@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/cutsiteTool.js

@@ -1,88 +0,0 @@
-import { Icon, Button, KeyCombo } from "@blueprintjs/core";
-import CutsiteFilter from "../CutsiteFilter";
-import React from "react";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-import { userDefinedHandlersAndOpts } from "../Editor/userDefinedHandlersAndOpts";
-import { pick } from "lodash-es";
-
-export default connectToEditor(
-  ({ readOnly, annotationVisibility = {}, toolBar = {} }) => {
-    return {
-      readOnly,
-      toggled: annotationVisibility.cutsites,
-      isOpen: toolBar.openItem === "cutsiteTool"
-    };
-  }
-)(({ toolbarItemProps, toggled, isOpen, annotationVisibilityToggle }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon data-test="cutsiteHideShowTool" icon="cut" />,
-        onIconClick: function () {
-          annotationVisibilityToggle("cutsites");
-        },
-        toggled,
-        tooltip: "Show cut sites",
-        tooltipToggled: "Hide cut sites",
-        Dropdown: CutsiteToolDropDown,
-        dropdowntooltip: (!isOpen ? "Show" : "Hide") + " Cut Site Options",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});
-// import show_cut_sites_img from "./veToolbarIcons/show_cut_sites.png";
-
-// function CutsiteToolIcon({ annotationVisibilityToggle }) {
-//   return (
-//     <div
-//       onClick={function() {
-//         annotationVisibilityToggle("cutsites");
-//       }}
-//     >
-//       <img src={show_cut_sites_img} alt="Show cut sites" />
-//     </div>
-//   );
-// }
-
-function CutsiteToolDropDown({
-  editorName,
-  toggleDropdown,
-  annotationVisibilityShow,
-  withDigestTool,
-  createNewDigest,
-
-  ...rest
-}) {
-  return (
-    <div className="veToolbarCutsiteFilterHolder">
-      <h6>
-        Filter Cut Sites{" "}
-        <span style={{ fontSize: 12, color: "grey" }}>
-          (Search by name or # of cuts)
-        </span>
-      </h6>
-      <CutsiteFilter
-        {...pick(rest, userDefinedHandlersAndOpts)}
-        editorName={editorName}
-        onChangeHook={function () {
-          annotationVisibilityShow("cutsites");
-        }}
-        closeDropDown={() => toggleDropdown({ forceClose: true })}
-      />
-      {withDigestTool && (
-        <Button
-          onClick={() => {
-            createNewDigest();
-            toggleDropdown();
-          }}
-        >
-          <span style={{ display: "flex" }}>
-            Virtual Digest &nbsp; <KeyCombo minimal combo="mod+shift+d" />
-          </span>
-        </Button>
-      )}
-    </div>
-  );
-}

package/cutsitesByRangeSelector.js

@@ -1,5 +0,0 @@
-// import cutsitesSelector from './cutsitesSelector';
-// export default function (state) {
-// 	var {cutsites} = cutsitesSelector(state)
-
-// }

package/cutsitesSelector.js

@@ -1,61 +0,0 @@
-import shortid from "shortid";
-import circularSelector from "./circularSelector";
-import sequenceSelector from "./sequenceSelector";
-import restrictionEnzymesSelector from "./restrictionEnzymesSelector";
-import cutsiteLabelColorSelector from "./cutsiteLabelColorSelector";
-import { createSelector } from "reselect";
-
-import { flatMap as flatmap, map } from "lodash-es";
-import { getCutsitesFromSequence } from "@teselagen/sequence-utils";
-import { getLowerCaseObj } from "../utils/arrayUtils";
-
-function cutsitesSelector(sequence, circular, enzymeList, cutsiteLabelColors) {
-  //get the cutsites grouped by enzyme
-  const cutsitesByName = getLowerCaseObj(
-    getCutsitesFromSequence(sequence, circular, map(enzymeList))
-  );
-  //tag each cutsite with a unique id
-  const cutsitesById = {};
-  Object.keys(cutsitesByName).forEach(function (enzymeName) {
-    const cutsitesForEnzyme = cutsitesByName[enzymeName];
-    cutsitesForEnzyme.forEach(function (cutsite) {
-      const numberOfCuts = cutsitesByName[enzymeName].length;
-      const uniqueId = shortid();
-      cutsite.id = uniqueId;
-      cutsite.numberOfCuts = numberOfCuts;
-      cutsite.annotationType = "cutsite";
-      cutsitesById[uniqueId] = cutsite;
-      const mergedCutsiteColors = Object.assign(
-        { single: "salmon", double: "lightblue", multi: "lightgrey" },
-        cutsiteLabelColors
-      );
-      if (numberOfCuts === 1) {
-        cutsite.labelColor = mergedCutsiteColors.single;
-        cutsite.labelClassname = "singleCutter";
-      } else if (numberOfCuts === 2) {
-        cutsite.labelColor = mergedCutsiteColors.double;
-        cutsite.labelClassname = "doubleCutter";
-      } else {
-        cutsite.labelColor = mergedCutsiteColors.multi;
-        cutsite.labelClassname = "multiCutter";
-      }
-    });
-  });
-  // create an array of the cutsites
-  const cutsitesArray = flatmap(cutsitesByName, function (cutsitesForEnzyme) {
-    return cutsitesForEnzyme;
-  });
-  return {
-    cutsitesByName,
-    cutsitesById,
-    cutsitesArray
-  };
-}
-
-export default createSelector(
-  sequenceSelector,
-  circularSelector,
-  restrictionEnzymesSelector,
-  cutsiteLabelColorSelector,
-  cutsitesSelector
-);

package/darkmode.css

@@ -1,98 +0,0 @@
-.bp3-dark .veAxisLine {
-  stroke: #f5f8fa !important;
-}
-.bp3-dark .veAxisTick,
-.bp3-dark .veCutsite {
-  fill: #f5f8fa;
-}
-
-.bp3-dark .veEditor:not(.tg-simple-dna-view) {
-  background: #293742 !important;
-}
-
-.veLabelLine {
-  stroke: black;
-  background: black;
-}
-.bp3-dark .veCaret,
-.bp3-dark .veLabelLine {
-  stroke: white;
-  background: white;
-}
-.bp3-dark .veLabelLine {
-  stroke: #f5f8fa !important;
-  background: #f5f8fa !important;
-}
-
-.bp3-dark .veEditor .veRowViewCaret {
-  background: #f5f8fa !important;
-}
-
-.bp3-dark .veEditor text {
-  fill: #f5f8fa;
-}
-
-.bp3-dark .veRowViewPartsContainer text,
-.bp3-dark .veLabelText.black {
-  fill: #f5f8fa !important;
-}
-
-.bp3-dark .tag-selection.selected {
-  border-color: #f5f8fa !important;
-}
-
-.bp3-dark .veLinearView text {
-  fill: #f5f8fa !important;
-}
-.bp3-dark .veCircularViewAxisNumber rect {
-  fill: #f5f8fa !important;
-}
-
-.bp3-dark .menu-bar {
-  background: none !important;
-}
-
-.alignmentViewTrackContainer {
-  background: white;
-}
-.bp3-dark .alignmentViewTrackContainer {
-  background: #293742;
-}
-.bp3-dark .alignmentViewTrackContainer text {
-  fill: #f5f8fa !important;
-}
-
-/* .bp3-dark .veRowViewAxis text {
-  stroke: #f5f8fa !important;
-} */
-
-.bp3-dark .translationLayer text {
-  fill: black !important;
-}
-
-.bp3-dark .step-group.active .step-text {
-  color: #2b95d6 !important;
-}
-
-.bp3-dark .step-group.active .step-mark {
-  background-color: #2b95d6 !important;
-  border-color: #2b95d6 !important;
-}
-
-.bp3-dark .tool-select-item:hover {
-  background: #0e5a8a !important;
-}
-
-.bp3-dark .veWhiteBackground {
-  background: #293742;
-}
-
-.bp3-dark .vePart path:first-of-type {
-  stroke-width: 1;
-  stroke: #df7ff1 !important;
-}
-
-.bp3-dark .vePart .veLabelText,
-.bp3-dark .veLabelText.vePart {
-  fill: #ac68cc !important;
-}

package/defaultConfig.js

@@ -1,150 +0,0 @@
-//only things specific to this menu should be included here
-//things that are shared between multiple menus, or that are command specific should be
-//defined in the commands/index.js file
-
-import viewSubmenu from "./viewSubmenu";
-export const copyOptionsMenu = {
-  text: "Copy Options",
-  showInSearchMenu: true,
-  submenu: [
-    { cmd: "toggleCopyFeatures", shouldDismissPopover: false },
-    { cmd: "toggleCopyPartialFeatures", shouldDismissPopover: false },
-    { cmd: "toggleCopyParts", shouldDismissPopover: false },
-    { cmd: "toggleCopyPartialParts", shouldDismissPopover: false }
-  ]
-};
-export const createNewAnnotationMenu = {
-  text: "Create",
-  cmd: "createMenuHolder",
-  showInSearchMenu: true
-};
-export default [
-  {
-    text: "File",
-    "data-test": "file",
-    submenu: [
-      {
-        cmd: "newSequence",
-        "data-test": "newSequence"
-      },
-      "renameSequence",
-      "saveSequence",
-      "saveSequenceAs",
-      "deleteSequence",
-      "duplicateSequence",
-      "--",
-      { cmd: "toggleReadOnlyMode", shouldDismissPopover: false },
-      "--",
-      "importSequence",
-      {
-        text: "Export Sequence",
-        showInSearchMenu: true,
-        submenu: [
-          { cmd: "exportSequenceAsGenbank" },
-          { cmd: "exportDNASequenceAsFasta" },
-          { cmd: "exportProteinSequenceAsFasta" },
-          { cmd: "exportSequenceAsTeselagenJson" }
-        ]
-      },
-      "--",
-      {
-        text: "Print",
-        cmd: "print"
-        // submenu: [{ cmd: "printCircularView" }, { cmd: "printLinearView" }]
-      },
-      { cmd: "viewRevisionHistory", text: "Revision History" },
-      { cmd: "viewProperties", text: "Properties", icon: "properties" }
-    ]
-  },
-  {
-    text: "Edit",
-    submenu: [
-      createNewAnnotationMenu,
-      "--",
-      "cut",
-      "copy",
-      copyOptionsMenu,
-      "paste",
-      "--",
-      "undo",
-      "redo",
-      "--",
-      "find",
-      "goTo",
-      "--",
-      "select",
-      "selectAll",
-      "selectInverse",
-      {
-        text: "Change Case",
-        cmd: "changeCaseCmd",
-        submenu: [
-          "flipCaseSequence",
-          "upperCaseSequence",
-          "lowerCaseSequence",
-          "upperCaseSelection",
-          "lowerCaseSelection"
-        ]
-      },
-      {
-        text: "Change Circular/Linear",
-        cmd: "changeCircularityCmd",
-        submenu: ["toggleCircular", "toggleLinear"]
-      },
-      // {
-      //   text: "Change Sequence Case For Selection",
-      //   submenu: [
-      //   ]
-      // },
-      "--",
-      "complementSelection",
-      "complementEntireSequence",
-      "reverseComplementSelection",
-      "reverseComplementEntireSequence",
-      "rotateToCaretPosition"
-    ]
-  },
-  {
-    text: "View",
-    submenu: viewSubmenu
-  },
-  {
-    text: "Tools",
-    cmd: "toolsCmd",
-    submenu: [
-      "openFilterCutsites",
-      "restrictionEnzymesManager",
-      "openCreateCustomEnzyme",
-      "simulateDigestion",
-      "simulatePCR",
-      {
-        text: "Remove Duplicates",
-        submenu: [
-          "showRemoveDuplicatesDialogFeatures",
-          "showRemoveDuplicatesDialogParts",
-          "showRemoveDuplicatesDialogPrimers"
-        ]
-      },
-      {
-        text: "Auto Annotate",
-        cmd: "autoAnnotateHolder",
-        submenu: [
-          "autoAnnotateFeatures",
-          "autoAnnotateParts",
-          "autoAnnotatePrimers"
-        ]
-      }
-    ]
-  },
-  // { isMenuSearch: true }
-  {
-    text: "Help",
-    submenu: [
-      { isMenuSearch: true },
-      "--",
-      "about",
-      { cmd: "versionNumber", shouldDismissPopover: false },
-      "hotkeyDialog"
-    ]
-  }
-];

package/deletionLayers.js

@@ -1,36 +0,0 @@
-//./deletionLayers.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-import omit from "lodash/omit";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const deletionLayerClear = createAction("deletionLayerClear");
-export const deletionLayerUpdate = createAction("DELETION_LAYER_UPDATE");
-export const deletionLayerDelete = createAction("DELETION_LAYER_DELETE");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [deletionLayerClear]: () => {
-      return {};
-    },
-    [deletionLayerUpdate]: (state, payload) => {
-      return {
-        ...state,
-        [payload.id]: {
-          color: "firebrick",
-          id: payload.id,
-          ...payload.range
-        }
-      };
-    },
-    [deletionLayerDelete]: (state, payload) => {
-      return omit(state, payload.id);
-    }
-  },
-  {}
-);

package/description.js

@@ -1,21 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const sequenceDescriptionUpdate = createAction(
-  "sequenceDescriptionUpdate"
-);
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [sequenceDescriptionUpdate]: (state, payload) => {
-      return payload;
-    }
-  },
-  ""
-);

package/digestTool.js

@@ -1,34 +0,0 @@
-import createAction from "./utils/createMetaAction";
-import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const updateSelectedFragment = createAction("updateSelectedFragment");
-export const updateComputePartialDigest = createAction(
-  "updateComputePartialDigest"
-);
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createMergedDefaultStateReducer(
-  {
-    [updateSelectedFragment]: (state, payload) => {
-      return {
-        ...state,
-        selectedFragment: payload
-      };
-    },
-    [updateComputePartialDigest]: (state, payload) => {
-      return {
-        ...state,
-        computePartialDigest: payload
-      };
-    }
-  },
-  {
-    selectedFragment: undefined,
-    computePartialDigest: false
-  }
-);

package/dnaToColor.js

@@ -1,17 +0,0 @@
-import { DNAComplementMap } from "@teselagen/sequence-utils";
-
-const dnaToColor = {
-  a: "lightgreen",
-  c: "#658fff",
-  g: "yellow",
-  t: "#EE6262"
-};
-export default dnaToColor;
-
-export function getDnaColor(char, isReverse) {
-  return (
-    dnaToColor[
-      isReverse ? DNAComplementMap[char.toLowerCase()] : char.toLowerCase()
-    ] || "lightgrey"
-  );
-}

package/downloadTool.js

@@ -1,39 +0,0 @@
-import React from "react";
-import { Icon, Menu } from "@blueprintjs/core";
-import { createCommandMenu } from "@teselagen/ui";
-import getCommands from "../commands";
-
-import { connectToEditor } from "../withEditorProps";
-import ToolbarItem from "./ToolbarItem";
-import withEditorProps from "../withEditorProps";
-
-export default connectToEditor()(({ toolbarItemProps }) => {
-  return (
-    <ToolbarItem
-      {...{
-        tooltip: "Export",
-        Dropdown,
-        noDropdownIcon: true,
-        onIconClick: "toggleDropdown",
-        Icon: <Icon data-test="veDownloadTool" icon="import" />,
-        ...toolbarItemProps
-      }}
-    />
-  );
-});
-
-const Dropdown = withEditorProps(props => {
-  return (
-    <Menu>
-      {createCommandMenu(
-        [
-          "exportSequenceAsGenbank",
-          "exportDNASequenceAsFasta",
-          "exportProteinSequenceAsFasta",
-          "exportSequenceAsTeselagenJson"
-        ],
-        getCommands({ props })
-      )}
-    </Menu>
-  );
-});

package/draggableClassnames.js

@@ -1,5 +0,0 @@
-export default {
-  caret: "veCaret",
-  selectionStart: "veSelectionLayerStart",
-  selectionEnd: "veSelectionLayerEnd"
-};