@teselagen/ove 0.7.28 → 0.7.29

package/partTagSearch.js

@@ -1,69 +0,0 @@
-import React from "react";
-import withEditorProps from "../withEditorProps";
-import { TgSelect, getKeyedTagsAndTagOptions } from "@teselagen/ui";
-import { flatMap } from "lodash-es";
-import { uniqBy } from "lodash-es";
-
-export const PartTagSearch = withEditorProps(PartToolDropdown);
-
-function PartToolDropdown({
-  sequenceData,
-  updateSelectedPartTags,
-  selectedPartTags,
-  allPartTags,
-  annotationVisibilityShow,
-  editTagsLink,
-  dontAutoOpen
-}) {
-  if (!sequenceData) return <div>No Parts Present</div>;
-  const keyedTags = getKeyedTagsAndTagOptions(allPartTags);
-
-  // this is what keyedTags looks like:
-  // keyedTags = {
-  //   '12:4': {label,value,id},
-  //   '12:1': {label,value,id},
-  //   '44': {label,value,id},
-  // }
-
-  const tags = uniqBy(
-    flatMap(sequenceData.parts, ({ tags }) => {
-      return flatMap(tags, t => {
-        const tag = keyedTags[t];
-        if (!tag) return [];
-        return tag;
-      });
-    }),
-    "value"
-  );
-  return (
-    <div style={{ width: "100%" }}>
-      <div>Search Parts By Tag: </div>
-      <div style={{ display: "flex" }}>
-        <TgSelect
-          value={selectedPartTags.parts}
-          onChange={(...args) => {
-            annotationVisibilityShow("parts");
-            updateSelectedPartTags(...args);
-          }}
-          isTagSelect
-          multi
-          popoverProps={{
-            usePortal: false,
-            modifiers: {
-              preventOverflow: { enabled: false },
-              hide: {
-                enabled: false
-              },
-              flip: {
-                boundariesElement: "viewport"
-              }
-            }
-          }}
-          options={tags}
-          autoOpen={!dontAutoOpen}
-        ></TgSelect>
-        {editTagsLink || null}
-      </div>
-    </div>
-  );
-}

package/partTool.js

@@ -1,45 +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 { partIcon } from "@teselagen/ui";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-import { PartTagSearch } from "../helperComponents/partTagSearch";
-
-export default connectToEditor(
-  ({ annotationVisibility = {}, toolBar = {} }) => {
-    return {
-      toggled: annotationVisibility.parts,
-      isOpen: toolBar.openItem === "partTool"
-    };
-  }
-)(({
-  allPartTags,
-  editTagsLink,
-  toolbarItemProps,
-  toggled,
-  annotationVisibilityToggle,
-  isOpen
-}) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon icon="doughnut-chart" />,
-        onIconClick: function () {
-          annotationVisibilityToggle("parts");
-        },
-        toggled,
-        editTagsLink,
-        allPartTags,
-        tooltip: "Show parts",
-        tooltipToggled: "Hide parts",
-        noDropdownIcon: !allPartTags,
-        Dropdown: PartTagSearch,
-        dropdowntooltip: (!isOpen ? "Show" : "Hide") + " Part Options",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/parts.js

@@ -1,19 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const upsertPart = createAction("UPSERT_PART");
-export const deletePart = createAction("DELETE_PART");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    ...upsertDeleteActionGenerator(upsertPart, deletePart)
-  },
-  {}
-);

package/partsSelector.js

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

package/polarToSpecialCartesian.js

@@ -1,7 +0,0 @@
-export default function polarToSpecialCartesian(radius, angle) {
-  //the 0 angle returns the 0,1 point on the unit circle instead of the 1,0 point like normal
-  return {
-    x: radius * Math.cos(angle - Math.PI / 2),
-    y: radius * Math.sin(angle - Math.PI / 2)
-  };
-}

package/positionCutsites.js

@@ -1,6 +0,0 @@
-export function positionCutsites(annotation) {
-  return {
-    start: annotation.topSnipPosition,
-    end: annotation.topSnipPosition
-  };
-}

package/prepareRowData.js

@@ -1,64 +0,0 @@
-import { mapAnnotationsToRows } from "@teselagen/sequence-utils";
-import { annotationTypes } from "@teselagen/sequence-utils";
-export default function prepareRowData(sequenceData, bpsPerRow) {
-  const sequenceLength = sequenceData.noSequence
-    ? sequenceData.size
-    : sequenceData.sequence.length;
-  const totalRows = Math.ceil(sequenceLength / bpsPerRow) || 1; //this check makes sure there is always at least 1 row!
-  const rows = [];
-  const rowMap = {};
-  if (sequenceData.isProtein) {
-    rowMap.primaryProteinSequence = mapAnnotationsToRows(
-      [
-        {
-          id: "primaryProteinSequence",
-          forward: true,
-          start: 0,
-          end: sequenceLength - 1,
-          proteinSequence: sequenceData.proteinSequence,
-          aminoAcids: sequenceData.aminoAcidDataForEachBaseOfDNA
-        }
-      ],
-      sequenceLength,
-      bpsPerRow
-    );
-  }
-  annotationTypes.forEach(function (type) {
-    rowMap[type] = mapAnnotationsToRows(
-      sequenceData[type],
-      sequenceLength,
-      bpsPerRow,
-      { splitForwardReverse: type === "primers" }
-    );
-  });
-
-  for (let rowNumber = 0; rowNumber < totalRows; rowNumber++) {
-    const row = {};
-    row.rowNumber = rowNumber;
-    row.start = rowNumber * bpsPerRow;
-    row.end =
-      (rowNumber + 1) * bpsPerRow - 1 < sequenceLength
-        ? (rowNumber + 1) * bpsPerRow - 1
-        : sequenceLength - 1;
-    if (row.end < 0) {
-      row.end = 0;
-    }
-    annotationTypes.forEach(function (type) {
-      row[type] = rowMap[type][rowNumber] || [];
-    });
-    if (sequenceData.isProtein) {
-      row.isProtein = true;
-      row.primaryProteinSequence =
-        rowMap.primaryProteinSequence &&
-        (rowMap.primaryProteinSequence[rowNumber] || []);
-    }
-    row.sequence = sequenceData.noSequence
-      ? {
-          length: row.end + 1 - row.start
-        }
-      : sequenceData.sequence.slice(row.start, row.end + 1);
-
-    rows[rowNumber] = row;
-  }
-  return rows;
-}

package/primerBases.js

@@ -1,221 +0,0 @@
-import React from "react";
-import { map } from "lodash-es";
-import { fudge2, realCharWidth } from "../constants";
-import getYOffset from "../../CircularView/getYOffset";
-import { getRangeLength } from "@teselagen/range-utils";
-import { getStructuredBases } from "./getStructuredBases";
-
-export function getBasesToShow({
-  hidePrimerBases,
-  annotation,
-  annotationRange,
-  charWidth,
-  bpsPerRow,
-  fullSequence,
-  iTree,
-  sequenceLength
-}) {
-  if (hidePrimerBases) return {};
-  const basesToShow = {};
-  if (annotation && annotation.bases) {
-    const fudge = charWidth - realCharWidth;
-    const { forward, primerBindsOn } = annotation;
-
-    const { basesNoInsertsWithMetaData, inserts, aRange } = getStructuredBases({
-      ...annotation,
-      fullSequence,
-      annotationRange,
-      sequenceLength
-    });
-
-    const annLen = getRangeLength(annotation, sequenceLength);
-    const aRangeLen = getRangeLength(annotationRange, sequenceLength);
-    const startOffset = annotationRange.start % bpsPerRow;
-    const endOffset = bpsPerRow - (annotationRange.end % bpsPerRow);
-    basesToShow.insertPaths = "";
-    basesToShow.insertTicks = "";
-    basesToShow.flipAnnotation = !forward;
-    basesToShow.extraHeight = 0;
-    const insertText = [];
-    const level1Height = -10;
-    const level2Height = 11;
-    inserts.forEach((i, n) => {
-      //loop thru all inserts
-      const indexToUse = forward ? i.index : annLen - i.index - 1;
-      if (
-        aRange.start - (primerBindsOn === "5prime" ? 1 : 0) <= indexToUse &&
-        aRange.end + (primerBindsOn === "5prime" ? 1 : 0) >= indexToUse
-      ) {
-        //only draw if insert falls within the annotation range
-        let xStart = i.index - aRange.start - Math.ceil(0.5 * i.bases.length); //calculate initial xStart
-        let xEnd = i.index - aRange.start + Math.floor(0.5 * i.bases.length);
-        if (aRange.end + 3 < xEnd) {
-          xStart -= xEnd - aRange.end - 3;
-          xEnd -= xEnd - aRange.end - 3;
-        }
-        if (i.index === 0) {
-          //for the first chunk, try to make it hang off the end if possible
-          xStart -= xEnd - 1;
-          xEnd -= xEnd - 1;
-        }
-        const forwAnd3Prime = forward;
-
-        if (xStart < -(forwAnd3Prime ? startOffset : endOffset)) {
-          //if the xStart is going to fall off the row to the left, correct it by moving the xStart to the right
-          const offsetLeft =
-            -(forwAnd3Prime ? startOffset : endOffset) - xStart;
-          xStart += offsetLeft;
-          xEnd += offsetLeft;
-        } else if (
-          xEnd + (forwAnd3Prime ? startOffset : endOffset) >
-          bpsPerRow
-        ) {
-          //if the xStart is going to fall off the row to the right, correct it by moving the xStart to the left
-          const offsetLeft =
-            bpsPerRow - xEnd - (forwAnd3Prime ? startOffset : endOffset);
-          xStart += offsetLeft;
-          xEnd += offsetLeft;
-        }
-        // use an interval tree to determine the level the primer insert should be on to not overlap with other inserts
-        const yOffset = getYOffset(iTree, xStart, xEnd);
-        iTree.insert(xStart, xEnd, {
-          //tnr: pass an initial level in the case that the underlying primer ranges themselves are overlapping
-          ...annotationRange,
-          yOffset
-        });
-
-        basesToShow.extraHeight = Math.max(
-          basesToShow.extraHeight,
-          15 + yOffset * 20
-        );
-        const insertStart =
-          (indexToUse - (forward ? aRange.start : aRange.end)) *
-          (!forward && primerBindsOn === "5prime" ? -1 : 1);
-        basesToShow.insertPaths += getInsertPath({
-          xStart,
-          xEnd,
-          charWidth,
-          level: yOffset,
-          insertStart
-        });
-
-        if (indexToUse !== aRange.end + 1 && indexToUse !== -1) {
-          basesToShow.insertTicks += getInsertTick({
-            charWidth,
-            height: level2Height,
-            insertStart
-          });
-        }
-        const textLength = Math.max(
-          0,
-          charWidth * i.bases.length - fudge - fudge2
-        );
-        insertText.push(
-          <text
-            style={{ pointerEvents: "none" }}
-            data-insert-bases={i.bases}
-            className="ve-monospace-font tg-primer-bases-insert"
-            textLength={textLength}
-            transform={
-              forward
-                ? ""
-                : `translate(${aRangeLen * charWidth},-5) scale(-1,-1) `
-            }
-            key={n}
-            x={
-              forward
-                ? (xStart - 1) * charWidth + fudge
-                : xStart * charWidth - fudge / 2
-            }
-            y={level1Height - yOffset * 20 - (forward ? 0 : 5)}
-          >
-            {i.bases.split("").map((b, i) => (
-              <tspan
-                key={i}
-                rotate={forward ? 0 : 180}
-                className="tg-no-match-seq"
-                textLength={textLength}
-              >
-                {b}
-              </tspan>
-            ))}
-          </text>
-        );
-      }
-    });
-
-    const textLength =
-      charWidth * basesNoInsertsWithMetaData.length - fudge - fudge2;
-    basesToShow.baseEl = (
-      <React.Fragment>
-        <text
-          {...{
-            textLength,
-            y: forward ? level2Height : -(basesToShow.extraHeight - 5),
-            x: forward ? fudge / 2 : fudge / 2 + 0.2 /* + diffLen * charWidth */
-          }}
-          style={{ pointerEvents: "none" }}
-          className="ve-monospace-font tg-primer-bases"
-        >
-          {map(
-            basesNoInsertsWithMetaData,
-            ({ b, isMatch, isAmbiguousMatch }, i) => {
-              return (
-                <tspan
-                  key={i}
-                  className={
-                    b === "&"
-                      ? "tg-no-show-seq"
-                      : isMatch
-                        ? ""
-                        : isAmbiguousMatch
-                          ? "tg-ambiguous-match-seq"
-                          : "tg-no-match-seq"
-                  }
-                  textLength={textLength}
-                >
-                  {b}
-                </tspan>
-              );
-            }
-          )}
-        </text>
-        {insertText}
-      </React.Fragment>
-    );
-  }
-  return basesToShow;
-}
-
-function getInsertTick({ insertStart, charWidth, height }) {
-  if (insertStart === 0) return "";
-  const insertLocation = insertStart * charWidth;
-
-  const jutUp = `
-  L ${insertLocation - 1},${height + 5}
-  L ${insertLocation - 1},${height - 4}
-  L ${insertLocation - 1},${height + 5}
-   `;
-  return jutUp;
-}
-
-function getInsertPath({ charWidth, xStart, xEnd, insertStart, level = 0 }) {
-  const insertLocation = insertStart * charWidth;
-  const insertHeight = 15;
-  const levelHeight = -5 - level * 20;
-  const leftX = (xStart - 1) * charWidth;
-  const rightX = (xEnd - 1) * charWidth;
-
-  const jutUp = `
-   L ${insertLocation - 6},${0}
-   L ${insertLocation - 6},${levelHeight}
-   L ${leftX},${levelHeight}
-   L ${leftX},${-insertHeight + levelHeight}
-
-   L ${rightX},${-insertHeight + levelHeight}
-   L ${rightX},${levelHeight}
-   L ${insertLocation + 4},${levelHeight}
-   L ${insertLocation + 4},${0}
-   `;
-  return jutUp;
-}

package/primerLengthsToHide.js

@@ -1,27 +0,0 @@
-import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const updatePrimerLengthsToHide = createAction(
-  "updatePrimerLengthsToHide"
-);
-export const togglePrimerLengthsToHide = createAction(
-  "togglePrimerLengthsToHide"
-);
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createMergedDefaultStateReducer(
-  {
-    [updatePrimerLengthsToHide]: (state, payload) => {
-      return { ...state, ...payload };
-    },
-    [togglePrimerLengthsToHide]: state => {
-      return { ...state, enabled: !state["enabled"] };
-    }
-  },
-  { enabled: false, min: 0, max: 40 }
-);

package/primers.js

@@ -1,19 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const upsertPrimer = createAction("UPSERT_PRIMER");
-export const deletePrimer = createAction("DELETE_PRIMER");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    ...upsertDeleteActionGenerator(upsertPrimer, deletePrimer)
-  },
-  {}
-);

package/primersSelector.js

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

package/printTool.js

@@ -1,31 +0,0 @@
-//TNRTODO this needs to be fixed and implemented
-import React from "react";
-import print from "./veToolbarIcons/print.png";
-
-export default () => {
-  return {
-    Icon: <img src={print} alt="Print Vector" />,
-    onIconClick: function () {
-      // var myPrintContent = document.getElementById('printdiv');
-      // var myPrintWindow = window.open(windowUrl, windowName, 'left=300,top=100,width=400,height=400');
-      // myPrintWindow.document.write(myPrintContent.innerHTML);
-      // myPrintWindow.document.getElementById('hidden_div').style.display='block'
-      // myPrintWindow.document.close();
-      // myPrintWindow.focus();
-      // myPrintWindow.print();
-      // myPrintWindow.close();
-      // return false;
-      // print();
-      // var content = document.getElementById("divcontents");
-      // document.appendChild(con)
-      // var pri = document.getElementById("ifmcontentstoprint").contentWindow;
-      // pri.document.open();
-      // pri.document.write(content.innerHTML);
-      // pri.document.close();
-      // pri.focus();
-      // pri.print();
-      // downloadSequenceData(sequenceData || )
-    },
-    tooltip: "Print Vector"
-  };
-};

package/propertiesTool.js

@@ -1,40 +0,0 @@
-import createAction from "./utils/createMetaAction";
-import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-// export const propertiesViewToggle = createAction(
-//   "TOGGLE_PROPERTIES_VIEW",
-//   () => {}
-// ); //NOTE!!:: second argument sanitizes actions so no payload is passed
-// export const propertiesViewOpen = createAction(
-//   "Open_PROPERTIES_VIEW",
-//   () => {}
-// ); //NOTE!!:: second argument sanitizes actions so no payload is passed
-export const propertiesViewTabUpdate = createAction("propertiesViewTabUpdate"); //NOTE!!:: second argument sanitizes actions so no payload is passed
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createMergedDefaultStateReducer(
-  {
-    [propertiesViewTabUpdate]: (
-      state,
-      tabId,
-      selectedAnnotationOrAnnotationId
-    ) => {
-      return {
-        ...state,
-        selectedAnnotationId: selectedAnnotationOrAnnotationId
-          ? selectedAnnotationOrAnnotationId.id ||
-            selectedAnnotationOrAnnotationId
-          : undefined,
-        tabId
-      };
-    }
-  },
-  {
-    tabId: "general"
-  }
-);

package/proteinUtils.js

@@ -1,3 +0,0 @@
-export function divideBy3(num, shouldDivideBy3) {
-  return shouldDivideBy3 ? Math.floor(num / 3) : num;
-}

package/pureNoFunc.js

@@ -1,18 +0,0 @@
-import { shouldUpdate } from "recompose";
-import { isEqualWith, isFunction } from "lodash-es";
-
-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;
-};
-
-const pure = BaseComponent => {
-  const hoc = shouldUpdate((props, nextProps) => !isEq(props, nextProps));
-  return hoc(BaseComponent);
-};
-
-export default pure;

package/readOnly.js

@@ -1,25 +0,0 @@
-//./caretPosition.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-import { noop } from "lodash-es";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const toggleReadOnlyMode = createAction("TOGGLE_READ_ONLY_MODE", noop); //NOTE!!:: second argument sanitizes actions so no payload is passed
-export const updateReadOnlyMode = createAction("UPDATE_READ_ONLY_MODE");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [updateReadOnlyMode]: (state, payload) => {
-      return payload;
-    },
-    [toggleReadOnlyMode]: state => {
-      return !state;
-    }
-  },
-  true
-);

package/redoTool.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.future &&
-      editorState.sequenceDataHistory.future.length
-    )
-  };
-})(({ toolbarItemProps, redo, disabled }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon data-test="veRedoTool" icon="redo" />,
-        disabled,
-        onIconClick: redo,
-        tooltip: (
-          <span>
-            Redo <span style={{ fontSize: 10 }}>(Cmd/Ctrl+Shift+Z)</span>
-          </span>
-        ),
-        ...toolbarItemProps
-      }}
-    />
-  );
-});