@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/undoTool.js

@@ -1,30 +0,0 @@
-import React from "react";
-import { Icon } from "@blueprintjs/core";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-
-export default connectToEditor(editorState => {
-  return {
-    disabled: !(
-      editorState.sequenceDataHistory &&
-      editorState.sequenceDataHistory.past &&
-      editorState.sequenceDataHistory.past.length
-    )
-  };
-})(({ toolbarItemProps, undo, disabled }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon data-test="veUndoTool" icon="undo" />,
-        disabled,
-        onIconClick: undo,
-        tooltip: (
-          <span>
-            Undo <span style={{ fontSize: 10 }}>(Cmd/Ctrl+Z)</span>
-          </span>
-        ),
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/updateEditor.js

@@ -1,200 +0,0 @@
-import { set } from "lodash-es";
-import { tidyUpSequenceData } from "@teselagen/sequence-utils";
-import { annotationTypes } from "@teselagen/sequence-utils";
-
-export default function updateEditor(
-  store,
-  editorName,
-  initialValues = {},
-  extraMeta = {},
-  { convertAnnotationsFromAAIndices } = {}
-) {
-  const {
-    sequenceData,
-    annotationVisibility,
-    annotationsToSupport,
-    findTool,
-    justPassingPartialSeqData
-  } = initialValues;
-  const currentEditor = store.getState().VectorEditor[editorName] || {};
-  const isAlreadyProteinEditor =
-    currentEditor.sequenceData && currentEditor.sequenceData.isProtein;
-  const isAlreadyRnaEditor =
-    currentEditor.sequenceData && currentEditor.sequenceData.isRna;
-  const isAlreadyOligoEditor =
-    currentEditor.sequenceData && currentEditor.sequenceData.isOligo;
-  const reverseSequenceShouldBeUpdate =
-    currentEditor.sequenceData?.isSingleStrandedDNA !==
-      sequenceData?.isSingleStrandedDNA ||
-    currentEditor.sequenceData?.isDoubleStrandedRNA !==
-      sequenceData?.isDoubleStrandedRNA;
-
-  const isAlreadySpecialEditor =
-    isAlreadyProteinEditor ||
-    isAlreadyRnaEditor ||
-    isAlreadyOligoEditor ||
-    reverseSequenceShouldBeUpdate;
-
-  let toSpread = {};
-  let payload;
-  if (justPassingPartialSeqData) {
-    payload = {
-      sequenceData: tidyUpSequenceData(
-        { ...currentEditor.sequenceData, ...sequenceData },
-        {
-          convertAnnotationsFromAAIndices,
-          //if we have sequence data coming in make sure to tidy it up for the user :)
-          annotationsAsObjects: true
-        }
-      )
-    };
-  } else {
-    if (sequenceData) {
-      const isDna =
-        !sequenceData.isOligo && !sequenceData.isRna && !sequenceData.isProtein;
-      if (sequenceData.isProtein && !isAlreadyProteinEditor) {
-        //we're editing a protein but haven't initialized the protein editor yet
-        toSpread = {
-          findTool: {
-            dnaOrAA: "AA",
-            ...findTool //we spread this here to allow the user to override this .. if they must!
-          },
-
-          annotationVisibility: {
-            caret: true,
-            sequence: false,
-            reverseSequence: false,
-            cutsites: false,
-            translations: false,
-            aminoAcidNumbers: false,
-            primaryProteinSequence: true,
-            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationsToSupport: {
-            features: true,
-            translations: false,
-            primaryProteinSequence: true,
-            parts: true,
-            orfs: false,
-            cutsites: false,
-            primers: false,
-            ...annotationsToSupport
-          }
-        };
-      } else if (sequenceData.isOligo && !isAlreadyOligoEditor) {
-        toSpread = {
-          findTool: {
-            dnaOrAA: "DNA",
-            ...findTool //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationVisibility: {
-            caret: true,
-            sequence: true,
-            cutsites: false,
-            reverseSequence: false,
-            translations: false,
-            aminoAcidNumbers: false,
-            primaryProteinSequence: false,
-            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationsToSupport: {
-            features: true,
-            translations: true,
-            primaryProteinSequence: false,
-            parts: true,
-            orfs: false,
-            cutsites: true,
-            primers: false,
-            ...annotationsToSupport //we spread this here to allow the user to override this .. if they must!
-          }
-        };
-      } else if (sequenceData.isRna && !isAlreadyRnaEditor) {
-        toSpread = {
-          findTool: {
-            dnaOrAA: "DNA",
-            ...findTool //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationVisibility: {
-            caret: true,
-            sequence: true,
-            cutsites: false,
-            reverseSequence: Boolean(sequenceData?.isDoubleStrandedRNA),
-            translations: false,
-            aminoAcidNumbers: false,
-            primaryProteinSequence: false,
-            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationsToSupport: {
-            features: true,
-            translations: true,
-            primaryProteinSequence: false,
-            parts: true,
-            orfs: true,
-            cutsites: true,
-            primers: true,
-            ...annotationsToSupport //we spread this here to allow the user to override this .. if they must!
-          }
-        };
-      } else if (isAlreadySpecialEditor && isDna) {
-        //we're editing dna but haven't initialized the dna editor yet
-        sequenceData.isProtein = false;
-        toSpread = {
-          findTool: {
-            dnaOrAA: "DNA",
-            ...findTool //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationVisibility: {
-            caret: true,
-            sequence: true,
-            reverseSequence: !sequenceData?.isSingleStrandedDNA,
-            translations: false,
-            aminoAcidNumbers: false,
-            primaryProteinSequence: false,
-            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
-          },
-          annotationsToSupport: {
-            features: true,
-            translations: true,
-            primaryProteinSequence: false,
-            parts: true,
-            orfs: true,
-            cutsites: true,
-            primers: true,
-            ...annotationsToSupport //we spread this here to allow the user to override this .. if they must!
-          }
-        };
-      }
-    }
-    payload = {
-      ...initialValues,
-      ...toSpread,
-      ...(sequenceData && {
-        sequenceData: tidyUpSequenceData(sequenceData, {
-          convertAnnotationsFromAAIndices,
-          //if we have sequence data coming in make sure to tidy it up for the user :)
-          annotationsAsObjects: true
-        })
-      })
-    };
-  }
-  annotationTypes.forEach(t => {
-    if (Object.keys(sequenceData?.[t] || {}).length > 100) {
-      set(payload, `annotationLabelVisibility.${t}`, false);
-    }
-  });
-  if (sequenceData && sequenceData.size > 20000) {
-    set(payload, "annotationVisibility.translations", false);
-    set(payload, "annotationVisibility.cutsites", false);
-  }
-
-  store.dispatch({
-    type: "VECTOR_EDITOR_UPDATE",
-    payload,
-    meta: {
-      mergeStateDeep: true,
-      editorName,
-      disregardUndo: true,
-      ...extraMeta
-    }
-  });
-}

package/updateLabelsForInViewFeatures.js

@@ -1,55 +0,0 @@
-import {
-  isElWithinAnotherEl,
-  isElWithinAnotherElWithDiff
-} from "../withEditorInteractions/isElementInViewport";
-
-export function updateLabelsForInViewFeatures({
-  rectElement = ".veLinearView"
-} = {}) {
-  const feats = Array.from(
-    document.querySelectorAll(`.veLinearView .veRowViewFeature`)
-  );
-  const parts = Array.from(
-    document.querySelectorAll(`.veLinearView .veRowViewPart`)
-  );
-  const primers = Array.from(
-    document.querySelectorAll(`.veLinearView .veRowViewPrimer`)
-  );
-  const els = [...feats, ...parts, ...primers];
-  const boundingRect = document
-    .querySelector(rectElement)
-    .getBoundingClientRect();
-
-  els.forEach(el => {
-    const elBounds = el.getBoundingClientRect();
-    const isElIn = isElWithinAnotherEl(elBounds, boundingRect);
-
-    if (isElIn) {
-      const label = el.querySelector(".veLabelText");
-      if (!label) return;
-      const labelBounds = label.getBoundingClientRect();
-      const [isLabelIn, diff] = isElWithinAnotherElWithDiff(labelBounds, {
-        left: Math.max(boundingRect.left, elBounds.left),
-        right: Math.min(boundingRect.right, elBounds.right)
-      });
-      if (!isLabelIn) {
-        const l = window.getComputedStyle(label, null),
-          t = l.getPropertyValue("transform");
-
-        // If t return other than "none"
-        // Split content into several value
-        // The fourth one is the translateX value
-
-        if (t !== "none") {
-          const v = t.split("(")[1],
-            // w = v.split(")")[0],
-            x = v.split(",");
-
-          const newX = Number(x[4]) + diff;
-          const newY = Number(x[5].replace(")", ""));
-          label.setAttribute("transform", `translate(${newX},${newY})`);
-        }
-      }
-    }
-  });
-}

package/updateLabelsForInViewFeaturesCircView.js

@@ -1,41 +0,0 @@
-// import {
-//   isElWithinAnotherEl,
-//   isElWithinAnotherElWithDiff
-// } from "../withEditorInteractions/isElementInViewport";
-
-// export function updateLabelsForInViewFeaturesCircView({
-//   rectElement = ".veCircularView",
-//   radius
-// } = {}) {
-//   const feats = Array.from(
-//     document.querySelectorAll(`.veCircularView .veFeature`)
-//   );
-//   // const parts = Array.from(
-//   //   document.querySelectorAll(`.veCircularView .vePart`)
-//   // );
-//   // const primers = Array.from(
-//   //   document.querySelectorAll(`.veCircularView .vePrimer`)
-//   // );
-//   const els = [...feats];
-//   // const els = [...feats, ...parts, ...primers];
-//   const boundingRect = document
-//     .querySelector(rectElement)
-//     .getBoundingClientRect();
-//   els.forEach((el) => {
-//     // const elBounds = el.getBoundingClientRect();
-//     // const isElIn = isElWithinAnotherEl(elBounds, boundingRect);
-//     const label = el.querySelector(".veLabelText");
-//     if (!label) return;
-//     const labelBounds = label.getBoundingClientRect();
-//     const [isLabelIn, diff] = isElWithinAnotherElWithDiff(labelBounds, {
-//       left: Math.max(boundingRect.left, 0 /*  elBounds.left */),
-//       right: Math.min(boundingRect.right, 0 /*  elBounds.right */)
-//     });
-//     if (!isLabelIn) {
-//       label.setAttribute("transform", `rotate(-40)`);
-//     }
-//     // if (isElIn) {
-
-//     // }
-//   });
-// }

package/updateTrackHelper.js

@@ -1,58 +0,0 @@
-import { insertItem, removeItem } from "../utils/arrayUtils";
-
-export function updateTrackHelper({
-  currentPairwiseAlignmentIndex,
-  pairwiseAlignments,
-  upsertAlignmentRun,
-  hasBeenTrimmed,
-  alignmentId,
-  alignmentTracks,
-  alignmentTrackIndex,
-  update
-}) {
-  const updateATs = (atsToUse, alignmentTrackIndex) => {
-    const removed = removeItem(atsToUse, alignmentTrackIndex);
-    return insertItem(
-      removed,
-      {
-        ...atsToUse[alignmentTrackIndex],
-        alignmentData: {
-          ...atsToUse[alignmentTrackIndex].alignmentData,
-          ...update
-        },
-        sequenceData: {
-          ...atsToUse[alignmentTrackIndex].sequenceData,
-          ...update
-        }
-      },
-      alignmentTrackIndex
-    );
-  };
-
-  upsertAlignmentRun({
-    id: alignmentId,
-    hasBeenTrimmed,
-    ...(pairwiseAlignments
-      ? {
-          pairwiseAlignments: pairwiseAlignments.map((ats, i) => {
-            if (alignmentTrackIndex === 0) {
-              return updateATs(ats, 0);
-            }
-            if (
-              currentPairwiseAlignmentIndex !== undefined
-                ? currentPairwiseAlignmentIndex === i
-                : alignmentTrackIndex - 1 === i
-            ) {
-              return updateATs(ats, 1);
-            }
-            return ats;
-          })
-        }
-      : {
-          alignmentTracks: updateATs(
-            alignmentTracks,
-            Number(alignmentTrackIndex)
-          )
-        })
-  });
-}

package/uppercaseSequenceMapFont.js

@@ -1,25 +0,0 @@
-import { createReducer } from "redux-act";
-
-//./caretPosition.js
-import createAction from "./utils/createMetaAction";
-// import createReducer from "./utils/createMergedDefaultStateReducer";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const updateSequenceCase = createAction("updateSequenceCase");
-
-const newVal = window.localStorage.getItem("uppercaseSequenceMapFont");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [updateSequenceCase]: (state, payload) => {
-      localStorage.setItem("uppercaseSequenceMapFont", payload);
-      return payload;
-    }
-  },
-  newVal || "noPreference" //  noPreference || uppercase || lowercase
-);

package/upsertDeleteActionGenerator.js

@@ -1,31 +0,0 @@
-import omit from "lodash/omit";
-import uuid from "shortid";
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default function upsertDeleteActionGenerator(
-  upsertAction,
-  deleteAction
-) {
-  return {
-    [upsertAction]: (state, payload) => {
-      const idToUse = payload.id || uuid();
-      return {
-        ...state,
-        [idToUse]: { ...(state[idToUse] || {}), ...payload, id: idToUse }
-      };
-    },
-    [deleteAction]: (state, payload) => {
-      let ids;
-      if (Array.isArray(payload)) {
-        ids = payload.map(val => {
-          return val.id || val;
-        });
-      } else {
-        ids = [payload.id || payload];
-      }
-      return omit(state, ids);
-    }
-  };
-}

package/useAAColorType.js

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

package/useAdditionalOrfStartCodons.js

@@ -1,24 +0,0 @@
-//./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

@@ -1,42 +0,0 @@
-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

@@ -1,31 +0,0 @@
-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

@@ -1,7 +0,0 @@
-/* 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

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

package/useMeltingTemp.js

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

package/useTmType.js

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

package/userDefinedHandlersAndOpts.js

@@ -1,61 +0,0 @@
-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.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>
-    );
-  }
-});