@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/searchLayersSelector.js

@@ -1,71 +0,0 @@
-import { findSequenceMatches } from "@teselagen/sequence-utils";
-import sequenceSelector from "./sequenceSelector";
-import { createSelector } from "reselect";
-import circularSelector from "./circularSelector";
-
-function searchLayersSelector(
-  sequence,
-  isCircular,
-  isOpen,
-  searchString,
-  ambiguousOrLiteral,
-  dnaOrAA,
-  isProtein,
-  proteinSequence
-) {
-  if (!searchString || !isOpen) {
-    return [];
-  }
-  if (isProtein) {
-    const searchingDna = dnaOrAA === "DNA";
-    const matches = findSequenceMatches(
-      searchingDna ? sequence : proteinSequence,
-      searchString,
-      {
-        isCircular: false,
-        isProteinSequence: true,
-        isAmbiguous: ambiguousOrLiteral === "AMBIGUOUS",
-        // isProteinSearch: dnaOrAA !== "DNA",
-        searchReverseStrand: false
-      }
-    ).sort(({ start }, { start: start2 }) => {
-      return start - start2;
-    });
-    return searchingDna
-      ? matches
-      : matches.map(({ start, end, ...rest }) => ({
-          ...rest,
-          isSearchLayer: true,
-          start: start * 3,
-          end: end * 3 + 2
-        }));
-  }
-  const matches = findSequenceMatches(sequence, searchString, {
-    isCircular,
-    isAmbiguous: ambiguousOrLiteral === "AMBIGUOUS",
-    isProteinSearch: dnaOrAA !== "DNA",
-    searchReverseStrand: true
-  }).sort(({ start }, { start: start2 }) => {
-    return start - start2;
-  });
-  return matches.map(match => ({
-    ...match,
-    forward: !match.bottomStrand,
-    className:
-      "veSearchLayer " +
-      (match.bottomStrand ? " veSearchLayerBottomStrand" : ""),
-    isSearchLayer: true
-  }));
-}
-
-export default createSelector(
-  sequenceSelector,
-  circularSelector,
-  state => state.findTool && state.findTool.isOpen,
-  state => state.findTool && state.findTool.searchText,
-  state => state.findTool && state.findTool.ambiguousOrLiteral,
-  state => state.findTool && state.findTool.dnaOrAA,
-  state => state.sequenceData.isProtein,
-  state => state.sequenceData.proteinSequence,
-  searchLayersSelector
-);

package/selectedAnnotations.js

@@ -1,89 +0,0 @@
-import { showContextMenu } from "@teselagen/ui";
-import without from "lodash/without";
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const annotationSelect = createAction("VE_ANNOTATION_SELECT");
-export const updateSelectedAnnotation = createAction(
-  "VE_ANNOTATION_UPDATE_SELECTED"
-);
-export const annotationDeselect = createAction("VE_ANNOTATION_DESELECT");
-export const annotationDeselectAll = createAction("VE_ANNOTATION_DESELECT_ALL");
-
-export function replacementLayerRightClicked({ event, annotation }, meta) {
-  event.preventDefault();
-  event.stopPropagation();
-  return function (dispatch /* getState */) {
-    const items = [
-      {
-        text: "Remove Edit",
-        onClick: function () {
-          dispatch({
-            type: "REPLACEMENT_LAYER_DELETE",
-            meta,
-            payload: { ...annotation }
-          });
-        }
-      }
-    ];
-
-    showContextMenu(items, undefined, event);
-  };
-}
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-const startingState = {
-  idMap: {},
-  idStack: []
-};
-export default createReducer(
-  {
-    [annotationSelect]: (state, payload) => {
-      if (!payload.id) throw new Error("Annotation must have an id!");
-      const newState = {
-        idMap: {
-          ...state.idMap,
-          [payload.id]: payload
-        },
-        idStack: [...state.idStack, payload.id]
-      };
-      return newState;
-    },
-    [annotationDeselect]: (state, payload) => {
-      const id = payload.id || payload;
-      const idMap = { ...state.idMap };
-      delete idMap[id];
-      const idStack = without(state.idStack, id);
-      return {
-        idMap,
-        idStack
-      };
-    },
-    [updateSelectedAnnotation]: (state, payload) => {
-      const id = payload.id;
-      const idMap = { ...state.idMap };
-      if (!idMap[id]) {
-        return state;
-      }
-      return {
-        idMap: {
-          ...idMap,
-          [id]: {
-            ...idMap[id],
-            ...payload
-          }
-        },
-        idStack: state.idStack
-      };
-    },
-    [annotationDeselectAll]: () => {
-      return startingState;
-    }
-  },
-  startingState
-);

package/selectedAnnotationsSelector.js

@@ -1 +0,0 @@
-export default state => state.selectedAnnotations;

package/selectedCutsitesSelector.js

@@ -1,21 +0,0 @@
-import { createSelector } from "reselect";
-import selectedAnnotationsSelector from "./selectedAnnotationsSelector";
-
-export default createSelector(
-  selectedAnnotationsSelector,
-  function (selectedAnnotations) {
-    const { idStack, idMap } = selectedAnnotations;
-    const cutsiteIdMap = {};
-    const cutsiteIdStack = idStack.filter(function (id) {
-      if (idMap[id].annotationType === "cutsite") {
-        cutsiteIdMap[id] = idMap[id];
-        return true;
-      }
-      return false;
-    });
-    return {
-      idStack: cutsiteIdStack,
-      idMap: cutsiteIdMap
-    };
-  }
-);

package/selectedPartTags.js

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

package/selectionLayer.js

@@ -1,25 +0,0 @@
-export function getAllSelectionLayers({
-  additionalSelectionLayers = [],
-  searchLayers = [],
-  selectionLayer
-}) {
-  const selectionLayers = [
-    ...additionalSelectionLayers,
-    ...searchLayers,
-    ...(Array.isArray(selectionLayer) ? selectionLayer : [selectionLayer])
-  ];
-  const doubleWrappedColor = "#edb2f1";
-  // const doubleWrappedColor = "#abdbfb";
-
-  if (selectionLayer.overlapsSelf) {
-    selectionLayers.push({
-      start: selectionLayer.end + 1,
-      end: selectionLayer.start - 1,
-      color: selectionLayer.isWrappedAddon ? undefined : doubleWrappedColor
-    });
-    if (selectionLayer.isWrappedAddon) {
-      selectionLayer.color = doubleWrappedColor;
-    }
-  }
-  return selectionLayers;
-}

package/sequence.js

@@ -1,12 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const addBps = createAction("addBps");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer({}, "");

package/sequenceDataHistory.js

@@ -1,43 +0,0 @@
-//./selectionLayer.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const addToUndoStack = createAction("ADD_TO_UNDO_STACK");
-export const veUndo = createAction("VE_UNDO_META");
-export const veRedo = createAction("VE_REDO_META");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [addToUndoStack]: (state, payload) => {
-      return {
-        ...state,
-        future: [],
-        past: [...(state.past || []), payload]
-      };
-    },
-    [veUndo]: (state, presentState) => {
-      return {
-        ...state,
-        past: (state.past || []).slice(0, -1),
-        future: (state.future || []).concat(presentState)
-      };
-    },
-    [veRedo]: (state, presentState) => {
-      return {
-        ...state,
-        future: (state.future || []).slice(0, -1),
-        past: (state.past || []).concat(presentState)
-      };
-    }
-  },
-  {
-    past: [],
-    future: []
-  }
-);

package/sequenceDataSelector.js

@@ -1,2 +0,0 @@
-const sequenceDataSelector = state => state.sequenceData;
-export default sequenceDataSelector;

package/sequenceLengthSelector.js

@@ -1,5 +0,0 @@
-import sequenceSelector from "./sequenceSelector";
-
-export default function (state) {
-  return sequenceSelector(state).length;
-}

package/sequenceSelector.js

@@ -1,4 +0,0 @@
-import sequenceDataSelector from "./sequenceDataSelector";
-export default function (state) {
-  return sequenceDataSelector(state).sequence;
-}

package/shouldFlipText.js

@@ -1,4 +0,0 @@
-export default function shouldFlipText(_angle) {
-  const angle = _angle > 2 * Math.PI ? _angle - 2 * Math.PI : _angle;
-  return angle > Math.PI * 0.5 && angle < Math.PI * 1.5;
-}

package/shouldRerender.js

@@ -1,27 +0,0 @@
-import { pick, isEqualWith, isFunction } from "lodash-es";
-const shouldRerender = (propKeys, stateKeys, that) => {
-  if (!that.hasRendered) {
-    that.hasRendered = true;
-    return true;
-  }
-  const nextProps = that.props;
-  const oldProps = that.oldProps || {};
-  const a = !isEq(pick(nextProps, propKeys), pick(oldProps, propKeys));
-  that.oldProps = nextProps;
-  const nextState = that.state;
-  const oldState = that.oldState || {};
-  const b =
-    !isEq(pick(nextState, stateKeys), pick(oldState, stateKeys)) || !isEq;
-  that.oldState = nextState;
-  return a || b;
-};
-export default shouldRerender;
-
-const isEq = (o1, o2) => {
-  const isEq = isEqualWith(o1, o2, function (val1, val2) {
-    if (isFunction(val1) && isFunction(val2)) {
-      return val1 === val2 || val1.toString() === val2.toString();
-    }
-  });
-  return isEq;
-};

package/showFileDialog.js

@@ -1,25 +0,0 @@
-// TODO maybe move to TRC or elsewhere
-let hiddenInput;
-let callback;
-
-function getInput(multiple) {
-  if (!hiddenInput) {
-    hiddenInput = document.createElement("input");
-    hiddenInput.type = "file";
-    hiddenInput.style.position = "absolute";
-    hiddenInput.style.visibility = "hidden";
-    hiddenInput.addEventListener("change", event => {
-      callback(event.target.files);
-    });
-
-    document.body.appendChild(hiddenInput);
-  }
-  hiddenInput.multiple = multiple ? "multiple" : undefined;
-  return hiddenInput;
-}
-
-export default function showFileDialog({ multiple = false, onSelect }) {
-  const input = getInput(multiple);
-  callback = onSelect;
-  input.click();
-}

package/showGCContent.js

@@ -1,23 +0,0 @@
-import { createReducer } from "redux-act";
-
-//./caretPosition.js
-import createAction from "./utils/createMetaAction";
-// import createReducer from "./utils/createMergedDefaultStateReducer";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const toggleShowGCContent = createAction("toggleShowGCContent");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [toggleShowGCContent]: (state, val) => {
-      localStorage.setItem("showGCContent", val);
-      return val;
-    }
-  },
-  window.localStorage.getItem("showGCContent")
-);

package/simpleDialog.css

@@ -1,13 +0,0 @@
-.simple-dialog .dialog-buttons {
-  display: flex;
-  flex-direction: row;
-  justify-content: flex-end;
-}
-
-.simple-dialog .dialog-buttons > * {
-  margin-left: 10px;
-}
-
-.simple-dialog .bp3-form-content {
-  height: 40px;
-}

package/specialCutsiteFilterOptions.js

@@ -1,22 +0,0 @@
-export default {
-  type2s: {
-    value: "type2s",
-    label: "Type IIS Enzymes",
-    isSpecialGroup: true
-  },
-  single: {
-    value: "single",
-    label: "Single cutters",
-    cutsThisManyTimes: 1
-  },
-  double: {
-    value: "double",
-    label: "Double cutters",
-    cutsThisManyTimes: 2
-  },
-  triple: {
-    value: "triple",
-    label: "Triple cutters",
-    cutsThisManyTimes: 3
-  }
-};

package/tagsToBoldSelector.js

@@ -1,2 +0,0 @@
-const tagsToBoldSelector = state => state.selectedPartTags.parts;
-export default tagsToBoldSelector;

package/toggle_views.svg

@@ -1 +0,0 @@
-<svg xmlns="http://www.w3.org/2000/svg" width="24" height="24" viewBox="0 0 24 24"><path d="M17 17h-10v-10h10v10zm7 3l-5-3v-10l5-3v16zm-24-16l5 3v10l-5 3v-16z"/></svg>

package/toolBar.js

@@ -1,23 +0,0 @@
-import createAction from "./utils/createMetaAction";
-import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const openToolbarItemUpdate = createAction("openToolbarItemUpdate");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createMergedDefaultStateReducer(
-  {
-    [openToolbarItemUpdate]: (state, payload) => {
-      return {
-        ...state,
-        openItem: payload
-      };
-    }
-  },
-  {
-    openItem: ""
-  }
-);

package/translationSearchMatchesSelector.js

@@ -1,14 +0,0 @@
-import { createSelector } from "reselect";
-import searchLayersSelector from "./searchLayersSelector";
-
-export default createSelector(
-  searchLayersSelector,
-  state => state.findTool && state.findTool.dnaOrAA,
-  state => state.findTool && state.findTool.highlightAll,
-  state => state.findTool && state.findTool.matchNumber,
-  (searchLayers, dnaOrAA, highlightAll, matchNumber) => {
-    if (dnaOrAA === "DNA") return [];
-    if (!highlightAll) return [searchLayers[matchNumber]];
-    return searchLayers;
-  }
-);

package/translations.js

@@ -1,20 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const _upsertTranslation = createAction("UPSERT_TRANSLATION");
-export const deleteTranslation = createAction("DELETE_TRANSLATION");
-
-const defaultValue = {};
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    ...upsertDeleteActionGenerator(_upsertTranslation, deleteTranslation)
-  },
-  defaultValue
-);

package/translationsRawSelector.js

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

package/translationsSelector.js

@@ -1,137 +0,0 @@
-import { reduce } from "lodash-es";
-import uuid from "shortid";
-import sequenceSelector from "./sequenceSelector";
-import orfsSelector from "./orfsSelector";
-import { createSelector } from "reselect";
-
-import { getAminoAcidDataForEachBaseOfDna } from "@teselagen/sequence-utils";
-import each from "lodash/each";
-import translationsRawSelector from "./translationsRawSelector";
-import translationSearchMatchesSelector from "./translationSearchMatchesSelector";
-import { normalizePositionByRangeLength } from "@teselagen/range-utils";
-import cdsFeaturesSelector from "./cdsFeaturesSelector";
-import circularSelector from "./circularSelector";
-
-function translationsSelector(
-  isCircular,
-  translationSearchMatches,
-  sequence,
-  orfs,
-  showOrfTranslations,
-  showOrfs,
-  cdsFeatures,
-  showCdsFeatureTranslations,
-  showFeatures,
-  translations,
-  frameTranslations
-) {
-  const translationsToPass = {
-    ...translationSearchMatches.reduce((acc, match) => {
-      if (!match) return acc;
-      const id = match.id || uuid();
-      acc[id] = {
-        ...match,
-        id,
-        translationType: "AA Search Match",
-        isOrf: true, //pass isOrf = true here in order to not have it show up in the properties window
-        forward: !match.bottomStrand
-      };
-      return acc;
-    }, {}),
-    ...reduce(
-      translations,
-      (acc, translation) => {
-        if (!translation.isOrf) {
-          acc[translation.id] = {
-            ...translation,
-            translationType: "User Created"
-          };
-        }
-        return acc;
-      },
-      {}
-    ),
-    ...(showOrfTranslations && showOrfs
-      ? reduce(
-          orfs,
-          (acc, orf) => {
-            acc[orf.id] = { ...orf, translationType: "ORF" };
-            return acc;
-          },
-          {}
-        )
-      : {}),
-    ...(showCdsFeatureTranslations &&
-      showFeatures &&
-      reduce(
-        cdsFeatures,
-        (acc, cdsFeature) => {
-          acc[cdsFeature.id] = {
-            ...cdsFeature,
-            translationType: "CDS Feature"
-          };
-          return acc;
-        },
-        {}
-      )),
-    ...reduce(
-      frameTranslations,
-      (acc, isActive, frameName) => {
-        const frameOffset = Number(frameName);
-        if (isActive) {
-          const id = uuid();
-          acc[id] = {
-            id,
-            start:
-              isCircular || frameOffset > 0
-                ? normalizePositionByRangeLength(
-                    0 + frameOffset + (frameOffset > 0 ? -1 : 1),
-                    sequence.length
-                  )
-                : 0,
-            end:
-              isCircular || frameOffset < 0
-                ? normalizePositionByRangeLength(
-                    sequence.length -
-                      1 +
-                      frameOffset +
-                      (frameOffset > 0 ? -1 : 1),
-                    sequence.length
-                  )
-                : sequence.length - 1,
-            translationType: "Frame",
-            forward: frameOffset > 0,
-            isOrf: true //pass isOrf = true here in order to not have it show up in the properties window
-          };
-        }
-        return acc;
-      },
-      {}
-    )
-  };
-  each(translationsToPass, function (translation) {
-    translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
-      sequence,
-      translation.forward,
-      translation
-    );
-  });
-  return translationsToPass;
-}
-
-export default createSelector(
-  circularSelector,
-  translationSearchMatchesSelector,
-  sequenceSelector,
-  orfsSelector,
-  state => state.annotationVisibility.orfTranslations,
-  state => state.annotationVisibility.orfs,
-  cdsFeaturesSelector,
-  state => state.annotationVisibility.cdsFeatureTranslations,
-  state => state.annotationVisibility.features,
-  translationsRawSelector,
-  state => state.frameTranslations,
-  state => state.sequenceData.isProtein,
-  state => state.sequenceData.proteinSequence,
-  translationsSelector
-);

package/typeField.js

@@ -1,24 +0,0 @@
-import React from "react";
-import { getFeatureToColorMap } from "@teselagen/sequence-utils";
-
-export const typeField = {
-  path: "type",
-  type: "string",
-  render: (name, { color }) => {
-    const colorToUse =
-      color || getFeatureToColorMap({ includeHidden: true })[name];
-    return (
-      <div style={{ display: "flex", alignItems: "center" }}>
-        <div
-          style={{
-            height: 20,
-            width: 20,
-            background: colorToUse,
-            marginRight: 3
-          }}
-        />
-        {name}
-      </div>
-    );
-  }
-};