@teselagen/ove 0.7.28 → 0.7.29

package/utils.js

@@ -1,37 +0,0 @@
-import React from "react";
-import { convertDnaCaretPositionOrRangeToAA } from "@teselagen/sequence-utils";
-import { convertRangeTo1Based } from "@teselagen/range-utils";
-
-export const sizeSchema = isProtein => ({
-  path: "size",
-  type: "number",
-  render: (val, _record) => {
-    const record = isProtein
-      ? convertDnaCaretPositionOrRangeToAA(_record)
-      : _record;
-    const base1Range = convertRangeTo1Based(record);
-    const hasJoinedLocations = record.locations && record.locations.length > 1;
-
-    return (
-      <span>
-        {isProtein ? Math.floor(val / 3) : val}{" "}
-        <span style={{ fontSize: 10 }}>
-          {hasJoinedLocations ? (
-            record.locations.map((loc, i) => {
-              const base1Range = convertRangeTo1Based(loc);
-              return (
-                <span key={i}>
-                  ({base1Range.start}-{base1Range.end})
-                </span>
-              );
-            })
-          ) : (
-            <span>
-              ({base1Range.start}-{base1Range.end})
-            </span>
-          )}
-        </span>
-      </span>
-    );
-  }
-});

package/versionHistory.js

@@ -1,26 +0,0 @@
-//./caretPosition.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-import { noop } from "lodash-es";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const toggleViewVersionHistory = createAction(
-  "TOGGLE_VIEW_VERSION_HISTORY",
-  noop
-); //NOTE!!:: second argument sanitizes actions so no payload is passed
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [toggleViewVersionHistory]: state => {
-      return { viewVersionHistory: !state.viewVersionHistory };
-    }
-  },
-  {
-    viewVersionHistory: false
-  }
-);

package/versionHistoryTool.js

@@ -1,21 +0,0 @@
-import React from "react";
-import { Icon } from "@blueprintjs/core";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-
-export default connectToEditor()(({
-  toolbarItemProps,
-  toggleViewVersionHistory
-}) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon icon="history" />,
-        onIconClick: toggleViewVersionHistory,
-        // disabled: hasBeenSaved || lastEdit,
-        tooltip: <span>View Version History</span>,
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/viewSubmenu.js

@@ -1,479 +0,0 @@
-import { MenuItem } from "@blueprintjs/core";
-import React from "react";
-import { InfoHelper } from "@teselagen/ui";
-import useAAColorType from "../utils/useAAColorType";
-import { LimitAnnotations } from "../utils/useAnnotationLimits";
-import { chromatogramMenu } from "../utils/useChromatogramPrefs";
-import useMeltingTemp from "../utils/useMeltingTemp";
-
-export const translationsSubmenu = [
-  {
-    cmd: "toggleTranslations",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "toggleCdsFeatureTranslations",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "toggleOrfTranslations",
-    shouldDismissPopover: false
-  },
-  { cmd: "toggleAminoAcidNumbers_dna", shouldDismissPopover: false }
-];
-export const orfsSubmenu = [
-  {
-    cmd: "toggleOrfs",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "toggleOrfTranslations",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "useGtgAndCtgAsStartCodons",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "minOrfSizeCmd",
-    shouldDismissPopover: false
-  }
-];
-export const cutsitesSubmenu = [
-  {
-    cmd: "toggleCutsites",
-    shouldDismissPopover: false
-  }
-];
-export const featuresSubmenu = [
-  {
-    cmd: "toggleFeatures",
-    shouldDismissPopover: false
-  },
-  "onConfigureFeatureTypesClick",
-  {
-    cmd: "featureTypesCmd",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "featureFilterIndividualCmd",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "filterFeatureLengthsCmd",
-    shouldDismissPopover: false
-  }
-];
-export const partsSubmenu = props => {
-  return [
-    {
-      cmd: "toggleParts",
-      shouldDismissPopover: false
-    },
-    {
-      cmd: "partFilterIndividualCmd",
-      shouldDismissPopover: false
-    },
-    ...(props.allPartTags
-      ? [
-          {
-            cmd: "filterPartsByTagCmd",
-            shouldDismissPopover: false
-          }
-        ]
-      : []),
-    {
-      cmd: "filterPartLengthsCmd",
-      shouldDismissPopover: false
-    }
-  ];
-};
-export const primersSubmenu = [
-  {
-    cmd: "togglePrimers",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "primerFilterIndividualCmd",
-    shouldDismissPopover: false
-  },
-  {
-    cmd: "filterPrimerLengthsCmd",
-    shouldDismissPopover: false
-  }
-];
-
-export const fullSequenceTranslationMenu = {
-  text: "Full Sequence Translation",
-  cmd: "fullSequenceTranslations",
-  submenu: [
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAA_allFrames",
-      text: "All Frames"
-      // frameNumber: "all" // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAA_frame1",
-      text: "Frame 1"
-      // frameNumber: 1 // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAA_frame2",
-      text: "Frame 2"
-      // frameNumber: 2 // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAA_frame3",
-      text: "Frame 3"
-      // frameNumber: 3 // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAAReverse_allFrames",
-      text: "All Reverse Frames"
-      // frameNumber: "all" // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAAReverse_frame1",
-      text: "Frame -1"
-      // frameNumber: 1 // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAAReverse_frame2",
-      text: "Frame -2"
-      // frameNumber: 2 // TODO ?
-    },
-    {
-      shouldDismissPopover: false,
-      cmd: "sequenceAAReverse_frame3",
-      text: "Frame -3"
-      // frameNumber: 3 // TODO ?
-    }
-  ]
-};
-export default [
-  // { cmd: "mapCaret" },
-  { cmd: "showAll", shouldDismissPopover: false },
-  { cmd: "hideAll", shouldDismissPopover: false },
-  {
-    cmd: "toggleChromatogram",
-    shouldDismissPopover: false,
-    submenu: [
-      { cmd: "toggleChromatogram", shouldDismissPopover: false },
-      chromatogramMenu
-    ]
-  },
-  { cmd: "toggleWarnings", shouldDismissPopover: false },
-  { cmd: "toggleAssemblyPieces", shouldDismissPopover: false },
-  { cmd: "toggleLineageAnnotations", shouldDismissPopover: false },
-  //deprecating
-  //{ cmd: "toggleFeatures", shouldDismissPopover: false },
-  {
-    cmd: "toggleFeatures",
-    // onClick: () => {}, //commenting this out to allow top level clicking -- https://github.com/TeselaGen/openVectorEditor/issues/865)
-    shouldDismissPopover: false,
-    submenu: featuresSubmenu
-  },
-  {
-    cmd: "toggleTranslations",
-    // onClick: () => {}, //commenting this out to allow top level clicking -- https://github.com/TeselaGen/openVectorEditor/issues/865)
-    shouldDismissPopover: false,
-    submenu: translationsSubmenu
-  },
-  { cmd: "togglePrimers", shouldDismissPopover: false },
-  // {
-  //   // TODO preprocess this as needed
-  //   cmd: "featureTypes",
-  //   itemId: "featureTypes",
-  //   //submenu of checklist of all feature types here
-  //   submenu: [{ text: "TO DO...", disabled: true }]
-  // },
-  {
-    cmd: "togglePartsWithSubmenu",
-    // onClick: () => {}, //commenting this out to allow top level clicking -- https://github.com/TeselaGen/openVectorEditor/issues/865)
-    shouldDismissPopover: false
-  },
-  { cmd: "toggleCutsites", shouldDismissPopover: false },
-  // TODO translations, cds feature translations?
-  {
-    cmd: "toggleOrfs",
-    // onClick: () => {}, //commenting this out to allow top level clicking -- https://github.com/TeselaGen/openVectorEditor/issues/865)
-    shouldDismissPopover: false,
-    submenu: orfsSubmenu
-  },
-  // { cmd: "complementary" },
-  // { cmd: "spaces" },
-  { divider: "" },
-  {
-    cmd: "toggleShowGCContent",
-    shouldDismissPopover: false,
-    text: "Percent GC Content of Selection"
-  },
-  {
-    text: "Melting Temp of Selection",
-    component: ToggleShowMeltingTemp
-  },
-  { divider: "" },
-  fullSequenceTranslationMenu,
-  { divider: "" },
-
-  { cmd: "toggleAxis", shouldDismissPopover: false },
-  { cmd: "toggleAxisNumbers", shouldDismissPopover: false },
-  {
-    cmd: "toggleAminoAcidNumbers_protein",
-    shouldDismissPopover: false
-  },
-  {
-    text: "Amino Acid Colors (by Hydrophobicity/by Family)",
-    component: function AAColorType(props) {
-      const [aaColorType, setAAColorType] = useAAColorType();
-      return (
-        <MenuItem
-          {...props}
-          text="Amino Acid Colors"
-          shouldDismissPopover={false}
-        >
-          <MenuItem
-            {...props}
-            text={
-              <div style={{ display: "flex" }}>
-                <span style={{ marginRight: 10 }}>Color By Hydrophobicity</span>
-                <InfoHelper
-                  content={
-                    <div style={{ color: "white" }}>
-                      <div
-                        style={{
-                          padding: 2,
-                          backgroundColor: "hsl(258.1, 100%, 69%)"
-                        }}
-                      >
-                        More Hydrophilic (4.5)
-                      </div>
-                      <div
-                        style={{
-                          padding: 2,
-                          backgroundColor: "hsl(356.9, 100%, 69%)"
-                        }}
-                      >
-                        More Hydrophobic (-4.5)
-                      </div>
-                    </div>
-                  }
-                ></InfoHelper>
-              </div>
-            }
-            shouldDismissPopover={false}
-            onClick={() => {
-              setAAColorType("byHydrophobicity");
-            }}
-            icon={aaColorType === "byHydrophobicity" ? "small-tick" : "blank"}
-          ></MenuItem>
-          <MenuItem
-            {...props}
-            text={
-              <div style={{ display: "flex" }}>
-                <span style={{ marginRight: 10 }}>Color By Family</span>
-                <InfoHelper
-                  content={
-                    <div style={{ color: "black" }}>
-                      <div style={{ padding: 2, backgroundColor: "#FFC0CB" }}>
-                        Positive: K, H, R
-                      </div>
-                      <div style={{ padding: 2, backgroundColor: "#EE82EE" }}>
-                        Negative: D, E
-                      </div>
-                      <div style={{ padding: 2, backgroundColor: "#D3D3D3" }}>
-                        Amidic: N, Q
-                      </div>
-                      <div style={{ padding: 2, backgroundColor: "#00FFFF" }}>
-                        Aliphatic: A, G, L, I, P, V
-                      </div>
-                      <div style={{ padding: 2, backgroundColor: "#FFA500" }}>
-                        Aromatic: F, W, Y
-                      </div>
-                      <div style={{ padding: 2, backgroundColor: "#FFFF00" }}>
-                        Sulfur: C, M
-                      </div>
-                      <div style={{ padding: 2, backgroundColor: "#90EE90" }}>
-                        Hydroxylic: S, T
-                      </div>
-                    </div>
-                  }
-                ></InfoHelper>
-              </div>
-            }
-            shouldDismissPopover={false}
-            onClick={() => {
-              setAAColorType("byFamily");
-            }}
-            icon={aaColorType === "byFamily" ? "small-tick" : "blank"}
-          ></MenuItem>
-        </MenuItem>
-      );
-    },
-    shouldDismissPopover: false
-  },
-  { cmd: "toggleDnaColors", shouldDismissPopover: false },
-  {
-    text: "Sequence",
-    submenu: [
-      { cmd: "toggleSequence", shouldDismissPopover: false },
-      { cmd: "toggleFivePrimeThreePrimeHints", shouldDismissPopover: false },
-      { cmd: "toggleReverseSequence", shouldDismissPopover: false },
-
-      {
-        text: "Case",
-        cmd: "sequenceCase",
-        submenu: [
-          {
-            cmd: "toggleSequenceMapFontUpper",
-            text: "Upper Case",
-            shouldDismissPopover: false
-          },
-          {
-            cmd: "toggleSequenceMapFontRaw",
-            text: "No Preference",
-            shouldDismissPopover: false
-          },
-          {
-            cmd: "toggleSequenceMapFontLower",
-            text: "Lower Case",
-            shouldDismissPopover: false
-          }
-        ]
-      },
-      {
-        cmd: "setRowViewSequenceSpacing",
-        shouldDismissPopover: false
-      }
-    ]
-  },
-
-  { divider: "" },
-  {
-    text: "Limits",
-    cmd: "limitsMenu",
-    submenu: [
-      {
-        text: "Max Features To Show",
-        component: LimitAnnotations,
-        type: "features"
-      },
-      {
-        text: "Max Parts To Show",
-        type: "parts",
-        component: LimitAnnotations
-      },
-      {
-        text: "Max Cut Sites To Show",
-        component: LimitAnnotations,
-        type: "cutsites"
-      },
-      {
-        text: "Max Primers To Show",
-        component: LimitAnnotations,
-        type: "primers"
-      },
-      {
-        text: "Max Warnings To Show",
-        component: LimitAnnotations,
-        type: "warnings"
-      },
-      {
-        text: "Max Assembly Pieces To Show",
-        component: LimitAnnotations,
-        type: "assemblyPieces"
-      },
-      {
-        text: "Max Lineage Annotations To Show",
-        component: LimitAnnotations,
-        type: "lineageAnnotations"
-      }
-    ]
-  },
-  {
-    text: "Labels",
-    submenu: [
-      { divider: "External Labels:" },
-      {
-        text: "Show All",
-        hiddenButSearchableText: "labels",
-        cmd: "showAllLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Hide All",
-        hiddenButSearchableText: "labels",
-        cmd: "hideAllLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Features",
-        hiddenButSearchableText: "labels",
-        cmd: "toggleFeatureLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Parts",
-        hiddenButSearchableText: "labels",
-        cmd: "togglePartLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Cutsites",
-        hiddenButSearchableText: "labels",
-        cmd: "toggleCutsiteLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Assembly Pieces",
-        hiddenButSearchableText: "labels",
-        cmd: "toggleAssemblyPieceLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "LineageAnnotations",
-        hiddenButSearchableText: "labels",
-        cmd: "toggleLineageAnnotationLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Warnings",
-        hiddenButSearchableText: "labels",
-        cmd: "toggleWarningLabels",
-        shouldDismissPopover: false
-      },
-      {
-        text: "Primers",
-        hiddenButSearchableText: "labels",
-        cmd: "togglePrimerLabels",
-        shouldDismissPopover: false
-      },
-
-      { divider: "" },
-
-      { cmd: "adjustLabelLineIntensity", shouldDismissPopover: false },
-      { cmd: "adjustLabelSize", shouldDismissPopover: false }
-    ]
-  }
-];
-
-function ToggleShowMeltingTemp(props) {
-  const [showMeltingTemp, setShowMeltingTemp] = useMeltingTemp();
-  return (
-    <MenuItem
-      {...props}
-      shouldDismissPopover={false}
-      onClick={() => {
-        setShowMeltingTemp(!showMeltingTemp);
-      }}
-      icon={showMeltingTemp ? "small-tick" : "blank"}
-    ></MenuItem>
-  );
-}

package/visibilityTool.js

@@ -1,39 +0,0 @@
-import { Icon, Menu } from "@blueprintjs/core";
-import React from "react";
-import { createCommandMenu } from "@teselagen/ui";
-import viewSubmenu from "../MenuBar/viewSubmenu";
-import getCommands from "../commands";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-import withEditorProps from "../withEditorProps";
-
-export default connectToEditor(({ toolBar = {} }) => {
-  return {
-    isOpen: toolBar.openItem === "visibilityTool"
-  };
-})(({ toolbarItemProps, isOpen }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon icon="eye-open" />,
-        onIconClick: "toggleDropdown",
-        Dropdown: VisibilityOptions,
-        noDropdownIcon: true,
-        toggled: isOpen,
-        tooltip: isOpen ? "Hide Visibility Options" : "Show Visibility Options",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});
-
-const VisibilityOptions = withEditorProps(function (props) {
-  return (
-    <Menu>
-      {createCommandMenu(viewSubmenu, getCommands({ props }), {
-        useTicks: true,
-        omitIcons: true
-      })}
-    </Menu>
-  );
-});