@teselagen/ove 0.0.13 → 0.0.15

package/src/RowItem/getXStartAndWidthFromNonCircularRange.js

@@ -0,0 +1,12 @@
+import { getRangeLength } from "@teselagen/range-utils";
+
+export default function getXStartAndWidthFromNonCircularRange(
+  range,
+  charWidth
+) {
+  const rangeLength = getRangeLength(range);
+  return {
+    width: rangeLength * charWidth,
+    xStart: range.start * charWidth
+  };
+}

package/src/RowItem/getXStartAndWidthOfRangeWrtRow.js

@@ -0,0 +1,27 @@
+import { normalizePositionByRangeLength } from "@teselagen/range-utils";
+import { isNumber } from "lodash";
+
+export default function getXStartAndWidthOfRangeWrtRow({
+  range,
+  row,
+  charWidth,
+  sequenceLength,
+  gapsBefore = 0,
+  gapsInside = 0
+}) {
+  const xStart =
+    ((!isNumber(gapsBefore) ? 0 : gapsBefore) +
+      normalizePositionByRangeLength(range.start - row.start, sequenceLength)) *
+    charWidth;
+  const obj = {
+    xStart,
+    width:
+      (gapsInside +
+        normalizePositionByRangeLength(
+          range.end + 1 - range.start,
+          sequenceLength + 1
+        )) *
+      charWidth
+  };
+  return obj;
+}

package/src/RowItem/getXStartAndWidthOfRowAnnotation.js

@@ -0,0 +1,19 @@
+export default function getXStartAndWidthOfRowAnnotation(
+  range,
+  bpsPerRow,
+  charWidth,
+  gapsBefore = 0,
+  gapsInside = 0
+) {
+  const startOffset = range.start % bpsPerRow;
+  const toReturn = {
+    startOffset,
+    xStart: (startOffset + gapsBefore) * charWidth,
+    width: getWidth(range, charWidth, gapsInside)
+  };
+  return toReturn;
+}
+
+export function getWidth(range, charWidth, gapsInside = 0) {
+  return (range.end + 1 - range.start + gapsInside) * charWidth;
+}

package/src/RowItem/index.js

@@ -0,0 +1,647 @@
+import {
+  normalizePositionByRangeLength,
+  getSequenceWithinRange,
+  getOverlapsOfPotentiallyCircularRanges
+} from "@teselagen/range-utils";
+import { map, camelCase, startCase, startsWith, flatMap, assign, noop } from "lodash";
+import { getComplementSequenceString } from "@teselagen/sequence-utils";
+import React, { useMemo } from "react";
+import pluralize from "pluralize";
+import SelectionLayer from "./SelectionLayer";
+import Sequence from "./Sequence";
+import Axis from "./Axis";
+import Orfs from "./Orfs";
+import Translations from "./Translations";
+import Labels from "./Labels";
+import Cutsites from "./Cutsites";
+import Caret from "./Caret";
+import StackedAnnotations from "./StackedAnnotations";
+import "./style.css";
+import Chromatogram from "./Chromatograms/Chromatogram";
+import { rowHeights } from "../RowView/estimateRowHeight";
+import { getAllSelectionLayers } from "../utils/selectionLayer";
+import { filter } from "lodash";
+import { defaultCharWidth } from "../constants/rowviewContants";
+import { CutsiteSelectionLayers } from "./CutsiteSelectionLayers";
+
+
+
+function filterRanges(ranges, extraProps = {}) {
+  if (!ranges) return ranges;
+  if (extraProps.onlyForward) {
+    ranges = filter(ranges, (a) => a.annotation.forward);
+  }
+  if (extraProps.onlyReverse) {
+    ranges = filter(ranges, (a) => !a.annotation.forward);
+  }
+  return ranges;
+}
+function getPropsForType(props, type, pluralType, extraProps) {
+  const upperPluralType = startCase(pluralType);
+  const annotationRanges = filterRanges(props.row[pluralType], extraProps);
+
+  const toRet = {
+    annotationColor: props[pluralType + "Color"],
+    annotationHeight:
+      props[pluralType + "Height"] || rowHeights[pluralType].height,
+    spaceBetweenAnnotations:
+      props["spaceBetweenAnnotations" + upperPluralType] ||
+      rowHeights[pluralType].spaceBetweenAnnotations,
+    marginTop:
+      props[pluralType + "MarginTop"] || rowHeights[pluralType].marginTop,
+    marginBottom:
+      props[pluralType + "MarginBottom"] || rowHeights[pluralType].marginBottom,
+    annotationRanges,
+    showLabels:
+      props.annotationLabelVisibility &&
+      props.annotationLabelVisibility[pluralType],
+    onClick: props[type + "Clicked"],
+    onRightClick: props[type + "RightClicked"],
+    onDoubleClick: props[type + "DoubleClicked"]
+  };
+
+  return toRet;
+}
+
+export default function RowItem(props) {
+  let {
+    noRedux,
+    charWidth = defaultCharWidth,
+    selectionLayer = { start: -1, end: -1 },
+    deletionLayers = {},
+    replacementLayers = {},
+    searchLayers = [],
+    rowTopComp,
+    rowBottomComp,
+    isProtein,
+    tickSpacing,
+    truncateLabelsThatDoNotFit = true,
+    aminoAcidNumbersHeight = rowHeights.aminoAcidNumbers.height,
+    cutsiteLabelHeight = rowHeights.cutsiteLabels.height,
+    sequenceHeight = rowHeights.sequence.height,
+    axisHeight = rowHeights.axis.height,
+    primerHeight = rowHeights.primers.height,
+    axisMarginTop = rowHeights.axis.marginTop,
+    width,
+    annotationVisibility = {},
+    annotationLabelVisibility = {},
+    additionalSelectionLayers = [],
+    caretPosition = -1,
+    row = {
+      sequence: "",
+      start: 0,
+      end: 0,
+      rowNumber: 0
+    },
+    readOnly,
+    isRowView,
+    emptyText,
+    alignmentType,
+    alignmentData,
+    sequenceLength = row.sequence.length,
+    chromatogramData,
+    fullSequence = "",
+    replacementLayerClicked = noop,
+    replacementLayerRightClicked = noop,
+    searchLayerClicked = noop,
+    backgroundRightClicked = noop,
+    selectionLayerRightClicked = noop,
+    searchLayerRightClicked = noop,
+    translationDoubleClicked = noop,
+    minHeight = 22,
+    bpsPerRow = sequenceLength,
+    editorName,
+    rowContainerStyle,
+    onScroll,
+    scrollData,
+    onlyShowLabelsThatDoNotFit,
+    labelLineIntensity,
+    isLinearView,
+    scalePct,
+    setScalePct,
+    extraAnnotationProps = {}
+  } = props;
+
+  const {
+    chromatogram: showChromatogram,
+    // orfLabels: showOrfLabel,
+    cutsites: showCutsites,
+    cutsitesInSequence: showCutsitesInSequence,
+    axis: showAxis,
+    axisNumbers: showAxisNumbers,
+    // yellowAxis: showYellowAxis,
+    aminoAcidNumbers: showAminoAcidNumbers,
+    dnaColors: showDnaColors,
+    fivePrimeThreePrimeHints,
+    reverseSequence: showReverseSequence,
+    sequence: showSequence,
+    height
+  } = annotationVisibility;
+
+  const { sequence = "", cutsites = [] } = row;
+
+  const reverseSequence = getComplementSequenceString(
+    (alignmentData && alignmentData.sequence) || sequence
+  );
+  const getGaps = useMemo(() => {
+    if (alignmentData) {
+      const gapMap = getGapMap(alignmentData.sequence);
+      //this function is used to calculate the number of spaces that come before or inside a range
+      return (rangeOrCaretPosition) => {
+        if (typeof rangeOrCaretPosition !== "object") {
+          return {
+            gapsBefore:
+              gapMap[Math.min(rangeOrCaretPosition, gapMap.length - 1)]
+          };
+        }
+        //otherwise it is a range!
+        const { start, end } = rangeOrCaretPosition;
+        const toReturn = {
+          gapsBefore: gapMap[start],
+          gapsInside:
+            gapMap[Math.min(end, gapMap.length - 1)] -
+            gapMap[Math.min(start, gapMap.length - 1)]
+        };
+
+        return toReturn;
+      };
+    } else {
+      return getGapsDefault;
+    }
+  }, [alignmentData]);
+
+  if (!row) {
+    return null;
+  }
+
+  if (!width) {
+    width = bpsPerRow * charWidth;
+  }
+  if (isLinearView) {
+    width -= ((charWidth || 12) * bpsPerRow.toString().length) / 2;
+  }
+  charWidth = charWidth || width / Math.max(bpsPerRow, 1);
+
+  const rowStyle = {
+    position: "relative",
+    minHeight,
+    height,
+    width: width + "px"
+  };
+
+  const annotationCommonProps = {
+    noRedux,
+    editorName,
+    charWidth,
+    bpsPerRow,
+    getGaps,
+    isProtein,
+    readOnly,
+    sequenceLength,
+    isRowView,
+    row: { start: row.start, end: row.end }
+  };
+
+  const drawLabels = (type, noDraw, { filterOpts, ...extraProps } = {}) => {
+    if (noDraw) {
+      return null;
+    }
+    const pluralType = pluralize(type);
+    const ranges = filterRanges(
+      annotationLabelVisibility[pluralType] && annotationVisibility[pluralType]
+        ? map(row[pluralType], (a) =>
+            assign(a, {
+              onClick: props[type + "Clicked"],
+              onRightClick: props[type + "RightClicked"],
+              onDoubleClick: props[type + "DoubleClicked"]
+            })
+          )
+        : [],
+      filterOpts
+    );
+    if (!ranges.length) return null;
+    return (
+      <Labels
+        {...annotationCommonProps}
+        onlyShowLabelsThatDoNotFit={onlyShowLabelsThatDoNotFit}
+        labelLineIntensity={labelLineIntensity}
+        rangeMax={bpsPerRow}
+        annotationRanges={ranges}
+        annotationHeight={cutsiteLabelHeight}
+        {...extraProps}
+      />
+    );
+  };
+
+  const drawAnnotations = (type, extraProps = {}) => {
+    const {
+      CompOverride,
+      shouldShow,
+      noPlural,
+      alignmentType,
+      onlyForward,
+      onlyReverse,
+      ...otherExtraProps
+    } = extraProps;
+    const pluralType = noPlural ? type : pluralize(type);
+    if (
+      shouldShow !== undefined
+        ? !shouldShow
+        : !annotationVisibility[pluralType] ||
+          Object.keys(row[pluralType] || {}).length <= 0
+    ) {
+      return null;
+    }
+    const CompToUse = CompOverride || StackedAnnotations;
+    return (
+      <CompToUse
+        truncateLabelsThatDoNotFit={truncateLabelsThatDoNotFit}
+        onlyShowLabelsThatDoNotFit={onlyShowLabelsThatDoNotFit}
+        type={type}
+        fullSequence={fullSequence}
+        containerClassName={camelCase("veRowView-" + pluralType + "Container")}
+        alignmentType={alignmentType}
+        {...annotationCommonProps}
+        {...getPropsForType(props, type, pluralType, extraProps)}
+        {...otherExtraProps}
+      />
+    );
+  };
+
+  // a t g a t c a g g
+  // 0 1 2 3 4 5 6 8 9
+  //0 1 2 3 4 5 6 7 9
+
+  const deletionLayersToDisplay = flatMap(
+    { ...replacementLayers, ...deletionLayers },
+    function (layer) {
+      if (layer.caretPosition > -1) {
+        return [];
+      }
+      const overlaps = getOverlapsOfPotentiallyCircularRanges(
+        layer,
+        row,
+        sequenceLength
+      );
+      return overlaps;
+    }
+  );
+  const deletionLayerStrikeThrough = deletionLayersToDisplay.length
+    ? deletionLayersToDisplay.map(function (layer, index) {
+        const left = (layer.start - row.start) * charWidth;
+        const width = (layer.end - layer.start + 1) * charWidth;
+        return (
+          <div
+            key={"deletionLayer" + index}
+            className="ve_sequence_strikethrough"
+            style={{
+              left,
+              width,
+              top: 10,
+              height: 2,
+              position: "absolute",
+              background: "black"
+            }}
+          />
+        );
+      })
+    : null;
+
+  const translationCommonProps = {
+    CompOverride: Translations,
+    showAminoAcidNumbers: showAminoAcidNumbers,
+    sequenceLength,
+    aminoAcidNumbersHeight
+  };
+  const partProps = {
+    getExtraInnerCompProps: function (annotationRange) {
+      const { annotation } = annotationRange;
+      const { color } = annotation;
+      const colorToUse = startsWith(color, "override_")
+        ? color.replace("override_", "")
+        : "#ac68cc";
+
+      let extraProps = {};
+      if (typeof extraAnnotationProps["part"] === "function") {
+        extraProps = extraAnnotationProps["part"](annotation);
+      }
+      return {
+        textColor: colorToUse,
+        stroke: colorToUse,
+        ...extraProps
+      };
+    },
+    alignmentType
+  };
+
+  return (
+    <div
+      style={rowContainerStyle}
+      onContextMenu={backgroundRightClicked}
+      onScroll={onScroll}
+      className="veRowItemWrapper"
+    >
+      {rowTopComp && rowTopComp}
+      <div className="veRowItem" style={rowStyle}>
+        {/* <div className="vespacer" /> */}
+
+        <SelectionLayer
+          className="veSearchLayerContainer"
+          customTitleStart="Search match"
+          // color="yellow"
+          // hideCarets
+          regions={searchLayers}
+          {...annotationCommonProps}
+          selectionLayerRightClicked={searchLayerRightClicked}
+          row={
+            alignmentData
+              ? { start: 0, end: alignmentData.sequence.length - 1 }
+              : row
+          }
+          onClick={searchLayerClicked}
+        />
+        <SelectionLayer
+          isDraggable
+          selectionLayerRightClicked={selectionLayerRightClicked}
+          {...annotationCommonProps}
+          row={
+            alignmentData
+              ? { start: 0, end: alignmentData.sequence.length - 1 }
+              : row
+          }
+          regions={getAllSelectionLayers({
+            additionalSelectionLayers,
+            selectionLayer
+          })}
+        />
+        {drawAnnotations("warning")}
+        {drawAnnotations("assemblyPiece")}
+        {drawAnnotations("lineageAnnotation")}
+        {drawLabels("part")}
+        {drawAnnotations("part", partProps)}
+        {drawAnnotations("orf", {
+          CompOverride: Orfs
+        })}
+        {charWidth > 4 &&
+          drawAnnotations("translation", {
+            ...translationCommonProps,
+            onDoubleClick: translationDoubleClicked
+          })}
+
+        {showChromatogram && chromatogramData && (
+          <Chromatogram
+            chromatogramData={chromatogramData}
+            alignmentData={alignmentData}
+            scalePct={scalePct}
+            setScalePct={setScalePct}
+            {...annotationCommonProps}
+          />
+        )}
+
+        {drawLabels("cutsite", !isRowView)}
+        {drawLabels("primer", false, {
+          filterOpts: { onlyForward: true }
+        })}
+
+        {drawAnnotations("primer", {
+          sequence: fullSequence,
+          isStriped: true,
+          annotationHeight: primerHeight,
+          onlyForward: true
+        })}
+        <div
+          className="veRowItemSequenceContainer"
+          style={{ position: "relative" }}
+        >
+          {showSequence && (
+            <Sequence
+              sequenceLength={sequenceLength}
+              cutsites={cutsites} //pass this in order to get children cutsites to re-render
+              showDnaColors={showDnaColors}
+              fivePrimeThreePrimeHints={fivePrimeThreePrimeHints}
+              scrollData={scrollData}
+              hideBps={charWidth < 7}
+              sequence={alignmentData ? alignmentData.sequence : row.sequence} //from alignment data and has "-"" chars in it
+              rowStart={row.start}
+              rowEnd={row.end}
+              height={sequenceHeight}
+              showCutsites={showCutsites}
+              charWidth={charWidth}
+              alignmentData={alignmentData}
+              {...annotationCommonProps}
+            >
+              {showCutsites && Object.keys(cutsites).length > 0 && (
+                <Cutsites
+                  sequenceLength={sequenceLength}
+                  annotationRanges={cutsites}
+                  topStrand
+                  {...annotationCommonProps}
+                />
+              )}
+              {deletionLayerStrikeThrough}
+            </Sequence>
+          )}
+          {emptyText}
+
+          {showReverseSequence && (
+            <Sequence
+              scrollData={scrollData}
+              sequenceLength={sequenceLength}
+              fivePrimeThreePrimeHints={fivePrimeThreePrimeHints}
+              isReverse
+              cutsites={cutsites} //pass this in order to get children cutsites to re-render
+              showDnaColors={showDnaColors}
+              hideBps={charWidth < 7}
+              length={reverseSequence.length}
+              showCutsites={showCutsites}
+              rowStart={row.start}
+              rowEnd={row.end}
+              sequence={reverseSequence}
+              height={sequenceHeight}
+              charWidth={charWidth}
+            >
+              {showCutsites && Object.keys(cutsites).length > 0 && (
+                <Cutsites
+                  topStrand={false}
+                  annotationRanges={cutsites}
+                  {...annotationCommonProps}
+                />
+              )}
+              {deletionLayerStrikeThrough}
+            </Sequence>
+          )}
+          {showCutsites && showCutsitesInSequence && (
+            <CutsiteSelectionLayers
+              {...{
+                editorName,
+                cutsites,
+                annotationCommonProps,
+                showReverseSequence,
+                sequenceHeight,
+                alignmentData,
+                row
+              }}
+            ></CutsiteSelectionLayers>
+          )}
+        </div>
+
+        {drawAnnotations("primer", {
+          sequence: fullSequence,
+          isStriped: true,
+          annotationHeight: primerHeight,
+          onlyReverse: true
+        })}
+        {drawLabels("primer", false, {
+          filterOpts: { onlyReverse: true }
+        })}
+        {drawLabels("feature")}
+        {drawAnnotations("feature")}
+
+        {map(replacementLayers, function (replacementLayer) {
+          if (!replacementLayer) return null;
+          const atCaret = replacementLayer.caretPosition > -1;
+          let normedCaretPos;
+          if (atCaret) {
+            normedCaretPos = normalizePositionByRangeLength(
+              replacementLayer.caretPosition,
+              sequenceLength
+            );
+          }
+          const insertedBpsLayer = {
+            ...replacementLayer,
+            start: atCaret ? normedCaretPos : replacementLayer.start,
+            end:
+              (atCaret ? normedCaretPos : replacementLayer.start) +
+              replacementLayer.sequence.length
+          };
+          const { sequence } = insertedBpsLayer;
+          const layerRangeOverlaps = getOverlapsOfPotentiallyCircularRanges(
+            insertedBpsLayer,
+            row,
+            sequenceLength
+          );
+          return layerRangeOverlaps.map(function (layer, index) {
+            const isStart = layer.start === insertedBpsLayer.start;
+            const seqInRow = getSequenceWithinRange(
+              {
+                start: layer.start - insertedBpsLayer.start,
+                end: layer.end - insertedBpsLayer.start
+              },
+              sequence
+            );
+            const startOffset = layer.start - row.start;
+            const width = seqInRow.length * charWidth;
+            const height = sequenceHeight;
+            const bufferBottom = 4;
+            const bufferLeft = 2;
+            const arrowHeight = isStart ? 8 : 0;
+            return (
+              <Sequence
+                sequenceLength={sequenceLength}
+                isReplacementLayer
+                showDnaColors={showDnaColors}
+                key={index}
+                sequence={seqInRow}
+                startOffset={startOffset}
+                height={height}
+                length={seqInRow.length}
+                charWidth={charWidth}
+              >
+                <svg
+                  style={{
+                    left: startOffset * charWidth,
+                    height: sequenceHeight,
+                    position: "absolute"
+                  }}
+                  ref="rowViewTextContainer"
+                  onClick={function (event) {
+                    replacementLayerClicked({
+                      annotation: replacementLayer,
+                      event
+                    });
+                  }}
+                  onContextMenu={function (event) {
+                    replacementLayerRightClicked({
+                      annotation: replacementLayer,
+                      event
+                    });
+                  }}
+                  className="rowViewTextContainer clickable"
+                  width={Math.max(0, Number(width))}
+                  height={Math.max(0, Number(height))}
+                >
+                  <polyline
+                    points={`${-bufferLeft},0 ${-bufferLeft},${-arrowHeight}, ${
+                      charWidth / 2
+                    },0 ${width},0 ${width},${
+                      height + bufferBottom
+                    } ${-bufferLeft},${height + bufferBottom} ${-bufferLeft},0`}
+                    fill="none"
+                    stroke="black"
+                    strokeWidth="2px"
+                  />
+                </svg>
+              </Sequence>
+            );
+          });
+        })}
+        {/* <DeletionLayers
+          deletionLayerClicked={deletionLayerClicked}
+          deletionLayerRightClicked={deletionLayerRightClicked}
+          deletionLayers={deletionLayers}
+          {...annotationCommonProps}
+        /> */}
+
+        {drawAnnotations("primaryProteinSequence", {
+          ...translationCommonProps,
+          noPlural: true
+        })}
+        {drawLabels("cutsite", isRowView)}
+        {showAxis && (
+          <Axis
+            scrollData={scrollData}
+            tickSpacing={tickSpacing}
+            showAxisNumbers={showAxisNumbers}
+            annotationHeight={axisHeight}
+            marginTop={axisMarginTop}
+            {...annotationCommonProps}
+            isLinearView={isLinearView}
+          />
+        )}
+        {caretPosition > -1 && (
+          <Caret
+            caretPosition={caretPosition}
+            {...{ ...annotationCommonProps, ...{ getGaps: undefined } }}
+            row={
+              alignmentData
+                ? { start: 0, end: alignmentData.sequence.length - 1 }
+                : row
+            }
+          />
+        )}
+      </div>
+      {rowBottomComp && rowBottomComp}
+    </div>
+  );
+}
+
+function getGapMap(sequence) {
+  const gapMap = [0]; //a map of position to how many gaps come before that position [0,0,0,5,5,5,5,17,17,17, ]
+  sequence.split("").forEach((char) => {
+    if (char === "-") {
+      gapMap[Math.max(0, gapMap.length - 1)] =
+        (gapMap[Math.max(0, gapMap.length - 1)] || 0) + 1;
+    } else {
+      gapMap.push(gapMap[gapMap.length - 1] || 0);
+      // gapMap[gapMap.length] =
+    }
+  });
+  return gapMap;
+}
+// var a = getGapMap("---tagccc---tagasdfw--gg")
+function getGapsDefault() {
+  return {
+    gapsBefore: 0,
+    gapsInside: 0
+  };
+}

package/src/RowItem/partOverhangs.js

@@ -0,0 +1,6 @@
+export const partOverhangs = [
+  "fivePrimeOverhang",
+  "fivePrimeUnderhang",
+  "threePrimeOverhang",
+  "threePrimeUnderhang"
+];