@teselagen/ove 0.7.27 → 0.7.28

package/tagsToBoldSelector.js

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

package/toggle_views.svg

@@ -0,0 +1 @@
+<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

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

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,20 @@
+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

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

package/translationsSelector.js

@@ -0,0 +1,137 @@
+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

@@ -0,0 +1,24 @@
+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>
+    );
+  }
+};

package/undoTool.js

@@ -0,0 +1,30 @@
+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.d.ts

@@ -1,3 +1 @@
-export default function updateEditor(store: any, editorName: any, initialValues?: {}, extraMeta?: {}, { convertAnnotationsFromAAIndices }?: {
-    convertAnnotationsFromAAIndices: any;
-}): void;
+export default function updateEditor(store: any, editorName: any, initialValues?: {}, extraMeta?: {}, { convertAnnotationsFromAAIndices }?: {}): void;

package/updateEditor.js

@@ -0,0 +1,200 @@
+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

@@ -0,0 +1,55 @@
+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

@@ -0,0 +1,41 @@
+// 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

@@ -0,0 +1,58 @@
+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

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

@@ -0,0 +1,31 @@
+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);
+    }
+  };
+}