@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/editorUtils.js

@@ -1,205 +0,0 @@
-import { getRangeLength, getSequenceWithinRange } from "@teselagen/range-utils";
-import React from "react";
-import { divideBy3 } from "./proteinUtils";
-import {
-  getInsertBetweenVals,
-  calculatePercentGC,
-  aliasedEnzymesByName
-} from "@teselagen/sequence-utils";
-import { get, sortBy } from "lodash-es";
-import VeWarning from "../helperComponents/VeWarning";
-import { normalizePositionByRangeLength } from "@teselagen/range-utils";
-import { filter } from "lodash-es";
-
-export function getSelectionMessage({
-  caretPosition = -1,
-  selectionLayer = { start: -1, end: -1 },
-  customTitle,
-  sequenceLength,
-  sequenceData,
-  showGCContent, //these are only passed in for the status bar
-  GCDecimalDigits, //these are only passed in for the status bar
-  isProtein
-}) {
-  let _selectionLayer = selectionLayer;
-  const isSelecting = selectionLayer.start > -1;
-  if (isSelecting) {
-    _selectionLayer = getSelFromWrappedAddon(selectionLayer, sequenceLength);
-    const length = getRangeLength(_selectionLayer, sequenceLength);
-    const GCContent = (numDecimalDigits = 0) =>
-      calculatePercentGC(
-        getSequenceWithinRange(_selectionLayer, sequenceData.sequence)
-      ).toFixed(numDecimalDigits);
-    const seqLen = divideBy3(length, isProtein);
-    return `${customTitle || "Selecting"} ${seqLen} ${
-      (isProtein ? "AA" : "bp") + (seqLen === 1 ? "" : "s")
-    } from ${divideBy3(_selectionLayer.start, isProtein) + 1} to ${divideBy3(
-      _selectionLayer.end + 1,
-      isProtein
-    )}${
-      showGCContent && !isProtein ? ` (${GCContent(GCDecimalDigits)}% GC)` : ""
-    }`;
-  } else if (caretPosition > -1) {
-    const insertBetween = getInsertBetweenVals(
-      caretPosition,
-      _selectionLayer,
-      sequenceLength
-    );
-    return (
-      `Caret Between ` +
-      (isProtein
-        ? `AAs ${divideBy3(insertBetween[0], true)} and ${divideBy3(
-            insertBetween[1] + 2,
-            true
-          )}`
-        : `Bases ${insertBetween[0]} and ${insertBetween[1]}`)
-    );
-  } else {
-    return "No Selection";
-  }
-}
-
-export function preventDefaultStopPropagation(e) {
-  if (e) {
-    e.stopPropagation();
-    e.preventDefault();
-  }
-}
-
-export function getNodeToRefocus(caretEl) {
-  let nodeToReFocus;
-  if (
-    caretEl &&
-    caretEl.closest &&
-    caretEl.closest(".veVectorInteractionWrapper")
-  ) {
-    nodeToReFocus = caretEl.closest(".veVectorInteractionWrapper");
-  }
-  return nodeToReFocus;
-}
-
-export function getEmptyText({ sequenceData, caretPosition }) {
-  return sequenceData.sequence.length === 0 && caretPosition === -1 ? (
-    <div className="veEmptySeqText">Insert Sequence Here</div>
-  ) : null;
-}
-
-export function tryToRefocusEditor() {
-  const ed = document.querySelector(".veVectorInteractionWrapper");
-  ed && ed.focus();
-}
-export function getCustomEnzymes() {
-  try {
-    const customEnzymes = JSON.parse(
-      window.localStorage.getItem("customEnzymes") || "{}"
-    );
-    return customEnzymes;
-  } catch (error) {
-    return {};
-  }
-}
-export function addCustomEnzyme(newEnz) {
-  const customEnzymes = getCustomEnzymes();
-  window.localStorage.setItem(
-    "customEnzymes",
-    JSON.stringify({
-      ...customEnzymes,
-      [newEnz.name.toLowerCase()]: newEnz
-    })
-  );
-}
-
-export function pareDownAnnotations(annotations, max) {
-  let annotationsToPass = annotations;
-  let paredDown = false;
-  if (Object.keys(annotations).length > max) {
-    paredDown = true;
-    const sortedAnnotations = sortBy(annotations, function (annotation) {
-      return -getRangeLength(annotation);
-    });
-    annotationsToPass = sortedAnnotations.slice(0, max).reduce(function (
-      obj,
-      item
-    ) {
-      obj[item.id] = item;
-      return obj;
-    }, {});
-  }
-  return [annotationsToPass, paredDown];
-}
-export function getParedDownWarning({ nameUpper, maxToShow, isAdjustable }) {
-  return (
-    <VeWarning
-      key={`ve-warning-max${nameUpper}ToDisplay`}
-      data-test={`ve-warning-max${nameUpper}ToDisplay`}
-      tooltip={`Warning: More than ${maxToShow} ${
-        nameUpper === "Cutsites" ? "Cut Sites" : nameUpper
-      }. Only displaying ${maxToShow} ${
-        isAdjustable ? "(Configure this under View > Limits)" : ""
-      } `}
-    />
-  );
-}
-
-export function getClientX(event) {
-  return event.clientX || get(event, "touches[0].clientX");
-}
-export function getClientY(event) {
-  return event.clientY || get(event, "touches[0].clientY");
-}
-
-export function hideAnnByLengthFilter(hideOpts, ann, seqLen) {
-  const featLength = getRangeLength(ann, seqLen);
-  return (
-    hideOpts.enabled && (featLength < hideOpts.min || featLength > hideOpts.max)
-  );
-}
-
-export function getSelFromWrappedAddon(selectionLayer, sequenceLength) {
-  const selToUse = {
-    ...selectionLayer
-  };
-  if (selectionLayer.isWrappedAddon) {
-    const oldEnd = selToUse.end;
-    selToUse.end = normalizePositionByRangeLength(
-      selToUse.start - 1,
-      sequenceLength
-    );
-    selToUse.start = normalizePositionByRangeLength(oldEnd + 1, sequenceLength);
-    delete selToUse.isWrappedAddon;
-  }
-  return selToUse;
-}
-
-export function getStripedPattern({ color, id }) {
-  return (
-    <pattern
-      id={`diagonalHatch-${id}`}
-      patternUnits="userSpaceOnUse"
-      width="4"
-      height="4"
-    >
-      <path
-        d="M-1,1 l2,-2
-           M0,4 l4,-4
-           M3,5 l2,-2"
-        style={{
-          stroke: color,
-          strokeWidth: 2,
-          fill: "blue",
-          opacity: 0.4
-        }}
-      />
-    </pattern>
-  );
-}
-export const getEnzymeAliases = enzyme => {
-  let lowerName = (enzyme.name && enzyme.name.toLowerCase()) || "";
-  if (typeof enzyme === "string") {
-    lowerName = enzyme.toLowerCase();
-  }
-  return filter(
-    (aliasedEnzymesByName[lowerName] || {}).aliases,
-    n => n.toLowerCase() !== lowerName //filter out current enzyme
-  );
-};

package/estimateRowHeight.js

@@ -1,184 +0,0 @@
-import { forEach } from "lodash-es";
-
-const debug = 0;
-// const debug = console.log("comment me back out!") || 1;
-
-export const rowHeights = {
-  rowJumpButtons: { height: 30 },
-  spacer: { height: 10 },
-  aminoAcidNumbers: { height: 9 },
-  translations: { spaceBetweenAnnotations: 2, marginTop: 5, height: 17 },
-  chromatogram: { height: 134 },
-  parts: { spaceBetweenAnnotations: 2, marginTop: 5, height: 15 },
-  primers: { spaceBetweenAnnotations: 2, marginTop: 5, height: 18 },
-  features: { spaceBetweenAnnotations: 2, marginTop: 5, height: 15 },
-  warnings: { spaceBetweenAnnotations: 2, marginTop: 5, height: 15 },
-  assemblyPieces: { spaceBetweenAnnotations: 2, marginTop: 5, height: 15 },
-  lineageAnnotations: { spaceBetweenAnnotations: 2, marginTop: 5, height: 15 },
-  orfs: { spaceBetweenAnnotations: 2, marginTop: 5, height: 15 },
-  //tnrtodo -- we should estimate external label height for parts/features/primers
-  cutsiteLabels: { spaceBetweenAnnotations: 0, height: 15 },
-  sequence: { height: 15 },
-  reverseSequence: { height: 15 },
-  axis: { marginTop: 5, height: 15 }
-};
-
-rowHeights.primaryProteinSequence = rowHeights.translations;
-
-Object.keys(rowHeights).forEach(k => {
-  rowHeights[k].type = k;
-  rowHeights[k].marginTop = rowHeights[k].marginTop || 0;
-  rowHeights[k].marginBottom = rowHeights[k].marginBottom || 0;
-  rowHeights[k].spaceBetweenAnnotations =
-    rowHeights[k].spaceBetweenAnnotations || 0;
-});
-const translations = {
-  getHeight: props => {
-    if (props.annotationVisibility.aminoAcidNumbers) {
-      return [rowHeights.aminoAcidNumbers.type, rowHeights.translations.type];
-    }
-    return rowHeights.translations.type;
-  },
-  hasYOffset: true
-};
-
-const annotationsToCompute = {
-  spacer: {
-    alwaysVisible: true,
-    height: rowHeights.spacer.type
-  },
-  primaryProteinSequence: translations,
-  translations,
-  parts: {
-    height: rowHeights.parts.type,
-    hasYOffset: true
-  },
-  primers: {
-    height: rowHeights.primers.type,
-    hasYOffset: true
-  },
-  features: {
-    height: rowHeights.features.type,
-    hasYOffset: true
-  },
-  chromatogram: {
-    height: rowHeights.chromatogram.type
-  },
-  warnings: {
-    height: rowHeights.warnings.type,
-    hasYOffset: true
-  },
-  orfs: {
-    height: rowHeights.orfs.type,
-    hasYOffset: true
-  },
-  sequence: {
-    height: rowHeights.sequence.type
-  },
-  reverseSequence: {
-    height: rowHeights.reverseSequence.type
-  },
-  axis: {
-    height: rowHeights.axis.type
-  },
-  cutsiteLabels: {
-    typeOverride: "cutsites",
-    height: rowHeights.cutsiteLabels.type,
-    hasYOffset: true
-  }
-};
-
-export default props => {
-  let {
-    index,
-    cache,
-    clearCache,
-    chromatogramData,
-    rowCount,
-    row,
-    showJumpButtons,
-    annotationVisibility
-  } = props;
-  if (clearCache) {
-    cache = {};
-  }
-
-  if (cache[index]) {
-    return cache[index];
-  }
-  if (!row) return 0;
-  let totalHeight = 0; //account for spacer
-  if (showJumpButtons && (index === 0 || index === rowCount - 1)) {
-    totalHeight += rowHeights.rowJumpButtons.height;
-  }
-  forEach(
-    annotationsToCompute,
-    (
-      { height: _height, alwaysVisible, getHeight, hasYOffset, typeOverride },
-      key
-    ) => {
-      const shouldShow =
-        alwaysVisible || annotationVisibility[typeOverride || key];
-      if (!shouldShow) return;
-      if (key === "chromatogram" && !chromatogramData) return;
-      const heightKeys = getHeight ? getHeight(props) : _height;
-      const [annotationHeight, marginHeight] = getSummedHeights(
-        heightKeys,
-        props
-      );
-
-      let heightToAdd = annotationHeight;
-      if (hasYOffset) {
-        const annotations = row[typeOverride || key];
-        if (hasYOffset) {
-          let maxYOffset = 0;
-          annotations &&
-            annotations.forEach(a => {
-              if (a.yOffset + 1 > maxYOffset) maxYOffset = a.yOffset + 1;
-            });
-          heightToAdd = maxYOffset * annotationHeight;
-        }
-      }
-      if (heightToAdd > 0) heightToAdd += marginHeight;
-
-      if (debug) {
-        heightToAdd !== 0 &&
-          console.info(`heightToAdd, key:`, heightToAdd, key);
-      }
-      totalHeight += heightToAdd;
-    }
-  );
-  if (debug) {
-    console.info(`totalHeight:`, totalHeight);
-  }
-  if (annotationVisibility.compactNames) {
-    totalHeight = Math.max(totalHeight, 31);
-  }
-  cache[index] = totalHeight;
-  return totalHeight;
-};
-
-function getHeights(heightKey, props) {
-  const annotationHeight = !heightKey
-    ? 0
-    : props[heightKey + "Height"] || (rowHeights[heightKey] || {}).height || 0;
-
-  const marginHeight =
-    (props[heightKey + "MarginTop"] ||
-      (rowHeights[heightKey] || {}).marginTop ||
-      0) +
-    (props[heightKey + "MarginBottom"] ||
-      (rowHeights[heightKey] || {}).marginBottom ||
-      0);
-  return [annotationHeight, marginHeight];
-}
-function getSummedHeights(heightKeys, props) {
-  let height = 0;
-  let marginHeight = 0;
-  (Array.isArray(heightKeys) ? heightKeys : [heightKeys]).forEach(k => {
-    const [h, m] = getHeights(k, props);
-    height += h;
-    marginHeight += m;
-  });
-  return [height, marginHeight];
-}

package/featureLengthsToHide.js

@@ -1,27 +0,0 @@
-import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const updateFeatureLengthsToHide = createAction(
-  "updateFeatureLengthsToHide"
-);
-export const toggleFeatureLengthsToHide = createAction(
-  "toggleFeatureLengthsToHide"
-);
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createMergedDefaultStateReducer(
-  {
-    [updateFeatureLengthsToHide]: (state, payload) => {
-      return { ...state, ...payload };
-    },
-    [toggleFeatureLengthsToHide]: state => {
-      return { ...state, enabled: !state["enabled"] };
-    }
-  },
-  { enabled: false, min: 0, max: 800 }
-);

package/featureTool.js

@@ -1,34 +0,0 @@
-import { Icon } from "@blueprintjs/core";
-// import { Checkbox, Button } from "@blueprintjs/core";
-import React from "react";
-// import { connect } from "react-redux";
-// import { convertRangeTo1Based } from "@teselagen/range-utils";
-import { featureIcon } from "@teselagen/ui";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-
-export default connectToEditor(
-  ({ annotationVisibility = {}, toolBar = {} }) => {
-    return {
-      toggled: annotationVisibility.features,
-      isOpen: toolBar.openItem === "featureTool"
-    };
-  }
-)(({ toolbarItemProps, toggled, annotationVisibilityToggle, isOpen }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon icon={featureIcon} />,
-        onIconClick: function () {
-          annotationVisibilityToggle("features");
-        },
-        toggled,
-        tooltip: "Show features",
-        tooltipToggled: "Hide features",
-        // Dropdown: ConnectedFeatureToolDropdown,
-        dropdowntooltip: (!isOpen ? "Show" : "Hide") + " Feature Options",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/features.js

@@ -1,19 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const upsertFeature = createAction("UPSERT_FEATURE");
-export const deleteFeature = createAction("DELETE_FEATURE");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    ...upsertDeleteActionGenerator(upsertFeature, deleteFeature)
-  },
-  {}
-);

package/featuresSelector.js

@@ -1,8 +0,0 @@
-import { createSelector } from "reselect";
-import sequenceDataSelector from "./sequenceDataSelector";
-
-function featuresRawSelector(sequenceData) {
-  return sequenceData.features;
-}
-
-export default createSelector(sequenceDataSelector, featuresRawSelector);

package/filteredCutsitesSelector.js

@@ -1,136 +0,0 @@
-import flatmap from "lodash/flatMap";
-import { createSelector } from "reselect";
-import cutsitesSelector from "./cutsitesSelector";
-import filteredRestrictionEnzymesSelector from "./filteredRestrictionEnzymesSelector";
-import specialCutsiteFilterOptions from "../constants/specialCutsiteFilterOptions";
-import { flatMap } from "lodash-es";
-import isEnzymeFilterAndSelector from "./isEnzymeFilterAndSelector";
-
-export default createSelector(
-  cutsitesSelector,
-  filteredRestrictionEnzymesSelector,
-  isEnzymeFilterAndSelector,
-  (state, addEnzs, enzymeGroupsOverride) => enzymeGroupsOverride,
-  function (
-    { cutsitesByName },
-    filteredRestrictionEnzymes,
-    isEnzymeFilterAnd,
-    enzymeGroupsOverride
-  ) {
-    const returnVal = {
-      cutsitesByName: {}
-    };
-    // const cutsitesByName = getLowerCaseObj(cutsitesByName);
-    const hiddenEnzymesByName = {};
-    let filteredEnzymes = [];
-    let enzymesFromGroups = [];
-    let hasUserGroup;
-    let groupCount = 0;
-    //handle adding enzymes that are included in user created groups
-    filteredRestrictionEnzymes.forEach(e => {
-      if (e.value.includes("__userCreatedGroup")) {
-        hasUserGroup = true;
-        const existingGroups = {
-          ...window.getExistingEnzymeGroups(),
-          ...enzymeGroupsOverride
-        };
-        const enzymes =
-          existingGroups[e.value.replace("__userCreatedGroup", "")] || [];
-        const zs = flatMap(enzymes, e => (e ? { value: e } : []));
-        filteredEnzymes = filteredEnzymes.concat(zs);
-        enzymesFromGroups = enzymesFromGroups.concat(zs);
-        groupCount += 1;
-      } else if (e.isHidden) {
-        hiddenEnzymesByName[e.value] = e;
-      } else {
-        if (!e) return;
-        groupCount += 1;
-        filteredEnzymes.push(e);
-      }
-    });
-    const cutSiteList = [];
-    if (!filteredEnzymes || (filteredEnzymes.length === 0 && !hasUserGroup)) {
-      returnVal.cutsitesByName = cutsitesByName;
-    } else {
-      //loop through each filter option ('Single Cutters', 'BamHI')
-      filteredEnzymes.forEach(function ({ value, ...rest }) {
-        if (!value) {
-          console.error(`Missing value for filtered enzyme`, rest);
-          return;
-        }
-        const lowerValue = value.toLowerCase();
-        const cutsThisManyTimes =
-          specialCutsiteFilterOptions[value] &&
-          specialCutsiteFilterOptions[value].cutsThisManyTimes;
-        if (value === "type2s") {
-          Object.keys(cutsitesByName).forEach(function (key) {
-            if (hiddenEnzymesByName[key]) return; //don't show that cutsite
-            if (
-              cutsitesByName[key].length &&
-              cutsitesByName[key][0]?.restrictionEnzyme?.isType2S
-            ) {
-              cutSiteList.push(key);
-              returnVal.cutsitesByName[key] = cutsitesByName[key];
-            }
-          });
-        } else if (cutsThisManyTimes > 0) {
-          //the cutter type is either 1,2,3 for single, double or triple cutters
-          Object.keys(cutsitesByName).forEach(function (key) {
-            if (hiddenEnzymesByName[key]) return; //don't show that cutsite
-            if (cutsitesByName[key].length === cutsThisManyTimes) {
-              cutSiteList.push(key);
-              returnVal.cutsitesByName[key] = cutsitesByName[key];
-            }
-          });
-        } else {
-          if (hiddenEnzymesByName[lowerValue]) return; //don't show that cutsite
-          //normal enzyme ('BamHI')
-          if (!cutsitesByName[lowerValue]) return;
-          cutSiteList.push(lowerValue);
-          returnVal.cutsitesByName[lowerValue] = cutsitesByName[lowerValue];
-        }
-      });
-    }
-
-    const enzymeCounts = {};
-    cutSiteList.forEach(
-      enzyme =>
-        (enzymeCounts[enzyme] = enzymeCounts[enzyme]
-          ? enzymeCounts[enzyme] + 1
-          : 1)
-    );
-
-    const intersectionCutSites = [];
-    Object.keys(enzymeCounts).forEach(key => {
-      if (enzymeCounts[key] === groupCount) intersectionCutSites.push(key);
-    });
-
-    returnVal.cutsiteIntersectionCount = intersectionCutSites.length;
-
-    const cutsbyname_AND = {};
-    intersectionCutSites.forEach(value => {
-      cutsbyname_AND[value] = cutsitesByName[value];
-    });
-
-    returnVal.cutsiteTotalCount = Object.keys(returnVal.cutsitesByName).length;
-
-    if (isEnzymeFilterAnd && returnVal.cutsiteIntersectionCount > 0) {
-      returnVal.cutsitesByName = cutsbyname_AND;
-    }
-
-    returnVal.cutsitesArray = flatmap(
-      returnVal.cutsitesByName,
-      cutsitesByNameArray => cutsitesByNameArray
-    );
-    returnVal.cutsitesById = returnVal.cutsitesArray.reduce(function (
-      obj,
-      item
-    ) {
-      if (item && item.id) {
-        obj[item.id] = item;
-      }
-      return obj;
-    }, {});
-    return returnVal;
-  }
-);

package/filteredFeaturesSelector.js

@@ -1,32 +0,0 @@
-import { createSelector } from "reselect";
-import { omitBy } from "lodash-es";
-import featuresSelector from "./featuresSelector";
-import sequenceLengthSelector from "./sequenceLengthSelector";
-import { hideAnnByLengthFilter } from "../utils/editorUtils";
-
-function filteredFeaturesSelector(
-  features,
-  seqLen,
-  featureIndividualToHide,
-  featureTypesToHide,
-  lengthsToHide
-) {
-  return omitBy(features, ann => {
-    const hideIndividually = featureIndividualToHide[ann.id];
-    const hideFeaturesByType = featureTypesToHide[ann.type];
-    return (
-      hideAnnByLengthFilter(lengthsToHide, ann, seqLen) ||
-      hideFeaturesByType ||
-      hideIndividually
-    );
-  });
-}
-
-export default createSelector(
-  featuresSelector,
-  sequenceLengthSelector,
-  state => state.annotationVisibility.featureIndividualToHide,
-  state => state.annotationVisibility.featureTypesToHide,
-  state => state.featureLengthsToHide,
-  filteredFeaturesSelector
-);