@teselagen/ove 0.7.26 → 0.7.28

package/useAAColorType.js

@@ -0,0 +1,8 @@
+import tgUseLocalStorageState from "tg-use-local-storage-state";
+
+const useAAColorType = () =>
+  tgUseLocalStorageState("aaColorType", {
+    isSimpleString: true,
+    defaultValue: "byHydrophobicity"
+  });
+export default useAAColorType;

package/useAdditionalOrfStartCodons.js

@@ -0,0 +1,24 @@
+//./caretPosition.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import { noop } from "lodash-es";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const useAdditionalOrfStartCodonsToggle = createAction(
+  "useAdditionalOrfStartCodonsToggle",
+  noop
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [useAdditionalOrfStartCodonsToggle]: state => {
+      return !state;
+    }
+  },
+  false
+);

package/useAnnotationLimits.js

@@ -0,0 +1,42 @@
+import React from "react";
+import { MenuItem } from "@blueprintjs/core";
+import tgUseLocalStorageState from "tg-use-local-storage-state";
+
+const useAnnotationLimits = () =>
+  tgUseLocalStorageState("annotationLimits", {
+    defaultValue: {
+      features: 50,
+      parts: 50,
+      primers: 50,
+      warnings: 50,
+      assemblyPieces: 50,
+      lineageAnnotations: 50,
+      cutsites: 100
+    }
+  });
+export default useAnnotationLimits;
+
+export function LimitAnnotations({ type, ...rest }) {
+  const [limits = {}, setLimits] = useAnnotationLimits();
+  return (
+    <MenuItem icon="blank" shouldDismissPopover={false} {...rest}>
+      {[50, 100, 200, 400].map(n => (
+        <MenuItem
+          shouldDismissPopover={false}
+          icon={
+            (
+              !limits[type]
+                ? n === 50 //if this hasn't been set yet, default it here
+                : limits[type] === n
+            )
+              ? "small-tick"
+              : "blank"
+          }
+          key={n}
+          text={n}
+          onClick={() => setLimits({ ...limits, [type]: n })}
+        ></MenuItem>
+      ))}
+    </MenuItem>
+  );
+}

package/useChromatogramPrefs.js

@@ -0,0 +1,31 @@
+import React from "react";
+import { MenuItem } from "@blueprintjs/core";
+import tgUseLocalStorageState from "tg-use-local-storage-state";
+
+const useShowChromQualScores = () => {
+  return tgUseLocalStorageState("showChromQualScores", { defaultValue: true });
+};
+
+const ShowChromQualScoresMenu = () =>
+  function ShowChromQualScoresMenu(props) {
+    const [showChromQualScores, setShowChromQualScores] =
+      useShowChromQualScores();
+    return (
+      <MenuItem
+        {...props}
+        text="Show Quality Scores"
+        shouldDismissPopover={false}
+        onClick={() => {
+          setShowChromQualScores(!showChromQualScores);
+        }}
+        icon={showChromQualScores ? "small-tick" : "blank"}
+      ></MenuItem>
+    );
+  };
+const chromatogramMenu = {
+  text: "Chromatogram (Quality Scores)",
+  cmd: "showChromQualScoresMenu",
+  component: ShowChromQualScoresMenu(),
+  shouldDismissPopover: false
+};
+export { chromatogramMenu, useShowChromQualScores };

package/useFormValue.js

@@ -0,0 +1,7 @@
+/* Copyright (C) 2018 TeselaGen Biotechnology, Inc. */
+import { useSelector } from "react-redux";
+import { get } from "lodash";
+
+export const useFormValue = (formName, field) => {
+  return useSelector(state => get(state.form?.[formName]?.values, field));
+};

package/useLadders.js

@@ -0,0 +1,6 @@
+import tgUseLocalStorageState from "tg-use-local-storage-state";
+
+const useLadders = () => {
+  return tgUseLocalStorageState("tg-additional-ladder", { defaultValue: [] });
+};
+export default useLadders;

package/useMeltingTemp.js

@@ -0,0 +1,7 @@
+import tgUseLocalStorageState from "tg-use-local-storage-state";
+
+const useMeltingTemp = () => {
+  return tgUseLocalStorageState("showMeltingTemp");
+};
+
+export default useMeltingTemp;

package/useTmType.js

@@ -0,0 +1,10 @@
+import tgUseLocalStorageState from "tg-use-local-storage-state";
+
+const useTmType = () => {
+  return tgUseLocalStorageState("tmType", {
+    isSimpleString: true,
+    defaultValue: "default"
+  });
+};
+
+export default useTmType;

package/userDefinedHandlersAndOpts.js

@@ -0,0 +1,61 @@
+export const userDefinedHandlersAndOpts = [
+  "beforeReadOnlyChange",
+  "defaultLinkedOligoMessage",
+  "allowMultipleFeatureDirections",
+  "getAdditionalEditAnnotationComps",
+  "getAdditionalCreateOpts",
+  "getLinkedOligoLink",
+  "additionalTopRightToolbarButtons",
+  "getCustomAutoAnnotateList",
+  "allowPartsToOverlapSelf",
+  "allowPrimerBasesToBeEdited",
+  "truncateLabelsThatDoNotFit",
+  "smartCircViewLabelRender",
+  "onConfigureFeatureTypesClick",
+  "allPartTags",
+  "bpLimit",
+  "editTagsLink",
+  "readOnly",
+  "shouldAutosave",
+  "hideSingleImport",
+  "beforeAnnotationCreate",
+  "disableSetReadOnly",
+  "allowAnnotationEditLocking",
+  "disableBpEditing",
+  "massageCmds",
+  "showReadOnly",
+  "showCircularity",
+  "onHiddenEnzymeAdd",
+  "showMoleculeType",
+  "showAvailability",
+  "showCicularViewInternalLabels",
+  "showGCContentByDefault",
+  "GCDecimalDigits",
+  "onlyShowLabelsThatDoNotFit",
+  "fullscreenMode",
+  "maxAnnotationsToDisplay",
+  "onNew",
+  "onImport",
+  "onSave",
+  "onSaveAs",
+  "alwaysAllowSave",
+  "generatePng",
+  "onRename",
+  "getVersionList",
+  "getSequenceAtVersion",
+  "onDuplicate",
+  "onSelectionOrCaretChanged",
+  "beforeSequenceInsertOrDelete",
+  "enzymeManageOverride",
+  "enzymeGroupsOverride",
+  "additionalEnzymes",
+  "onDelete",
+  "onCopy",
+  "autoAnnotateFeatures",
+  "autoAnnotateParts",
+  "autoAnnotatePrimers",
+  "onCreateNewFromSubsequence",
+  "onPreviewModeFullscreenClose",
+  "onPaste",
+  "menuFilter"
+];

package/utils/getAnnotationNameAndStartStopString.d.ts

@@ -7,8 +7,4 @@ export default function getAnnotationNameAndStartStopString({ name, start, end,
     annotationTypePlural: any;
     overlapsSelf: any;
     isWrappedAddon: any;
-}, { startText, isProtein, readOnly }?: {
-    startText: any;
-    isProtein: any;
-    readOnly: any;
-}): string;
+}, { startText, isProtein, readOnly }?: {}): string;

package/utils/selectionLayer.d.ts

@@ -1,5 +1,5 @@
 export function getAllSelectionLayers({ additionalSelectionLayers, searchLayers, selectionLayer }: {
-    additionalSelectionLayers?: any[] | undefined;
-    searchLayers?: any[] | undefined;
+    additionalSelectionLayers?: never[] | undefined;
+    searchLayers?: never[] | undefined;
     selectionLayer: any;
 }): any[];

package/utils.js

@@ -0,0 +1,37 @@
+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

@@ -0,0 +1,26 @@
+//./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

@@ -0,0 +1,21 @@
+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
+      }}
+    />
+  );
+});