@teselagen/ove 0.0.13 → 0.0.15

package/src/AlignmentView/index.js

@@ -0,0 +1,2058 @@
+import { HorizontalPanelDragHandle } from "./HorizontalPanelDragHandle";
+import {
+  DragDropContext,
+  Droppable,
+  Draggable as DndDraggable
+} from "@hello-pangea/dnd";
+import Clipboard from "clipboard";
+import React from "react";
+import { connect } from "react-redux";
+import {
+  Button,
+  Intent,
+  Popover,
+  Menu,
+  MenuItem,
+  Tooltip,
+  Icon,
+  Spinner,
+  AnchorButton,
+  EditableText
+} from "@blueprintjs/core";
+import {
+  InfoHelper,
+  Loading,
+  showContextMenu,
+  withStore
+} from "@teselagen/ui";
+import { store } from "@risingstack/react-easy-state";
+import {
+  throttle,
+  // cloneDeep,
+  map,
+  some,
+  forEach,
+  isFunction,
+  unset,
+  omit
+} from "lodash";
+import { getSequenceDataBetweenRange } from "@teselagen/sequence-utils";
+import ReactList from "@teselagen/react-list";
+import ReactDOM from "react-dom";
+
+import { NonReduxEnhancedLinearView } from "../LinearView";
+import Minimap, { getTrimmedRangesToDisplay } from "./Minimap";
+import { compose, branch, renderComponent } from "recompose";
+import AlignmentVisibilityTool from "./AlignmentVisibilityTool";
+import * as alignmentActions from "../redux/alignments";
+import estimateRowHeight from "../RowView/estimateRowHeight";
+import prepareRowData from "../utils/prepareRowData";
+import withEditorProps from "../withEditorProps";
+
+import "./style.css";
+import {
+  editorDragged,
+  editorClicked,
+  editorDragStarted,
+  updateSelectionOrCaret,
+  editorDragStopped
+} from "../withEditorInteractions/clickAndDragUtils";
+import { ResizeSensor } from "@blueprintjs/core";
+import ReactDraggable from "react-draggable";
+import draggableClassnames from "../constants/draggableClassnames";
+import Caret from "../RowItem/Caret";
+import { debounce } from "lodash";
+import { view } from "@risingstack/react-easy-state";
+import { noop } from "lodash";
+import { massageTickSpacing } from "../utils/massageTickSpacing";
+import { getClientX, getClientY } from "../utils/editorUtils";
+
+import UncontrolledSliderWithPlusMinusBtns from "../helperComponents/UncontrolledSliderWithPlusMinusBtns";
+import { updateLabelsForInViewFeatures } from "../utils/updateLabelsForInViewFeatures";
+
+import PinchHelper from "../helperComponents/PinchHelper/PinchHelper";
+import { showDialog } from "../GlobalDialogUtils";
+import { GlobalDialog } from "../GlobalDialog";
+import { array_move } from "../ToolBar/array_move";
+import classNames from "classnames";
+import { getTrackFromEvent } from "./getTrackFromEvent";
+import { PerformantSelectionLayer } from "./PerformantSelectionLayer";
+import { PairwiseAlignmentView } from "./PairwiseAlignmentView";
+import { updateTrackHelper } from "./updateTrackHelper";
+// import { getGaps } from "./getGaps";
+import { isTargetWithinEl } from "./isTargetWithinEl";
+import { EditTrackNameDialog } from "./EditTrackNameDialog";
+import { coerceInitialValue } from "./coerceInitialValue";
+
+let charWidthInLinearViewDefault = 12;
+try {
+  const newVal = JSON.parse(
+    window.localStorage.getItem("charWidthInLinearViewDefault")
+  );
+  if (newVal) charWidthInLinearViewDefault = newVal;
+} catch (e) {
+  console.error(
+    "error setting charWidthInLinearViewDefault from local storage:",
+    e
+  );
+}
+
+export class AlignmentView extends React.Component {
+  bindOutsideChangeHelper = {};
+  constructor(props) {
+    super(props);
+    window.scrollAlignmentToPercent = this.scrollAlignmentToPercent;
+    if (window.Cypress)
+      window.Cypress.scrollAlignmentToPercent = this.scrollAlignmentToPercent;
+    this.onShortcutCopy = document.addEventListener(
+      "keydown",
+      this.handleAlignmentCopy
+    );
+  }
+  getMaxLength = () => {
+    const { alignmentTracks } = this.props;
+    const { sequenceData = { sequence: "" }, alignmentData } =
+      alignmentTracks[0];
+    const data = alignmentData || sequenceData;
+    return data.noSequence ? data.size : data.sequence.length;
+  };
+
+  getNearestCursorPositionToMouseEvent(rowData, event, callback) {
+    this.charWidth = this.getCharWidthInLinearView();
+    //loop through all the rendered rows to see if the click event lands in one of them
+    let nearestCaretPos = 0;
+    const rowDomNode = this.veTracksAndAlignmentHolder;
+    const boundingRowRect = rowDomNode.getBoundingClientRect();
+    const maxEnd = this.getMaxLength();
+    if (
+      getClientX(event) - boundingRowRect.left - this.state.nameDivWidth <
+      0
+    ) {
+      nearestCaretPos = 0;
+    } else {
+      const clickXPositionRelativeToRowContainer =
+        getClientX(event) - boundingRowRect.left - this.state.nameDivWidth;
+      const numberOfBPsInFromRowStart = Math.floor(
+        (clickXPositionRelativeToRowContainer + this.charWidth / 2) /
+          this.charWidth
+      );
+      nearestCaretPos = numberOfBPsInFromRowStart + 0;
+      if (nearestCaretPos > maxEnd + 1) {
+        nearestCaretPos = maxEnd + 1;
+      }
+    }
+    if (this.props.sequenceData && this.props.sequenceData.isProtein) {
+      nearestCaretPos = Math.round(nearestCaretPos / 3) * 3;
+    }
+    if (this.props.sequenceLength === 0) nearestCaretPos = 0;
+    const callbackVals = {
+      updateSelectionOrCaret: this.updateSelectionOrCaret,
+      nearestCaretPos,
+      sequenceLength: this.getSequenceLength(),
+      caretPosition: this.easyStore.caretPosition,
+      selectionLayer: this.easyStore.selectionLayer,
+      easyStore: this.easyStore,
+      caretPositionUpdate: this.caretPositionUpdate,
+      selectionLayerUpdate: this.selectionLayerUpdate,
+      event,
+      doNotWrapOrigin: true,
+      shiftHeld: event.shiftKey,
+      // caretGrabbed: event.target.className === "cursor",
+      selectionStartGrabbed: event.target.classList.contains(
+        draggableClassnames.selectionStart
+      ),
+      selectionEndGrabbed: event.target.classList.contains(
+        draggableClassnames.selectionEnd
+      )
+    };
+    callback(callbackVals);
+  }
+
+  componentWillUnmount() {
+    if (window.Cypress) {
+      delete window.scrollAlignmentToPercent;
+      delete window.Cypress.scrollAlignmentToPercent;
+      delete window.updateAlignmentSelection;
+      delete window.Cypress.updateAlignmentSelection;
+    }
+    const { removeAlignmentFromRedux, id } = this.props;
+    removeAlignmentFromRedux({ id });
+    this.onShortcutCopy &&
+      document.removeEventListener("keydown", this.handleAlignmentCopy);
+  }
+  handleAlignmentCopy = (event) => {
+    if (
+      event.key === "c" &&
+      !event.shiftKey &&
+      (event.metaKey === true || event.ctrlKey === true)
+    ) {
+      const input = document.createElement("textarea");
+      document.body.appendChild(input);
+      const seqDataToCopy = this.getAllAlignmentsFastaText();
+      input.value = seqDataToCopy;
+      input.select();
+      const copySuccess = document.execCommand("copy");
+      if (!copySuccess) {
+        window.toastr.error("Selection Not Copied");
+      } else {
+        window.toastr.success("Selection Copied");
+      }
+      document.body.removeChild(input);
+      event.preventDefault();
+    }
+  };
+  getAllAlignmentsFastaText = () => {
+    const selectionLayer =
+      this.props.store.getState().VectorEditor.__allEditorsOptions.alignments[
+        this.props.id
+      ].selectionLayer || {};
+    const { alignmentTracks } = this.props;
+    const seqDataOfAllTracksToCopy = [];
+    alignmentTracks.forEach((track) => {
+      const seqDataToCopy = getSequenceDataBetweenRange(
+        track.alignmentData,
+        selectionLayer
+      ).sequence;
+      seqDataOfAllTracksToCopy.push(
+        `>${track.alignmentData.name}\r\n${seqDataToCopy}\r\n`
+      );
+    });
+    return seqDataOfAllTracksToCopy.join("");
+  };
+  state = {
+    alignmentName: this.props.alignmentName,
+    isTrackDragging: false,
+    charWidthInLinearView: charWidthInLinearViewDefault,
+    scrollAlignmentView: false,
+    width: 0,
+    nameDivWidth: 140
+  };
+  easyStore = store({
+    selectionLayer: { start: -1, end: -1 },
+    caretPosition: -1,
+    percentScrolled: 0,
+    viewportWidth: 400,
+    verticalVisibleRange: { start: 0, end: 0 }
+  });
+
+  getMinCharWidth = (noNameDiv) => {
+    const toReturn = Math.min(
+      Math.max(
+        this.state.width - (noNameDiv ? 0 : this.state.nameDivWidth) - 5,
+        1
+      ) / this.getSequenceLength(),
+      10
+    );
+    if (isNaN(toReturn)) return 10;
+    return toReturn;
+  };
+
+  getSequenceLength = () => {
+    const { alignmentTracks: [template] = [] } = this.props;
+    return template.alignmentData.sequence.length || 1;
+  };
+  async componentDidUpdate(prevProps) {
+    if (
+      prevProps.scrollPercentageToJumpTo !==
+        this.props.scrollPercentageToJumpTo &&
+      this.props.scrollPercentageToJumpTo !== undefined
+    ) {
+      this.scrollAlignmentToPercent(this.props.scrollPercentageToJumpTo);
+    }
+    //autosave if necessary!
+    if (
+      this.props.shouldAutosave &&
+      prevProps &&
+      prevProps.stateTrackingId &&
+      this.props.stateTrackingId !== prevProps.stateTrackingId
+    ) {
+      this.setState({ saveMessage: "Alignment Saving.." });
+      this.setState({ saveMessageLoading: true });
+
+      let cleanedTracks;
+      if (this.props.pairwiseAlignments) {
+        cleanedTracks = this.props.pairwiseAlignments.map(cleanTracks);
+      } else {
+        cleanedTracks = cleanTracks(this.props.alignmentTracks);
+      }
+
+      await this.props.handleAlignmentSave(cleanedTracks, this.props);
+      this.setState({ saveMessage: "Alignment Saved" });
+      this.setState({ saveMessageLoading: false });
+      setTimeout(() => {
+        this.setState({ saveMessage: undefined });
+        this.setState({ saveMessageLoading: false });
+      }, 5000);
+    }
+  }
+  componentDidMount() {
+    const updateAlignmentSelection = (newRangeOrCaret) => {
+      this.updateSelectionOrCaret(false, newRangeOrCaret, {
+        forceReduxUpdate: true
+      });
+    };
+    window.updateAlignmentSelection = updateAlignmentSelection;
+    if (window.Cypress)
+      window.Cypress.updateAlignmentSelection = updateAlignmentSelection;
+    setTimeout(() => {
+      updateLabelsForInViewFeatures({ rectElement: ".alignmentHolder" });
+    }, 0);
+    setTimeout(() => {
+      this.setVerticalScrollRange();
+    }, 500);
+  }
+
+  annotationClicked = ({
+    event,
+    annotation,
+    gapsBefore = 0,
+    gapsInside = 0
+  }) => {
+    event.preventDefault && event.preventDefault();
+    event.stopPropagation && event.stopPropagation();
+    this.updateSelectionOrCaret(event.shiftKey, {
+      ...annotation,
+      start: annotation.start + gapsBefore,
+      end: annotation.end + gapsBefore + gapsInside
+    });
+  };
+
+  updateSelectionOrCaret = (
+    shiftHeld,
+    newRangeOrCaret,
+    { forceReduxUpdate } = {}
+  ) => {
+    const sequenceLength = this.getSequenceLength();
+
+    updateSelectionOrCaret({
+      doNotWrapOrigin: true,
+      shiftHeld,
+      sequenceLength,
+      newRangeOrCaret,
+      caretPosition: this.easyStore.caretPosition,
+      selectionLayer: this.easyStore.selectionLayer,
+      selectionLayerUpdate: forceReduxUpdate
+        ? this.forceReduxSelectionLayerUpdate
+        : this.selectionLayerUpdate,
+      caretPositionUpdate: this.caretPositionUpdate
+    });
+  };
+
+  caretPositionUpdate = (position) => {
+    const { caretPosition = -1, alignmentId } = this.props;
+    if (caretPosition === position) {
+      return;
+    }
+    this.easyStore.caretPosition = position;
+    this.easyStore.selectionLayer = { start: -1, end: -1 };
+    this.debouncedAlignmentRunUpdate({
+      alignmentId,
+      selectionLayer: { start: -1, end: -1 },
+      caretPosition: position
+    });
+  };
+
+  debouncedAlignmentRunUpdate = debounce(this.props.alignmentRunUpdate, 1000);
+
+  forceReduxSelectionLayerUpdate = (newSelection) => {
+    this.selectionLayerUpdate(newSelection, { forceReduxUpdate: true });
+  };
+
+  selectionLayerUpdate = (newSelection, { forceReduxUpdate } = {}) => {
+    const { selectionLayer = { start: -1, end: -1 }, alignmentId } = this.props;
+    if (!newSelection) return;
+    const { start, end } = newSelection;
+
+    if (selectionLayer.start === start && selectionLayer.end === end) {
+      return;
+    }
+    this.easyStore.caretPosition = -1;
+    this.easyStore.selectionLayer = newSelection;
+
+    (forceReduxUpdate
+      ? this.props.alignmentRunUpdate
+      : this.debouncedAlignmentRunUpdate)({
+      alignmentId,
+      selectionLayer: newSelection,
+      caretPosition: -1
+    });
+  };
+
+  getCharWidthInLinearView = () => {
+    if (this.props.isFullyZoomedOut) {
+      return this.getMinCharWidth();
+    } else {
+      return Math.max(this.getMinCharWidth(), this.state.charWidthInLinearView);
+    }
+  };
+  getNumBpsShownInLinearView = () => {
+    const toReturn =
+      (this.state.width - this.state.nameDivWidth) /
+      this.getCharWidthInLinearView();
+    return toReturn || 0;
+  };
+  setVerticalScrollRange = throttle(() => {
+    if (
+      this &&
+      this.InfiniteScroller &&
+      this.InfiniteScroller.getFractionalVisibleRange &&
+      this.easyStore
+    ) {
+      let [start, end] = this.InfiniteScroller.getFractionalVisibleRange();
+      if (this.props.hasTemplate) {
+        end = end + 1;
+      }
+      if (
+        this.easyStore.verticalVisibleRange.start !== start ||
+        this.easyStore.verticalVisibleRange.end !== end
+      )
+        this.easyStore.verticalVisibleRange = { start, end };
+    }
+  }, 100);
+  handleScroll = () => {
+    // tnr: maybe add this in at some point
+    // this.updateMinimapHighlightForScroll(
+    //   this.oldMinimapScrollTracker || this.alignmentHolder.scrollTop,
+    //   this.alignmentHolder.scrollTop
+    // );
+    // this.oldMinimapScrollTracker = this.alignmentHolder.scrollTop;
+    // if (this.alignmentHolder.scrollTop !== this.oldMinimapScrollTracker) {
+    // }
+    if (this.alignmentHolder.scrollTop !== this.oldAlignmentHolderScrollTop) {
+      setTimeout(() => {
+        this.setVerticalScrollRange();
+        this.oldAlignmentHolderScrollTop = this.alignmentHolder.scrollTop;
+      }, 100);
+    }
+    if (this.blockScroll) {
+      //we have to block the scroll sometimes when adjusting the minimap so things aren't too jumpy
+      return;
+    }
+
+    const scrollPercentage =
+      this.alignmentHolder.scrollLeft /
+      (this.alignmentHolder.scrollWidth - this.alignmentHolder.clientWidth);
+    this.easyStore.percentScrolled = scrollPercentage || 0;
+    if (!this.isZooming) {
+      this.easyStore.percentScrolledPreZoom = this.easyStore.percentScrolled;
+    }
+    if (this.alignmentHolderTop) {
+      this.alignmentHolderTop.scrollLeft = this.alignmentHolder.scrollLeft;
+    }
+    updateLabelsForInViewFeatures({ rectElement: ".alignmentHolder" });
+  };
+  handleTopScroll = () => {
+    this.alignmentHolder.scrollLeft = this.alignmentHolderTop.scrollLeft;
+  };
+  /**
+   * Responsible for handling resizing the highlighted region of the minimap
+   * @param {*} newSliderSize
+   * @param {*} newPercent
+   */
+  onMinimapSizeAdjust = (newSliderSize, newPercent) => {
+    const percentageOfSpace = newSliderSize / this.state.width;
+    const seqLength = this.getSequenceLength();
+    const numBpsInView = seqLength * percentageOfSpace;
+    const newCharWidth =
+      (this.state.width - this.state.nameDivWidth) / numBpsInView;
+    this.blockScroll = true;
+    this.setCharWidthInLinearView({ charWidthInLinearView: newCharWidth });
+    setTimeout(() => {
+      this.scrollAlignmentToPercent(newPercent);
+      this.blockScroll = false;
+      updateLabelsForInViewFeatures({ rectElement: ".alignmentHolder" });
+    });
+  };
+
+  setCharWidthInLinearView = ({ charWidthInLinearView }) => {
+    window.localStorage.setItem(
+      "charWidthInLinearViewDefault",
+      charWidthInLinearView
+    );
+    this.setState({ charWidthInLinearView });
+    charWidthInLinearViewDefault = JSON.parse(
+      window.localStorage.getItem("charWidthInLinearViewDefault")
+    );
+  };
+
+  scrollToCaret = () => {
+    let el = window.document.querySelector(".veCaret:not(.zoomSelection)"); //adding .veRowViewCaret breaks this for some reason
+    if (!el) {
+      el = window.document.querySelector(".veCaret"); //adding .veRowViewCaret breaks this for some reason
+    }
+    if (!el) {
+      return;
+    }
+    el.scrollIntoView({ inline: "center", block: "nearest" });
+  };
+
+  scrollAlignmentToPercent = (scrollPercentage) => {
+    const scrollPercentageToUse = Math.min(Math.max(scrollPercentage, 0), 1);
+    this.easyStore.percentScrolled = scrollPercentageToUse;
+    this.alignmentHolder.scrollLeft =
+      scrollPercentageToUse *
+      (this.alignmentHolder.scrollWidth - this.alignmentHolder.clientWidth);
+    if (this.alignmentHolderTop) {
+      this.alignmentHolderTop.scrollLeft =
+        scrollPercentageToUse *
+        (this.alignmentHolderTop.scrollWidth -
+          this.alignmentHolderTop.clientWidth);
+    }
+  };
+  scrollYToTrack = (trackIndex) => {
+    this.InfiniteScroller.scrollTo(trackIndex);
+  };
+
+  estimateRowHeight = (index, cache) => {
+    const { alignmentVisibilityToolOptions, alignmentTracks } = this.props;
+    const track = alignmentTracks[index];
+    if (!track) return 100;
+    const { sequenceData } = track;
+    this.rowData = prepareRowData(sequenceData, sequenceData.sequence.length);
+    return estimateRowHeight({
+      index,
+      cache,
+      // clearCache: this.clearCache,
+      row: this.rowData[index],
+      annotationVisibility:
+        alignmentVisibilityToolOptions.alignmentAnnotationVisibility,
+      annotationLabelVisibility:
+        alignmentVisibilityToolOptions.alignmentAnnotationLabelVisibility
+    });
+  };
+
+  getMaxLinearViewWidth = () => {
+    let maxWidth = 0;
+    const charWidthInLinearView = this.getCharWidthInLinearView();
+    forEach(this.props.alignmentTracks, (t) => {
+      const w = (t.alignmentData || t.sequenceData).sequence.length;
+      if (w > maxWidth) maxWidth = w;
+    });
+    return maxWidth * charWidthInLinearView;
+  };
+
+  renderItem = (_i, key, isTemplate, cloneProps) => {
+    const charWidthInLinearView = this.getCharWidthInLinearView();
+    const {
+      alignmentTrackIndex,
+      pairwiseAlignments,
+      currentPairwiseAlignmentIndex,
+      pairwiseOverviewAlignmentTracks,
+      alignmentTracks = [],
+      upsertAlignmentRun,
+      alignmentId,
+      noClickDragHandlers,
+      handleSelectTrack,
+      allowTrackRearrange,
+      isPairwise,
+      linearViewOptions,
+      alignmentVisibilityToolOptions,
+      hasTemplate,
+      allowTrackNameEdit,
+      ...rest
+    } = this.props;
+    const isDragDisabled = !allowTrackRearrange || isPairwise;
+    let i;
+    if (isTemplate) {
+      i = _i;
+    } else if (hasTemplate) {
+      i = _i + 1;
+    } else {
+      i = _i;
+    }
+
+    const track = alignmentTracks[i];
+    if (!track) return null;
+    const {
+      sequenceData,
+      alignmentData,
+      isReversed,
+      wasTrimmed,
+      additionalSelectionLayers,
+      chromatogramData
+      // mismatches
+    } = track;
+    const seqLen = this.getMaxLength();
+
+    const trimmedRangesToDisplay = getTrimmedRangesToDisplay({
+      seqLen,
+      trimmedRange: alignmentData?.trimmedRange
+    });
+    const linearViewWidth =
+      (alignmentData || sequenceData).sequence.length * charWidthInLinearView;
+    const name = sequenceData.name || sequenceData.id;
+
+    //tnw: commenting this out for now since it can significantly slow down the alignment visualization
+    /**
+     * for alignment of sanger seq reads to a ref seq, have translations show up at the bp pos of ref seq's CDS features across all seq reads
+     **/
+    // let sequenceDataWithRefSeqCdsFeatures;
+    // if (this.props.alignmentType === "SANGER SEQUENCING") {
+    //   if (i !== 0) {
+    //     sequenceDataWithRefSeqCdsFeatures = cloneDeep(sequenceData);
+    //     const refSeqCdsFeaturesBpPos = [];
+    //     alignmentTracks[0].sequenceData.features.forEach((feature) => {
+    //       if (feature.type === "CDS") {
+    //         const editedFeature = cloneDeep(feature);
+    //         // in seq reads, ref seq's CDS feature translations need to show up at the bp pos of alignment, not the original bp pos
+    //         // actual position in the track
+    //         const absoluteFeatureStart =
+    //           getGaps(feature.start, alignmentTracks[0].alignmentData.sequence)
+    //             .gapsBefore + feature.start;
+    //         const gapsBeforeSeqRead = getGaps(
+    //           0,
+    //           alignmentData.sequence
+    //         ).gapsBefore;
+    //         const bpsFromSeqReadStartToFeatureStartIncludingGaps =
+    //           absoluteFeatureStart - gapsBeforeSeqRead;
+    //         const absoluteFeatureEnd =
+    //           getGaps(feature.end, alignmentTracks[0].alignmentData.sequence)
+    //             .gapsBefore + feature.end;
+    //         // const gapsBeforeFeatureInSeqRead = getGaps(feature.start - gapsBeforeSeqRead, alignmentData.sequence).gapsBefore
+    //         const gapsAfterSeqRead =
+    //           alignmentData.sequence.length -
+    //           alignmentData.sequence.replace(/-+$/g, "").length;
+    //         const seqReadLengthWithoutGapsBeforeAfter =
+    //           alignmentData.sequence.length -
+    //           gapsBeforeSeqRead -
+    //           gapsAfterSeqRead;
+    //         const absoluteSeqReadStart = gapsBeforeSeqRead;
+    //         const absoluteSeqReadEnd =
+    //           absoluteSeqReadStart + seqReadLengthWithoutGapsBeforeAfter;
+    //         let featureStartInSeqRead;
+    //         if (absoluteFeatureEnd < absoluteSeqReadStart) {
+    //           // if the feature ends before the seq read starts, do nothing
+    //         } else if (absoluteFeatureStart > absoluteSeqReadEnd) {
+    //           // if the feature starts after the seq read ends, do nothing
+    //         } else if (
+    //           absoluteFeatureStart < absoluteSeqReadStart &&
+    //           absoluteFeatureEnd > absoluteSeqReadStart
+    //         ) {
+    //           // if the feature starts before the seq read starts but doesn't end before the seq read starts
+    //           const arrayOfCodonStartPos = [];
+    //           for (
+    //             let i = absoluteFeatureStart;
+    //             i < absoluteSeqReadStart + 6;
+    //             i += 3
+    //           ) {
+    //             arrayOfCodonStartPos.push(i);
+    //           }
+    //           // want to start translation at the codon start pos closest to seq read start
+    //           const absoluteTranslationStartInFrame =
+    //             arrayOfCodonStartPos.reduce((prev, curr) =>
+    //               Math.abs(curr - absoluteSeqReadStart) <
+    //                 Math.abs(prev - absoluteSeqReadStart) &&
+    //               curr >= absoluteSeqReadStart
+    //                 ? curr
+    //                 : prev
+    //             );
+    //           const seqReadTranslationStartInFrame =
+    //             absoluteTranslationStartInFrame - gapsBeforeSeqRead;
+    //           editedFeature.start = seqReadTranslationStartInFrame;
+    //           const shortenedFeatureLength =
+    //             Math.abs(absoluteFeatureEnd - absoluteFeatureStart) -
+    //             (absoluteTranslationStartInFrame - absoluteFeatureStart);
+    //           editedFeature.end = editedFeature.start + shortenedFeatureLength;
+    //           refSeqCdsFeaturesBpPos.push(editedFeature);
+    //         } else {
+    //           // if the feature is fully contained within the seq read start/end
+    //           const seqReadStartToFeatureStartIncludingGaps =
+    //             alignmentData.sequence
+    //               .replace(/^-+/g, "")
+    //               .replace(/-+$/g, "")
+    //               .slice(0, bpsFromSeqReadStartToFeatureStartIncludingGaps);
+    //           const arrayOfGaps = seqReadStartToFeatureStartIncludingGaps.match(
+    //             new RegExp("-", "g")
+    //           );
+    //           let numOfGapsFromSeqReadStartToFeatureStart = 0;
+    //           if (arrayOfGaps !== null) {
+    //             numOfGapsFromSeqReadStartToFeatureStart = arrayOfGaps.length;
+    //           }
+    //           featureStartInSeqRead =
+    //             bpsFromSeqReadStartToFeatureStartIncludingGaps -
+    //             numOfGapsFromSeqReadStartToFeatureStart;
+    //           editedFeature.start = featureStartInSeqRead;
+    //           const featureLength = Math.abs(feature.end - feature.start);
+    //           editedFeature.end = editedFeature.start + featureLength;
+    //           refSeqCdsFeaturesBpPos.push(editedFeature);
+    //         }
+    //       }
+    //     });
+    //     // add ref seq's CDS features to seq reads (not the actual sequenceData) to generate translations at those bp pos
+    //     if (refSeqCdsFeaturesBpPos.length !== 0) {
+    //       sequenceDataWithRefSeqCdsFeatures.features.push(
+    //         ...refSeqCdsFeaturesBpPos
+    //       );
+    //       // use returned aligned sequence rather than original sequence because after bowtie2, may be reverse complement or have soft-clipped ends
+    //       sequenceDataWithRefSeqCdsFeatures.sequence =
+    //         alignmentData.sequence.replace(/-/g, "");
+    //     }
+    //   }
+    // }
+    const tickSpacing = massageTickSpacing(
+      Math.ceil(120 / charWidthInLinearView)
+    );
+
+    const { compactNames } =
+      alignmentVisibilityToolOptions.alignmentAnnotationVisibility;
+    const selectionLayer = [
+      this.state[`tempTrimBefore${i}`] || trimmedRangesToDisplay[0],
+      this.state[`tempTrimAfter${i}`] || trimmedRangesToDisplay[1]
+    ]
+      .filter((i) => i)
+      .map((i) => ({
+        ...i,
+        hideCarets: true,
+        ignoreGaps: true,
+        className: "tg-trimmed-region",
+        color: "gray"
+      }));
+    const innerRenderItem = (provided = {}, snapshot) => (
+      <div
+        ref={provided?.innerRef}
+        {...provided?.draggableProps}
+        className={classNames("alignmentViewTrackContainer", {
+          isDragDisabled
+        })}
+        data-alignment-track-index={i}
+        style={{
+          boxShadow: isTemplate
+            ? "red 0px -1px 0px 0px inset, red 0px 1px 0px 0px inset"
+            : "0px -1px 0px 0px inset",
+          display: "flex",
+          ...provided?.draggableProps?.style,
+          ...(snapshot?.isDragging && { left: unset })
+        }}
+        key={i}
+      >
+        <div
+          className="alignmentTrackName"
+          style={{
+            position: "sticky",
+            left: 0,
+            zIndex: 10,
+            borderBottom: `1px solid ${isTemplate ? "red" : "lightgray"}`,
+            borderRight: `1px solid ${isTemplate ? "red" : "lightgray"}`,
+            width: this.state.nameDivWidth - 3,
+            padding: 2,
+            marginRight: 3,
+            paddingBottom: 0,
+            minWidth: this.state.nameDivWidth - 3,
+            overflow: "hidden",
+            scrollbarWidth: "none",
+            whiteSpace: "nowrap"
+          }}
+          title={name}
+          key={i}
+        >
+          <div
+            {...provided?.dragHandleProps}
+            style={{
+              ...(compactNames && {
+                display: "flex",
+                alignItems: "flex-start"
+              }),
+              cursor:
+                !isPairwise && allowTrackRearrange && !isTemplate ? "move" : ""
+            }}
+          >
+            <div
+              className="alignmentTrackNameDiv"
+              style={{
+                background: "#3FA6DA",
+                display: "inline-block",
+                color: "white",
+                borderRadius: 5,
+                paddingRight: 5,
+                ...(compactNames && {
+                  marginRight: 5
+                })
+              }}
+            >
+              {allowTrackNameEdit && (
+                <Button
+                  onClick={() => {
+                    showDialog({
+                      ModalComponent: EditTrackNameDialog,
+                      props: {
+                        initialValues: {
+                          name
+                        },
+                        updateName: ({ newName }) => {
+                          updateTrackHelper({
+                            currentPairwiseAlignmentIndex,
+                            pairwiseAlignments,
+                            upsertAlignmentRun,
+                            alignmentId,
+                            alignmentTracks,
+                            alignmentTrackIndex: i,
+                            update: { name: newName }
+                          });
+                        }
+                      }
+                    });
+                  }}
+                  small
+                  data-tip="Edit Track Name"
+                  className="edit-track-name-btn"
+                  icon={<Icon size={12} color="lightgrey" icon="edit"></Icon>}
+                  minimal
+                ></Button>
+              )}
+              {sequenceData.seqLink && (
+                <AnchorButton
+                  href={sequenceData.seqLink}
+                  data-tip={sequenceData.seqLinkTooltip}
+                  target="_blank"
+                  small
+                  icon={
+                    <Icon size={12} color="white" icon="document-open"></Icon>
+                  }
+                  minimal
+                ></AnchorButton>
+              )}
+              {name}
+            </div>
+            <div style={{ fontSize: 10, marginTop: 2, marginBottom: 2 }}>
+              {/* <Icon //tnr: add this once we support forward/reverse for each track
+                color="darkgrey"
+                style={{ marginRight: 10 }}
+                icon="arrow-right"
+              ></Icon> */}
+              {isReversed && (
+                <span
+                  style={{
+                    backgroundColor: isReversed ? "#E76A6E" : "#4C90F0",
+                    padding: 2,
+                    paddingLeft: 4,
+                    color: "white",
+                    marginRight: 2,
+                    borderRadius: "5px"
+                  }}
+                  data-tip={
+                    isReversed
+                      ? "The alignment algorithm matched the reverse complement of this input sequence"
+                      : "The original sequence was NOT reversed complemented by the alignment algorithm"
+                  }
+                >
+                  {isReversed ? "REV" : "FWD"}{" "}
+                </span>
+              )}
+              {wasTrimmed && (
+                <span
+                  style={{
+                    backgroundColor: "#13C9BA",
+                    padding: 2,
+                    paddingLeft: 4,
+                    color: "white",
+                    marginRight: 2,
+                    borderRadius: "5px"
+                  }}
+                  data-tip="This sequence was trimmed and resubmitted for alignment"
+                >
+                  TRIMMED
+                </span>
+              )}
+              {sequenceData.sequence.length} bps
+            </div>
+          </div>
+          <HorizontalPanelDragHandle
+            onDrag={({ dx }) => {
+              this.setState({
+                nameDivWidth: Math.min(
+                  this.state.nameDivWidth - dx,
+                  this.state.width - 20
+                )
+              });
+            }}
+          />
+        </div>
+
+        {handleSelectTrack && !isTemplate && (
+          <div
+            onClick={() => {
+              handleSelectTrack(i);
+            }}
+            style={{
+              position: "absolute",
+              opacity: 0,
+              height: "100%",
+              left: this.state.nameDivWidth,
+              width: linearViewWidth,
+              fontWeight: "bolder",
+              cursor: "pointer",
+              padding: 5,
+              textAlign: "center",
+              zIndex: 400
+            }}
+            className="alignmentViewSelectTrackPopover veWhiteBackground"
+          >
+            Inspect track
+          </div>
+        )}
+        <NonReduxEnhancedLinearView
+          {...{
+            ...rest,
+            caretPosition: this.state[`tempTrimmingCaret${i}`] || -1,
+            selectionLayer,
+            isInAlignment: true,
+            // : { start: -1, end: -1 },
+            annotationVisibilityOverrides:
+              alignmentVisibilityToolOptions.alignmentAnnotationVisibility,
+            linearViewAnnotationLabelVisibilityOverrides:
+              alignmentVisibilityToolOptions.alignmentAnnotationLabelVisibility,
+            marginWith: 0,
+            orfClicked: this.annotationClicked,
+            primerClicked: this.annotationClicked,
+            translationClicked: this.annotationClicked,
+            cutsiteClicked: this.annotationClicked,
+            translationDoubleClicked: this.annotationClicked,
+            deletionLayerClicked: this.annotationClicked,
+            replacementLayerClicked: this.annotationClicked,
+            featureClicked: this.annotationClicked,
+            partClicked: this.annotationClicked,
+            searchLayerClicked: this.annotationClicked,
+            editorDragStarted: noop, //override these since we're defining the handlers above
+            editorDragStopped: noop, //override these since we're defining the handlers above
+            editorDragged: noop, //override these since we're defining the handlers above
+            hideName: true,
+            sequenceData,
+            // sequenceDataWithRefSeqCdsFeatures,
+            tickSpacing,
+            allowSeqDataOverride: true, //override the sequence data stored in redux so we can track the caret position/selection layer in redux but not have to update the redux editor
+            editorName: `${isTemplate ? "template_" : ""}alignmentView${i}`,
+            alignmentData,
+            chromatogramData,
+            height: "100%",
+            vectorInteractionWrapperStyle: {
+              overflowY: "hidden"
+            },
+            marginWidth: 0,
+            linearViewCharWidth: charWidthInLinearView,
+            ignoreGapsOnHighlight: true,
+            ...(linearViewOptions &&
+              (isFunction(linearViewOptions)
+                ? linearViewOptions({
+                    index: i,
+                    isTemplate,
+                    alignmentVisibilityToolOptions,
+                    sequenceData,
+                    alignmentData,
+                    chromatogramData
+                  })
+                : linearViewOptions)),
+            additionalSelectionLayers,
+            dimensions: {
+              width: linearViewWidth
+            },
+            width: linearViewWidth,
+            paddingBottom: 5,
+            scrollDataPassed: this.easyStore
+          }}
+        />
+      </div>
+    );
+    if (isTemplate) return innerRenderItem();
+    if (cloneProps)
+      return innerRenderItem(cloneProps.provided, cloneProps.snapshot);
+    const idToUse = alignmentData.id || sequenceData.id || i + "_index_id";
+    return (
+      <DndDraggable
+        key={idToUse.toString()}
+        index={i}
+        isDragDisabled={isDragDisabled}
+        draggableId={idToUse.toString()}
+      >
+        {innerRenderItem}
+      </DndDraggable>
+    );
+  };
+  handleResize = throttle(([e]) => {
+    this.easyStore.viewportWidth =
+      e.contentRect.width - this.state.nameDivWidth || 400;
+    this.setState({ width: e.contentRect.width });
+  }, 200);
+
+  removeMinimapHighlightForMouseLeave = () => {
+    const minimapLaneEl = document.querySelector(`.minimapLane.lane-hovered`);
+    if (!minimapLaneEl) return;
+    minimapLaneEl.classList.remove("lane-hovered");
+  };
+  updateMinimapHighlightForMouseMove = (event) => {
+    this.latestMouseY = getClientY(event); //we use this variable later
+    this.updateMinimapHighlight();
+  };
+  updateMinimapHighlight = () => {
+    const rows = document.querySelectorAll(`.alignmentViewTrackContainer`);
+    const rowsLength = document.querySelectorAll(`.minimapLane`).length;
+    if (rowsLength <= 4) {
+      return; // no need to include this functionality here
+    }
+    some(rows, (rowDomNode) => {
+      const boundingRowRect = rowDomNode.getBoundingClientRect();
+      if (
+        this.latestMouseY > boundingRowRect.top &&
+        this.latestMouseY < boundingRowRect.top + boundingRowRect.height
+      ) {
+        const prevMinimapLaneEl = document.querySelector(
+          `.minimapLane.lane-hovered`
+        );
+        if (prevMinimapLaneEl) {
+          prevMinimapLaneEl.classList.remove("lane-hovered");
+        }
+        const i = Number(rowDomNode.getAttribute("data-alignment-track-index"));
+
+        //then the click falls within this row
+        const minimapLaneEl = document.querySelector(
+          `.minimapLane:nth-child(${i + 1})`
+        );
+        if (!minimapLaneEl) return;
+        minimapLaneEl.classList.add("lane-hovered");
+        return true; //break the loop early because we found the row the click event landed in
+      }
+    });
+  };
+  onTrackDragStart = () => {
+    this.setState({ isTrackDragging: true });
+  };
+  onTrackDragEnd = ({ destination, source }) => {
+    this.setState({ isTrackDragging: false });
+    if (!destination) {
+      return;
+    }
+    const { upsertAlignmentRun, alignmentId, alignmentTracks } = this.props;
+    upsertAlignmentRun({
+      id: alignmentId,
+      alignmentTracks: array_move(
+        alignmentTracks,
+        source.index,
+        destination.index
+      )
+    });
+  };
+
+  render() {
+    const charWidthInLinearView = this.getCharWidthInLinearView();
+    const {
+      alignmentTracks = [],
+      height,
+      minimapLaneHeight,
+      minimapLaneSpacing,
+      isInPairwiseOverviewView,
+      isPairwise,
+      currentPairwiseAlignmentIndex,
+      hasTemplate,
+      noVisibilityOptions,
+      updateAlignmentSortOrder,
+      alignmentSortOrder,
+      handleBackButtonClicked,
+      noClickDragHandlers,
+      upsertAlignmentRun,
+      alignmentId,
+      allowTrimming,
+      additionalSelectionLayerRightClickedOptions,
+      selectionLayerRightClicked,
+      additionalTopEl,
+      handleAlignmentRename,
+      alignmentVisibilityToolOptions
+    } = this.props;
+    const sequenceLength = this.getMaxLength();
+    if (
+      !alignmentTracks ||
+      !alignmentTracks[0] ||
+      !alignmentTracks[0].alignmentData
+    ) {
+      console.error("corrupted data!", this.props);
+      return "corrupted data!";
+    }
+
+    const getTrackVis = (alignmentTracks, isTemplate, allTracks) => {
+      const rowData = {};
+      const innerTrackVis = (drop_provided, drop_snapshot) => {
+        return (
+          <div
+            className="alignmentTracks "
+            style={{
+              overflowY: "auto",
+              display: "flex",
+              zIndex: 10
+            }}
+          >
+            <div
+              style={{
+                overflowX: "auto",
+                width: this.state.width
+              }}
+              ref={(ref) => {
+                this[isTemplate ? "alignmentHolderTop" : "alignmentHolder"] =
+                  ref;
+              }}
+              onContextMenu={(e) => {
+                if (
+                  !allowTrimming ||
+                  isTargetWithinEl(e, ".alignmentTrackName")
+                ) {
+                  return;
+                }
+
+                this.getTrackTrimmingOptions({
+                  e,
+                  allTracks,
+                  upsertAlignmentRun,
+                  alignmentId,
+                  currentPairwiseAlignmentIndex
+                });
+              }}
+              onMouseLeave={this.removeMinimapHighlightForMouseLeave}
+              onMouseMove={this.updateMinimapHighlightForMouseMove}
+              dataname="scrollGroup"
+              className="alignmentHolder"
+              onScroll={isTemplate ? this.handleTopScroll : this.handleScroll}
+            >
+              <ReactDraggable
+                disabled={this.state.isTrackDragging}
+                bounds={{ top: 0, left: 0, right: 0, bottom: 0 }}
+                onDrag={
+                  noClickDragHandlers
+                    ? noop
+                    : (event) => {
+                        if (this.state.isTrackDragging) return;
+                        this.getNearestCursorPositionToMouseEvent(
+                          rowData,
+                          event,
+                          editorDragged
+                        );
+                      }
+                }
+                onStart={
+                  noClickDragHandlers
+                    ? noop
+                    : (event) => {
+                        if (isTargetWithinEl(event, ".alignmentTrackName")) {
+                          return this.setState({ isTrackDragging: true });
+                        }
+                        if (this.state.isTrackDragging) return;
+                        this.getNearestCursorPositionToMouseEvent(
+                          rowData,
+                          event,
+                          editorDragStarted
+                        );
+                      }
+                }
+                onStop={
+                  noClickDragHandlers
+                    ? noop
+                    : (...args) => {
+                        setTimeout(() => {
+                          this.setState({ isTrackDragging: false });
+                        }, 0);
+                        editorDragStopped(...args);
+                      }
+                }
+              >
+                <div
+                  ref={(ref) => (this.veTracksAndAlignmentHolder = ref)}
+                  className={classNames("veTracksAndAlignmentHolder", {
+                    isTrackDragging: this.state.isTrackDragging
+                  })}
+                  // onContextMenu={
+                  //tnrtodo add copy single track/all tracks logic here
+                  // (event) => {
+                  // this.getNearestCursorPositionToMouseEvent(
+                  //   rowData,
+                  //   event,
+                  //   () => {
+                  //   }
+                  // );
+                  // }
+                  // }
+                  onClick={
+                    noClickDragHandlers
+                      ? noop
+                      : (event) => {
+                          if (this.state.isTrackDragging) return;
+                          if (isTargetWithinEl(event, ".alignmentTrackName")) {
+                            return;
+                          }
+                          this.getNearestCursorPositionToMouseEvent(
+                            rowData,
+                            event,
+                            editorClicked
+                          );
+                        }
+                  }
+                >
+                  <PerformantSelectionLayer
+                    leftMargin={this.state.nameDivWidth}
+                    className="veAlignmentSelectionLayer"
+                    isDraggable
+                    selectionLayerRightClicked={
+                      selectionLayerRightClicked
+                        ? (...args) => {
+                            selectionLayerRightClicked(...args, this.props);
+                          }
+                        : (...args) => {
+                            const { event } = args[0];
+                            const track = getTrackFromEvent(event, allTracks);
+
+                            const alignmentData = track.alignmentData;
+                            const { name } = alignmentData;
+                            showContextMenu(
+                              [
+                                ...(additionalSelectionLayerRightClickedOptions
+                                  ? additionalSelectionLayerRightClickedOptions(
+                                      ...args,
+                                      this.props
+                                    )
+                                  : []),
+                                {
+                                  text: "Copy Selection of All Alignments as Fasta",
+                                  className:
+                                    "copyAllAlignmentsFastaClipboardHelper",
+                                  hotkey: "cmd+c",
+                                  willUnmount: () => {
+                                    this
+                                      .copyAllAlignmentsFastaClipboardHelper &&
+                                      this.copyAllAlignmentsFastaClipboardHelper.destroy();
+                                  },
+                                  didMount: () => {
+                                    this.copyAllAlignmentsFastaClipboardHelper =
+                                      new Clipboard(
+                                        `.copyAllAlignmentsFastaClipboardHelper`,
+                                        {
+                                          action: "copyAllAlignmentsFasta",
+                                          text: () => {
+                                            return this.getAllAlignmentsFastaText();
+                                          }
+                                        }
+                                      );
+                                  },
+                                  onClick: () => {
+                                    window.toastr.success("Selection Copied");
+                                  }
+                                },
+                                {
+                                  text: `Copy Selection of ${name} as Fasta`,
+                                  className:
+                                    "copySpecificAlignmentFastaClipboardHelper",
+                                  willUnmount: () => {
+                                    this
+                                      .copySpecificAlignmentFastaClipboardHelper &&
+                                      this.copySpecificAlignmentFastaClipboardHelper.destroy();
+                                  },
+                                  didMount: () => {
+                                    this.copySpecificAlignmentFastaClipboardHelper =
+                                      new Clipboard(
+                                        `.copySpecificAlignmentFastaClipboardHelper`,
+                                        {
+                                          action: "copySpecificAlignmentFasta",
+                                          text: () => {
+                                            const { selectionLayer } =
+                                              this.props.store.getState()
+                                                .VectorEditor
+                                                .__allEditorsOptions.alignments[
+                                                this.props.id
+                                              ] || {};
+                                            const seqDataToCopy =
+                                              getSequenceDataBetweenRange(
+                                                alignmentData,
+                                                selectionLayer
+                                              ).sequence;
+                                            const seqDataToCopyAsFasta = `>${name}\r\n${seqDataToCopy}\r\n`;
+                                            return seqDataToCopyAsFasta;
+                                          }
+                                        }
+                                      );
+                                  },
+                                  onClick: () => {
+                                    window.toastr.success(
+                                      "Selection Copied As Fasta"
+                                    );
+                                  }
+                                },
+                                {
+                                  text: `Copy Selection of ${name}`,
+                                  className:
+                                    "copySpecificAlignmentAsPlainClipboardHelper",
+                                  willUnmount: () => {
+                                    this
+                                      .copySpecificAlignmentAsPlainClipboardHelper &&
+                                      this.copySpecificAlignmentAsPlainClipboardHelper.destroy();
+                                  },
+                                  didMount: () => {
+                                    this.copySpecificAlignmentAsPlainClipboardHelper =
+                                      new Clipboard(
+                                        `.copySpecificAlignmentAsPlainClipboardHelper`,
+                                        {
+                                          action: "copySpecificAlignmentFasta",
+                                          text: () => {
+                                            const { selectionLayer } =
+                                              this.props.store.getState()
+                                                .VectorEditor
+                                                .__allEditorsOptions.alignments[
+                                                this.props.id
+                                              ] || {};
+                                            const seqDataToCopy =
+                                              getSequenceDataBetweenRange(
+                                                alignmentData,
+                                                selectionLayer
+                                              ).sequence;
+                                            return seqDataToCopy;
+                                          }
+                                        }
+                                      );
+                                  },
+                                  onClick: () => {
+                                    window.toastr.success("Selection Copied");
+                                  }
+                                }
+                              ],
+                              undefined,
+                              event
+                            );
+                          }
+                    }
+                    easyStore={this.easyStore}
+                    sequenceLength={sequenceLength}
+                    charWidth={this.getCharWidthInLinearView()}
+                    row={{ start: 0, end: sequenceLength - 1 }}
+                  ></PerformantSelectionLayer>
+                  <PerformantCaret
+                    leftMargin={this.state.nameDivWidth}
+                    className="veAlignmentSelectionLayer"
+                    isDraggable
+                    sequenceLength={sequenceLength}
+                    charWidth={this.getCharWidthInLinearView()}
+                    row={{ start: 0, end: sequenceLength - 1 }}
+                    easyStore={this.easyStore}
+                  />
+                  {isTemplate ? (
+                    this.renderItem(0, 0, isTemplate)
+                  ) : (
+                    <ReactList
+                      ref={(c) => {
+                        this.InfiniteScroller = c;
+                        const domNode = ReactDOM.findDOMNode(c);
+                        if (domNode instanceof HTMLElement) {
+                          drop_provided.innerRef(domNode);
+                        }
+                      }}
+                      type="variable"
+                      itemSizeEstimator={this.estimateRowHeight}
+                      itemRenderer={this.renderItem}
+                      length={
+                        alignmentTracks.length +
+                        (drop_snapshot.isUsingPlaceholder ? 1 : 0)
+                      }
+                    />
+                  )}
+                </div>
+              </ReactDraggable>
+            </div>
+          </div>
+        );
+      };
+      if (isTemplate) return innerTrackVis();
+      else
+        return (
+          <Droppable
+            mode="virtual"
+            renderClone={(provided, snapshot, { source: { index } }) => {
+              return this.renderItem(index, index, false, {
+                provided,
+                snapshot
+              });
+            }}
+            direction="vertical"
+            droppableId={"droppable" + isTemplate ? "_no_drop" : ""}
+          >
+            {innerTrackVis}
+          </Droppable>
+        );
+    };
+
+    const [firstTrack, ...otherTracks] = alignmentTracks;
+    const totalWidthOfMinimap = this.state.width;
+    const totalWidthInAlignmentView = 14 * this.getSequenceLength();
+    const minSliderSize = Math.min(
+      totalWidthOfMinimap * (totalWidthOfMinimap / totalWidthInAlignmentView),
+      totalWidthOfMinimap
+    );
+    const viewportHeight = Math.max(
+      document.documentElement.clientHeight,
+      window.innerHeight || 0
+    );
+
+    /**
+     * Parameters to be passed to our Pinch Handler component
+     * OnPinch is the method to be executed when the pinch gesture is registered
+     * Pinch Handler for minimap
+     */
+    const pinchHandler = {
+      onPinch: ({ delta: [d] }) => {
+        this.bindOutsideChangeHelper.triggerChange(({ value, changeValue }) => {
+          // changeValue(d);
+          if (d > 0) {
+            if (value > 8) {
+              changeValue(value + 0.4);
+            } else {
+              changeValue(value + 0.2);
+            }
+          } else if (d < 0) {
+            if (value > 8) {
+              changeValue(value - 0.4);
+            } else {
+              changeValue(value - 0.2);
+            }
+          }
+        });
+        updateLabelsForInViewFeatures();
+      }
+    };
+
+    return (
+      <PinchHelper {...pinchHandler}>
+        <ResizeSensor onResize={this.handleResize}>
+          <div
+            style={{
+              height: height || (isPairwise ? "auto" : viewportHeight * 0.88),
+              display: "flex",
+              flexDirection: "column",
+              justifyContent: "space-between",
+              position: "relative",
+              overflowY: "auto",
+              ...this.props.style
+              // borderTop: "1px solid black"
+            }}
+            className="alignmentView"
+          >
+            <DragDropContext
+              onDragStart={this.onTrackDragStart}
+              onDragEnd={this.onTrackDragEnd}
+            >
+              <div
+                style={{
+                  display: "flex",
+                  flexDirection: "column",
+                  position: "relative",
+                  overflowY: "auto"
+                }}
+                className="alignmentView-top-container"
+              >
+                <div
+                  style={{
+                    paddingTop: "3px",
+                    paddingBottom: "5px",
+                    borderBottom: "1px solid",
+                    display: "flex",
+                    minHeight: "32px",
+                    width: "100%",
+                    flexWrap: "nowrap",
+                    flexDirection: "row",
+                    flex: "0 0 auto"
+                  }}
+                  className="ve-alignment-top-bar"
+                >
+                  {handleBackButtonClicked && (
+                    <Tooltip content="Back to Pairwise Alignment Overview">
+                      <Button
+                        icon="arrow-left"
+                        onClick={() => {
+                          // this.setState({
+                          //   charWidthInLinearView: charWidthInLinearViewDefault
+                          // });
+                          handleBackButtonClicked();
+                          this.caretPositionUpdate(-1);
+                        }}
+                        small
+                        intent={Intent.PRIMARY}
+                        minimal
+                        style={{ marginRight: 10 }}
+                        className="alignmentViewBackButton"
+                      />
+                    </Tooltip>
+                  )}
+
+                  <div style={{ display: "flex" }}>
+                    <EditableText
+                      disabled={!handleAlignmentRename}
+                      onChange={(v) => {
+                        this.setState({
+                          alignmentName: v
+                        });
+                      }}
+                      maxLength={399} //stop the name from being tooo long
+                      value={this.state.alignmentName}
+                      onConfirm={async (v) => {
+                        if (!v) {
+                          this.setState({
+                            alignmentName: this.props.alignmentName
+                          });
+                          return;
+                        }
+                        if (v === this.props.alignmentName) {
+                          return; //already saved this name
+                        }
+                        this.setState({ saveMessage: "Alignment Renaming.." });
+                        this.setState({ saveMessageLoading: true });
+                        await handleAlignmentRename(v, this.props);
+                        this.setState({ saveMessage: "Rename Successful" });
+                        this.setState({ saveMessageLoading: false });
+                        setTimeout(() => {
+                          this.setState({ saveMessage: undefined });
+                          this.setState({ saveMessageLoading: false });
+                        }, 5000);
+                      }}
+                      selectAllOnFocus={true}
+                      className="veAlignmentName"
+                    ></EditableText>
+                    &nbsp;&nbsp;&nbsp;
+                    <div
+                      className="veAlignmentType"
+                      style={{
+                        paddingTop: "3px",
+                        fontSize: "14px",
+                        color: "grey",
+                        maxWidth: "300px",
+                        overflow: "hidden",
+                        textOverflow: "ellipsis",
+                        whiteSpace: "nowrap"
+                      }}
+                      title={
+                        this.props.alignmentType || "Unknown Alignment Type"
+                      }
+                    >
+                      {this.props.alignmentType || "Unknown Alignment Type"}
+                    </div>
+                  </div>
+
+                  {this.props.unmappedSeqs && (
+                    <InfoHelper
+                      size={20}
+                      content={
+                        <div>
+                          This alignment had sequences that did not map to the
+                          template sequence:
+                          {this.props.unmappedSeqs.map(
+                            ({ sequenceData }, i) => (
+                              <div key={i}>{sequenceData.name}</div>
+                            )
+                          )}
+                        </div>
+                      }
+                      intent="warning"
+                      icon="warning-sign"
+                    ></InfoHelper>
+                  )}
+                  {!isInPairwiseOverviewView && (
+                    <UncontrolledSliderWithPlusMinusBtns
+                      noWraparound
+                      bindOutsideChangeHelper={this.bindOutsideChangeHelper}
+                      onClick={() => {
+                        setTimeout(this.scrollToCaret, 0);
+                      }}
+                      minCharWidth={this.getMinCharWidth()}
+                      onChange={async (zoomLvl) => {
+                        this.isZooming = true;
+                        setTimeout(() => {
+                          this.isZooming = false;
+                        }, 10);
+                        // zoomLvl is in the range of 0 to 10
+                        const minCharWidth = this.getMinCharWidth();
+                        const scaleFactor = Math.pow(12 / minCharWidth, 1 / 10);
+                        const newCharWidth =
+                          minCharWidth * Math.pow(scaleFactor, zoomLvl);
+                        await this.setCharWidthInLinearView({
+                          charWidthInLinearView: newCharWidth
+                        });
+                        await this.scrollToCaret();
+                        await updateLabelsForInViewFeatures({
+                          rectElement: ".alignmentHolder"
+                        });
+                      }}
+                      coerceInitialValue={coerceInitialValue}
+                      title="Adjust Zoom Level"
+                      style={{ paddingTop: "4px", width: 100 }}
+                      className="veZoomAlignmentSlider ove-slider"
+                      labelRenderer={false}
+                      initialValue={charWidthInLinearView}
+                      stepSize={0.05} //was 0.01
+                      max={10}
+                      min={0}
+                      clickStepSize={0.5}
+                    />
+                  )}
+                  {!noVisibilityOptions && !isInPairwiseOverviewView && (
+                    <AlignmentVisibilityTool
+                      currentPairwiseAlignmentIndex={
+                        currentPairwiseAlignmentIndex
+                      }
+                      {...alignmentVisibilityToolOptions}
+                    />
+                  )}
+                  {updateAlignmentSortOrder && !isInPairwiseOverviewView && (
+                    <Popover
+                      minimal
+                      content={
+                        <Menu>
+                          <MenuItem
+                            active={true || alignmentSortOrder}
+                            onClick={() => {
+                              updateAlignmentSortOrder("Position");
+                            }}
+                            text="Position"
+                          />
+                          <MenuItem
+                            active={false || alignmentSortOrder}
+                            onClick={() => {
+                              updateAlignmentSortOrder("Alphabetical");
+                            }}
+                            text="Alphabetical"
+                          />
+                        </Menu>
+                      }
+                      target={
+                        <Button
+                          small
+                          text="Sort Order"
+                          rightIcon="caret-down"
+                          icon="sort"
+                        />
+                      }
+                    />
+                  )}
+                  {additionalTopEl}
+                  {this.state.saveMessage && (
+                    <div
+                      className="ove-menu-toast"
+                      style={{
+                        display: "flex",
+                        alignItems: "center",
+                        marginLeft: "auto",
+                        marginRight: 10
+                      }}
+                    >
+                      {this.state.saveMessageLoading ? (
+                        <div>
+                          <Spinner size={15}></Spinner>
+                        </div>
+                      ) : (
+                        <Icon icon="tick-circle" intent="success"></Icon>
+                      )}{" "}
+                      &nbsp;
+                      {this.state.saveMessage}
+                    </div>
+                  )}
+                </div>
+                {hasTemplate ? (
+                  <React.Fragment>
+                    <div className="alignmentTrackFixedToTop">
+                      {getTrackVis([firstTrack], true, alignmentTracks)}
+                    </div>
+                    {getTrackVis(otherTracks, false, alignmentTracks)}
+                  </React.Fragment>
+                ) : (
+                  getTrackVis(alignmentTracks, false, alignmentTracks)
+                )}
+              </div>
+            </DragDropContext>
+            {!isInPairwiseOverviewView && (
+              <div
+                className="alignmentViewBottomBar"
+                style={{
+                  // flexGrow: 1,
+                  // minHeight: "-webkit-min-content", //https://stackoverflow.com/questions/28029736/how-to-prevent-a-flex-item-from-shrinking-smaller-than-its-content
+                  maxHeight: 210,
+                  marginTop: 4,
+                  paddingTop: 4,
+                  borderTop: "1px solid lightgrey",
+                  display: "flex"
+                }}
+              >
+                <Minimap
+                  {...{
+                    selectionLayerComp: (
+                      <React.Fragment>
+                        <PerformantSelectionLayer
+                          is
+                          hideCarets
+                          className="veAlignmentSelectionLayer veMinimapSelectionLayer"
+                          easyStore={this.easyStore}
+                          sequenceLength={sequenceLength}
+                          charWidth={this.getMinCharWidth(true)}
+                          row={{ start: 0, end: sequenceLength - 1 }}
+                        ></PerformantSelectionLayer>
+                        <PerformantCaret
+                          style={{
+                            opacity: 0.2
+                          }}
+                          className="veAlignmentSelectionLayer veMinimapSelectionLayer"
+                          sequenceLength={sequenceLength}
+                          charWidth={this.getMinCharWidth(true)}
+                          row={{ start: 0, end: sequenceLength - 1 }}
+                          easyStore={this.easyStore}
+                        />
+                      </React.Fragment>
+                    ),
+                    alignmentTracks,
+                    dimensions: {
+                      width: Math.max(this.state.width, 10) || 10
+                    },
+                    nameDivOffsetPercent: 0,
+                    // this.state.nameDivWidth / this.getMaxLinearViewWidth(),
+                    scrollYToTrack: this.scrollYToTrack,
+                    onSizeAdjust: this.onMinimapSizeAdjust,
+                    minSliderSize,
+                    laneHeight:
+                      minimapLaneHeight ||
+                      (alignmentTracks.length > 5 ? 10 : 17),
+                    laneSpacing:
+                      minimapLaneSpacing ||
+                      (alignmentTracks.length > 5 ? 2 : 1),
+                    easyStore: this.easyStore,
+                    numBpsShownInLinearView: this.getNumBpsShownInLinearView(),
+                    scrollAlignmentView: this.state.scrollAlignmentView
+                  }}
+                  onMinimapScrollX={this.scrollAlignmentToPercent}
+                />
+              </div>
+            )}
+            <GlobalDialog
+            // {...pickedUserDefinedHandlersAndOpts}
+            // dialogOverrides={pick(this.props, [
+            //   "AddOrEditFeatureDialogOverride",
+            //   "AddOrEditPartDialogOverride",
+            //   "AddOrEditPrimerDialogOverride"
+            // ])}
+            />
+          </div>
+        </ResizeSensor>
+      </PinchHelper>
+    );
+  }
+
+  getTrackTrimmingOptions({
+    e,
+    allTracks,
+    upsertAlignmentRun,
+    currentPairwiseAlignmentIndex,
+    alignmentId
+  }) {
+    const track = getTrackFromEvent(e, allTracks);
+
+    this.getNearestCursorPositionToMouseEvent(
+      this.rowData,
+      e,
+      ({ nearestCaretPos }) => {
+        this.setState({
+          [`tempTrimmingCaret${track.index}`]: nearestCaretPos
+        });
+        const afterDisabled =
+          nearestCaretPos <= track.alignmentData.trimmedRange?.start;
+        const beforeDisabled =
+          nearestCaretPos > track.alignmentData.trimmedRange?.end;
+        showContextMenu(
+          [
+            {
+              divider: (
+                <div
+                  style={{
+                    color: "#137cbd",
+                    fontSize: 13,
+                    fontWeight: "bold"
+                  }}
+                >{`Trim ${
+                  track.sequenceData.name || track.sequenceData.id
+                }...`}</div>
+              )
+            },
+            {
+              text: "Ignore Before",
+              disabled: beforeDisabled,
+              icon: "drawer-left-filled",
+              onMouseOver: () =>
+                !beforeDisabled &&
+                this.setState({
+                  [`tempTrimBefore${track.index}`]: {
+                    start: 0,
+                    end: nearestCaretPos - 1
+                  }
+                }),
+              onMouseLeave: () =>
+                this.setState({
+                  [`tempTrimBefore${track.index}`]: undefined
+                }),
+              onClick: () => {
+                updateTrackHelper({
+                  currentPairwiseAlignmentIndex,
+                  upsertAlignmentRun,
+                  alignmentId,
+                  alignmentTracks: allTracks,
+                  alignmentTrackIndex: track.index,
+                  hasBeenTrimmed: true,
+                  update: {
+                    trimmedRange: {
+                      start: nearestCaretPos,
+                      end:
+                        track.alignmentData.trimmedRange?.end ||
+                        this.getMaxLength() - 1
+                    }
+                  }
+                });
+              }
+            },
+            {
+              text: "Ignore After",
+              disabled: afterDisabled,
+              icon: "drawer-right-filled",
+              onMouseOver: () =>
+                !afterDisabled &&
+                this.setState({
+                  [`tempTrimAfter${track.index}`]: {
+                    start: nearestCaretPos,
+                    end: this.getMaxLength() - 1
+                  }
+                }),
+              onMouseLeave: () =>
+                this.setState({
+                  [`tempTrimAfter${track.index}`]: undefined
+                }),
+              onClick: () => {
+                updateTrackHelper({
+                  currentPairwiseAlignmentIndex,
+                  upsertAlignmentRun,
+                  alignmentId,
+                  alignmentTracks: allTracks,
+                  alignmentTrackIndex: track.index,
+                  hasBeenTrimmed: true,
+                  update: {
+                    trimmedRange: {
+                      start: track.alignmentData.trimmedRange?.start || 0,
+                      end: nearestCaretPos - 1
+                    }
+                  }
+                });
+              }
+            },
+            {
+              divider: ""
+            },
+            {
+              text: "Clear Trim(s)",
+              disabled: !(track?.alignmentData?.trimmedRange?.start > -1),
+              icon: "trash",
+              onClick: () => {
+                updateTrackHelper({
+                  currentPairwiseAlignmentIndex,
+                  upsertAlignmentRun,
+                  alignmentId,
+                  alignmentTracks: allTracks,
+                  alignmentTrackIndex: track.index,
+                  hasBeenTrimmed: false,
+                  update: {
+                    trimmedRange: undefined
+                  }
+                });
+              }
+            }
+          ],
+          undefined,
+          e,
+          () => {
+            this.setState({
+              [`tempTrimmingCaret${track.index}`]: undefined
+            });
+          }
+        );
+      }
+    );
+    e.preventDefault();
+    e.stopPropagation();
+  }
+}
+
+export default compose(
+  withStore,
+  withEditorProps,
+  connect(
+    (state, ownProps) => {
+      // const {id}
+      const {
+        VectorEditor: {
+          __allEditorsOptions: { alignments }
+        }
+      } = state;
+      const { id: alignmentId, updateAlignmentViewVisibility } = ownProps;
+      const alignment = { ...alignments[alignmentId], id: alignmentId };
+      const {
+        stateTrackingId,
+        unmappedSeqs,
+        alignmentTracks,
+        pairwiseAlignments,
+        alignmentType,
+        scrollPercentageToJumpTo,
+        pairwiseOverviewAlignmentTracks,
+        loading,
+        alignmentAnnotationVisibility,
+        alignmentAnnotationLabelVisibility,
+        caretPosition = -1,
+        selectionLayer = { start: -1, end: -1 }
+      } = alignment || {};
+      if (loading) {
+        return {
+          loading: true
+        };
+      }
+      if (!alignmentTracks && !pairwiseAlignments)
+        return {
+          noTracks: true
+        };
+      const templateLength = (
+        pairwiseAlignments ? pairwiseAlignments[0][0] : alignmentTracks[0]
+      ).alignmentData.sequence.length;
+
+      const alignmentAnnotationsToToggle = [
+        "features",
+        "parts",
+        "sequence",
+        "reverseSequence",
+        "axis",
+        "translations",
+        "cdsFeatureTranslations",
+        "chromatogram",
+        "dnaColors",
+        "compactNames"
+      ];
+      const togglableAlignmentAnnotationSettings = {};
+      map(alignmentAnnotationsToToggle, (annotation) => {
+        if (annotation in alignmentAnnotationVisibility) {
+          togglableAlignmentAnnotationSettings[annotation] =
+            alignmentAnnotationVisibility[annotation];
+        }
+      });
+
+      const annotationsWithCounts = [];
+      if (alignmentTracks) {
+        let totalNumOfFeatures = 0;
+        let totalNumOfParts = 0;
+        alignmentTracks.forEach((seq) => {
+          if (seq.sequenceData.features) {
+            totalNumOfFeatures += seq.sequenceData.features.length;
+          }
+          if (seq.sequenceData.parts) {
+            totalNumOfParts += seq.sequenceData.parts.length;
+          }
+        });
+        annotationsWithCounts.push({
+          features: totalNumOfFeatures,
+          parts: totalNumOfParts
+        });
+      } else if (pairwiseAlignments) {
+        pairwiseAlignments.forEach((pairwise) => {
+          let totalNumOfFeatures = 0;
+          let totalNumOfParts = 0;
+          pairwise.forEach((seq) => {
+            if (seq.sequenceData.features) {
+              totalNumOfFeatures += seq.sequenceData.features.length;
+            }
+            if (seq.sequenceData.parts) {
+              totalNumOfParts += seq.sequenceData.parts.length;
+            }
+          });
+          annotationsWithCounts.push({
+            features: totalNumOfFeatures,
+            parts: totalNumOfParts
+          });
+        });
+      }
+
+      return {
+        isAlignment: true,
+        selectionLayer,
+        unmappedSeqs,
+        caretPosition,
+        alignmentId,
+        stateTrackingId,
+        sequenceData: {
+          //pass fake seq data in so editor interactions work
+          sequence: Array.from(templateLength)
+            .map(() => "a")
+            .join("")
+        },
+        pairwiseAlignments,
+        alignmentType,
+        alignmentTracks,
+        scrollPercentageToJumpTo,
+        pairwiseOverviewAlignmentTracks,
+        //manipulate the props coming in so we can pass a single clean prop to the visibility options tool
+        alignmentVisibilityToolOptions: {
+          alignmentAnnotationVisibility,
+          alignmentAnnotationLabelVisibility,
+          alignmentAnnotationVisibilityToggle: (updates) => {
+            setTimeout(() => {
+              updateLabelsForInViewFeatures({
+                rectElement: ".alignmentHolder"
+              });
+            }, 0);
+
+            updateAlignmentViewVisibility({
+              ...alignment,
+              alignmentAnnotationVisibility: {
+                ...alignment.alignmentAnnotationVisibility,
+                ...updates
+              }
+            });
+          },
+          alignmentAnnotationLabelVisibilityToggle: (name) => {
+            updateAlignmentViewVisibility({
+              ...alignment,
+              alignmentAnnotationLabelVisibility: {
+                ...alignment.alignmentAnnotationLabelVisibility,
+                [name]: !alignment.alignmentAnnotationLabelVisibility[name]
+              }
+            });
+          },
+          togglableAlignmentAnnotationSettings,
+          annotationsWithCounts
+        }
+      };
+    },
+    {
+      ...alignmentActions
+    }
+  ),
+  branch(
+    ({ loading }) => loading,
+    renderComponent(() => {
+      return <Loading bounce />;
+    })
+  ),
+  branch(
+    ({ noTracks }) => noTracks,
+    renderComponent(() => {
+      return (
+        <div style={{ minHeight: 30, minWidth: 150 }}>"No Tracks Found"</div>
+      );
+    })
+  ),
+  branch(
+    ({ pairwiseAlignments }) => pairwiseAlignments,
+    renderComponent((props) => {
+      return <PairwiseAlignmentView {...props} />;
+    })
+  )
+)(AlignmentView);
+
+const PerformantCaret = view(({ easyStore, ...rest }) => {
+  return <Caret caretPosition={easyStore.caretPosition} {...rest} />;
+});
+
+function cleanTracks(alignmentTracks) {
+  return alignmentTracks.map((t) => {
+    return omit(t, [
+      "matchHighlightRanges",
+      "additionalSelectionLayers",
+      "mismatches"
+    ]);
+  });
+}