@teselagen/ove 0.7.26 → 0.7.28

package/selectedCutsitesSelector.js

@@ -0,0 +1,21 @@
+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

@@ -0,0 +1,21 @@
+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

@@ -0,0 +1,25 @@
+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/selectors/annotationSearchSelector.d.ts

@@ -1,5 +1,5 @@
 export const searchableTypes: string[];
-declare const _default: ((state: any) => any[][]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, ...args_2: any[]) => any[][], {
+declare const _default: ((state: any) => any[][]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, ...args: any[]) => any[][], {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/sequence.js

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

package/sequenceDataHistory.js

@@ -0,0 +1,43 @@
+//./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

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

package/sequenceLengthSelector.js

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

package/sequenceSelector.js

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

package/shouldFlipText.js

@@ -0,0 +1,4 @@
+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

@@ -0,0 +1,27 @@
+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

@@ -0,0 +1,25 @@
+// 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

@@ -0,0 +1,23 @@
+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

@@ -0,0 +1,13 @@
+.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

@@ -0,0 +1,22 @@
+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/src/Editor/DropHandler.js

@@ -28,7 +28,8 @@ export default class DropHandler extends React.Component {
           ".dna",
           ".prot",
           ".ab1",
-          ".json"
+          ".json",
+          ".fastq"
         ]}
         onDropRejected={() => {
           window.toastr.error("Error: Incorrect File Type");

package/src/Editor/index.js

@@ -55,8 +55,6 @@ import { getClientX, getClientY } from "../utils/editorUtils";
 import PCRTool from "../PCRTool/PCRTool";
 import classNames from "classnames";
 
-
-
 // if (process.env.NODE_ENV !== 'production') {
 //   const {whyDidYouUpdate} = require('why-did-you-update');
 //   whyDidYouUpdate(React);

package/src/RowItem/StackedAnnotations/getStructuredBases.js

@@ -28,11 +28,25 @@ export function getStructuredBases({
       }
     }
   }
-  const aRange = {
-    //tnr: this probably needs to be changed in case annotation wraps origin
-    start: annotationRange.start - start,
-    end: annotationRange.end - start
-  };
+
+  const wrapsOrigin = start > end;
+  let aRange;
+  if (!wrapsOrigin) {
+    aRange = {
+      //tnr: this probably needs to be changed in case annotation wraps origin
+      start: annotationRange.start - start,
+      end: annotationRange.end - start
+    };
+  } else {
+    aRange = {
+      start: annotationRange.start === 0 ? sequenceLength - start : 0,
+      end:
+        annotationRange.start === 0
+          ? annLen - 1
+          : getRangeLength(annotationRange) - 1
+    };
+  }
+
   const r = {
     aRange,
     basesNoInserts: basesToUse,
@@ -63,7 +77,7 @@ export function getStructuredBases({
     forward ? r.basesNoInserts : r.basesNoInserts.split("").reverse().join("")
   );
   r.basesNoInsertsWithMetaData = basesForRange.split("").map((b, i) => {
-    const indexOfBase = i + annotationRange.start;
+    const indexOfBase = (i + annotationRange.start) % sequenceLength;
     let seqForBase = (fullSequence && fullSequence[indexOfBase]) || "";
     if (!forward) {
       seqForBase = getComplementSequenceString(seqForBase);

package/src/ToolBar/cutsiteTool.js

@@ -69,7 +69,7 @@ function CutsiteToolDropDown({
         onChangeHook={function () {
           annotationVisibilityShow("cutsites");
         }}
-        closeDropDown={toggleDropdown}
+        closeDropDown={() => toggleDropdown({ forceClose: true })}
       />
       {withDigestTool && (
         <Button

package/src/helperComponents/PropertiesDialog/TranslationProperties.js

@@ -44,7 +44,8 @@ class TranslationProperties extends React.Component {
     const translationsToUse = map(translations, translation => {
       let aaString = "";
       for (let i = 0; i < translation.aminoAcids.length; i++) {
-        aaString += translation.aminoAcids[i].aminoAcid.value;
+        // sometimes the `translation.aminoAcids[i].aminoAcid` is null
+        aaString += translation.aminoAcids[i].aminoAcid?.value || '';
       }
       return {
         ...translation,