b5;
+    box-shadow: inset 0 0 60px rgba(0, 0, 0, 0.2);
+    border-radius: 5px;
+    z-index: 1000;
+    box-sizing: border-box;
+  }
+  .flexlayout__edge_rect {
+    position: absolute;
+    z-index: 1000;
+    box-shadow: inset 0 0 5px rgba(0, 0, 0, 0.2);
+    background-color: gray;
+  }
+  .flexlayout__drag_rect {
+    position: absolute;
+    cursor: move;
+    color: white;
+    background-color: #121212;
+    border: 2px solid #333333;
+    box-shadow: inset 0 0 60px rgba(0, 0, 0, 0.3);
+    border-radius: 5px;
+    z-index: 1000;
+    box-sizing: border-box;
+    opacity: 0.9;
+    text-align: center;
+    display: flex;
+    justify-content: center;
+    flex-direction: column;
+    overflow: hidden;
+    padding: 10px;
+    word-wrap: break-word;
+    font-size: medium;
+    font-family: Roboto, Arial, sans-serif;
+  }
+
+.flexlayout__tabset {
+    overflow: hidden;
+    background: none;
+  }
+  .flexlayout__tabset_header {
+
+  }
+  .flexlayout__tabset_header_content {
+    flex-grow: 1;
+  }
+  .flexlayout__tabset_tabbar_outer {
+    box-sizing: border-box;
+    position: absolute;
+    left: 0;
+    right: 0;
+    overflow: hidden;
+    display: flex;
+    background: none;
+  }
+  .flexlayout__tabset_tabbar_outer_top {
+    /* border-bottom: 1px solid #262626; */
+  }
+  .flexlayout__tabset_tabbar_outer_bottom {
+    /* border-top: 1px solid #262626; */
+  }
+  .flexlayout__tabset_tabbar_inner {
+    position: relative;
+    box-sizing: border-box;
+    display: flex;
+    flex-grow: 1;
+    overflow: hidden;
+  }
+  .flexlayout__tabset_tabbar_inner_tab_container {
+    display: flex;
+    box-sizing: border-box;
+    position: absolute;
+    top: 0;
+    bottom: 0;
+    width: 10000px;
+  }
+  .flexlayout__tabset_tabbar_inner_tab_container_top {
+
+  }
+  .flexlayout__tabset_tabbar_inner_tab_container_bottom {
+
+  }
+  .flexlayout__tabset-selected {
+    // background-color: #111c25;
+  }
+  .flexlayout__tabset-maximized {
+  }
+  .flexlayout__tab {
+    overflow: hidden;
+    position: absolute;
+    box-sizing: border-box;
+  }
+  .flexlayout__tab_button {
+    display: inline-flex;
+    align-items: center;
+    box-sizing: border-box;
+    cursor: pointer;
+    padding: 0px 8px 0px 8px;
+    margin-right: 8px;
+    background-color: #2f2f2f;
+  }
+  .flexlayout__tabset-selected .flexlayout__tab_button--selected {
+    color: white; 
+    background-color: #6db1e8;
+  }
+  @media (hover: hover) {
+    .flexlayout__tab_button:hover {
+    }
+  }
+  .flexlayout__tab_button--unselected {
+    color: gray;
+  }
+  .flexlayout__tab_button_top {
+  }
+  .flexlayout__tab_button_bottom {
+  }
+  .flexlayout__tab_button_leading {
+    display: inline-block;
+  }
+  .flexlayout__tab_button_content {
+    font-size: $ms-font-size-14;
+    font-weight: $ms-font-weight-semibold;
+    display: inline-block;
+  }
+  .flexlayout__tab_button_textbox {
+    border: none;
+    /* color: green;
+    background-color: #262626; */
+  }
+  .flexlayout__tab_button_textbox:focus {
+    outline: none;
+  }
+
+  .flexlayout__tab_button_trailing {
+    margin-left: 8px;
+  }
+
+  .flexlayout__tab_button--selected .flexlayout__tab_button_trailing {
+    color: white;
+  }
+
+  .flexlayout__tab_button_trailing, .flexlayout__tab_button_trailing i {
+    width: 8px;
+    height: 8px;
+    font-size: 8px;    
+  }
+
+  .flexlayout__splitter {
+    background-color: $ms-color-gray140;
+  }
+
+.toolOptionsPanel {
+  width: 100%;
+  height: 44px;
+  background-color: $ms-color-gray190;
+  border-bottom: 1px solid $ms-color-gray150;
+  justify-content: center;
+}
\ No newline at end of file

app/src/App.tsx

+import './App.scss';
+import React, { useEffect, useReducer } from 'react';
+import TopBar from './components/TopBar';
+import { Icon, Label, Separator, Slider, Stack } from '@fluentui/react';
+import { useState } from 'react';
+import * as FlexLayout from "flexlayout-react";
+import { IIcons } from 'flexlayout-react/declarations/view/Layout';
+import { initialWorkspaceState, WorkspaceActionKind, workspaceReducer, WorkspaceStorage } from './modules/storage/models/workspace';
+import { RightPanel } from './components/RightPanel';
+import { GraphicsLibrary } from "./modules/graphics/index";
+import { ChromatinViewport } from './components/viewports/ChromatinViewport';
+import { D1Viewport } from './components/viewports/D1Viewport';
+import { ConfigurationActionKind, configurationReducer, ConfigurationState, defaultChromatinViewportConfiguration, defaultForceGraphViewportConfiguration, defaultDistanceViewportConfiguration, ViewportConfigurationType } from './modules/storage/models/viewports';
+import { TADViewport } from './components/viewports/TADViewport';
+import { isNumber } from 'lodash';
+import { CursorClick24Regular, Lasso24Regular } from '@fluentui/react-icons';
+import { NewXYZDataDialog } from './components/dialogs/NewXYZDataDialog';
+// import New1DDataDialog from './dialogs/New1DDataDialog';
+import { DataAction, DataActionKind, dataReducer, DataState } from './modules/storage/models/data';
+import { SelectionActionKind, selectionReducer, SelectionState } from './modules/storage/models/selections';
+import { clearBrowser, loadFromBrowser, saveToBrowser } from './modules/storage/inBrowserStorage';
+import { saveToFile, loadFromFile } from './modules/storage/fileStorage';
+import { ImportWorkspaceDialog } from './components/dialogs/ImportWorkspaceDialog';
+import { ApplicationState, APPLICATION_STATE_VERSION } from './modules/storage/state';
+import { ForceGraphViewport } from './components/viewports/ForceGraphViewport';
+import { ToolsList } from './components/Tools/ToolsList';
+import { ToolOptions } from './components/Tools/ToolOptions';
+import { NewGenomicDataDialog } from './components/dialogs/NewGenomicDataDialog';
+
+export enum Tool {
+  PointSelection = 0,
+  SphereSelection = 1,
+}
+
+function App(): JSX.Element {
+  const [adapter, setAdapter] = useState<GPUAdapter | null>(null);
+  const [device, setDevice] = useState<GPUDevice | null>(null);
+  const [deviceError, setDeviceError] = useState<GPUUncapturedErrorEvent | null>(null);
+  const [graphicsLibrary, setGraphicsLibrary] = useState<GraphicsLibrary | null>(null);
+
+  //#region Adapter, Device, Library Initialization
+  useEffect(() => {
+    async function waitForAdapter() {
+      const adapter = await navigator.gpu.requestAdapter({
+        powerPreference: "high-performance",
+      });
+
+      setAdapter(adapter);
+    }
+
+    waitForAdapter();
+  }, []);
+
+  useEffect(() => {
+    if (adapter == null) {
+      return;
+    }
+
+    const waitForDevice = async function () {
+      const device = await adapter.requestDevice({
+        requiredFeatures: ['timestamp-query']
+      });
+      device.onuncapturederror = (error: GPUUncapturedErrorEvent) => {
+        setDeviceError(error);
+      };
+
+      setDeviceError(null);
+      setDevice(device);
+    }
+
+    waitForDevice();
+  }, [adapter]);
+
+  useEffect(() => {
+    if (adapter == null || device == null) {
+      return;
+    }
+
+    setGraphicsLibrary(() => new GraphicsLibrary(adapter, device));
+  }, [adapter, device]);
+  //#endregion
+
+  //#region Application Data
+
+  const initialState: ApplicationState = {
+    version: APPLICATION_STATE_VERSION,
+    data: {
+      dataMaxId: 0,
+      data: [],
+    },
+    configurations: {
+      maxId: 0,
+      configurations: [],
+    },
+    selections: {
+      maxId: 0,
+      selections: [],
+    },
+    workspace: {
+      workspaceData: initialWorkspaceState
+    }
+  }
+
+
+  const [data, dispatchData] = useReducer(
+    dataReducer,
+    initialState.data as DataState
+  );
+  const [workspace, dispatchWorkspace] = useReducer(
+    workspaceReducer,
+    initialState.workspace?.workspaceData as FlexLayout.IJsonModel
+  );
+  const [configurations, dispatchConfigurations] = useReducer(
+    configurationReducer,
+    initialState.configurations as ConfigurationState
+  );
+  const [selections, dispatchSelections] = useReducer(
+    selectionReducer,
+    initialState.selections as SelectionState
+  );
+
+
+
+  function setCurrentState(state: ApplicationState) {
+    if (state.version == null || state.version < APPLICATION_STATE_VERSION) {
+      throw "The workspace you are trying to load was created in a version of Chromazoom that is no longer supported."
+    }
+    if (state.data)
+      dispatchData({
+        type: DataActionKind.SET,
+        state: state.data
+      });
+    if (state.workspace)
+      dispatchWorkspace({
+        type: WorkspaceActionKind.REPLACE,
+        model: state.workspace.workspaceData
+      });
+    if (state.configurations)
+      dispatchConfigurations({
+        type: ConfigurationActionKind.SET,
+        state: state.configurations
+      });
+    if (state.selections)
+      dispatchSelections({
+        type: SelectionActionKind.SET,
+        state: state.selections
+      });
+  }
+
+  function getCurrentState(): ApplicationState {
+    return {
+      data,
+      configurations,