@teselagen/ove 0.7.28 → 0.7.29

package/PointedAnnotation.js

@@ -1,347 +0,0 @@
-import Color from "color";
-import classnames from "classnames";
-import withHover from "../../helperComponents/withHover";
-import getAnnotationNameAndStartStopString from "../../utils/getAnnotationNameAndStartStopString";
-
-import React, { useState } from "react";
-import { doesLabelFitInAnnotation } from "../utils";
-import { noop } from "lodash-es";
-import getAnnotationClassnames from "../../utils/getAnnotationClassnames";
-import { getStripedPattern } from "../../utils/editorUtils";
-import { ANNOTATION_LABEL_FONT_WIDTH } from "../constants";
-import { partOverhangs } from "../partOverhangs";
-import { Tooltip } from "@blueprintjs/core";
-
-function PointedAnnotation(props) {
-  const {
-    className,
-    widthInBps,
-    charWidth,
-    height,
-    rangeType,
-    forward,
-    arrowheadType,
-    name: _name = "",
-    customName,
-    type,
-    readOnly,
-    isStriped,
-    onMouseLeave,
-    onMouseOver,
-    isProtein,
-    id,
-    extraHeight,
-    flipAnnotation,
-    insertPaths,
-    insertTicks,
-    hideName,
-    color = "orange",
-    fill,
-    stroke,
-    opacity,
-    onClick = noop,
-    onDoubleClick = noop,
-    textColor,
-    onRightClick = noop,
-    gapsInside,
-    gapsBefore,
-    annotation,
-    truncateLabelsThatDoNotFit,
-    onlyShowLabelsThatDoNotFit
-  } = props;
-
-  const name = customName || _name;
-  let pointiness = props.pointiness || 4;
-  let arrowPointiness = props.arrowPointiness || 1;
-  const [isOpen, setOpen] = useState(false);
-  const [isOpen2, setOpen2] = useState(false);
-  if (arrowheadType === "NONE") {
-    pointiness = 0;
-    arrowPointiness = 0;
-  }
-  const _rangeType = annotation.rangeTypeOverride || rangeType;
-
-  const classNames = getAnnotationClassnames(annotation, {
-    isProtein,
-    type,
-    viewName: "RowView"
-  });
-  let partOverhangStart;
-  let partOverhangEnd;
-
-  partOverhangs.forEach(h => {
-    const overhangBps = props[h];
-    if (overhangBps) {
-      if (h.includes("fivePrime")) {
-        partOverhangStart = overhangBps;
-        if (h.includes("Underhang")) {
-          partOverhangStart += " Underhang";
-        } else if (h.includes("Overhang")) {
-          partOverhangStart += " Overhang";
-        }
-      } else {
-        partOverhangEnd = overhangBps;
-        if (h.includes("Underhang")) {
-          partOverhangEnd += " Underhang";
-        } else if (h.includes("Overhang")) {
-          partOverhangEnd += " Overhang";
-        }
-      }
-    }
-  });
-
-  const width = (widthInBps + gapsInside) * charWidth;
-  let charWN = charWidth; //charWN is normalized
-  if (charWidth < 15) {
-    //allow the arrow width to adapt
-    if (width > 15) {
-      charWN = 15; //tnr: replace 15 here with a non-hardcoded number..
-    } else {
-      charWN = width;
-    }
-  }
-  charWN = arrowPointiness * charWN;
-
-  const widthMinusOne = width - charWN;
-  let path;
-  let hasAPoint = false;
-  const endLine = annotation.overlapsSelf
-    ? `L 0,${height / 2}
-  L -10,${height / 2}
-  L 0,${height / 2} `
-    : "";
-  const bottomLine = `${insertTicks || ""} L 0,${height}`;
-  const startLines = `M 0,0
-  ${insertPaths || ""}`;
-  const arrowLine = annotation.overlapsSelf
-    ? `L ${width + 10},${height / 2}
-  L ${width},${height / 2} `
-    : "";
-
-  // starting from the top left of the annotation
-  if (_rangeType === "middle") {
-    //draw a rectangle
-    path = `
-        ${startLines}
-        L ${width - pointiness / 2},0
-        Q ${width + pointiness / 2},${height / 2} ${
-          width - pointiness / 2
-        },${height}
-        ${bottomLine}
-        Q ${pointiness},${height / 2} ${0},${0}
-        z`;
-  } else if (_rangeType === "start") {
-    path = `
-        ${startLines}
-        L ${width - pointiness / 2},0
-
-        Q ${width + pointiness / 2},${height / 2} ${
-          width - pointiness / 2
-        },${height}
-
-        ${bottomLine}
-        ${endLine}
-        z`;
-  } else if (_rangeType === "beginningAndEnd") {
-    hasAPoint = true;
-    path = `
-        ${startLines}
-        L ${widthMinusOne},0
-        L ${width},${height / 2}
-        ${arrowLine}
-        L ${widthMinusOne},${height}
-        ${bottomLine}
-        ${endLine}
-        z`;
-  } else {
-    hasAPoint = true;
-    path = `
-      ${startLines}
-      L ${widthMinusOne},0
-      L ${width},${height / 2}
-      ${arrowLine}
-      L ${widthMinusOne},${height}
-      ${bottomLine}
-      Q ${pointiness},${height / 2} ${0},${0}
-      z`;
-  }
-  let nameToDisplay = name;
-  let textOffset =
-    width / 2 -
-    (name.length * 5) / 2 -
-    (hasAPoint ? (pointiness / 2) * (forward ? 1 : -1) : 0);
-  if (
-    !doesLabelFitInAnnotation(name, { width }, charWidth) ||
-    (!onlyShowLabelsThatDoNotFit &&
-      ["parts", "features"].includes(annotation.annotationTypePlural))
-  ) {
-    if (truncateLabelsThatDoNotFit) {
-      const fractionToDisplay =
-        width / (name.length * ANNOTATION_LABEL_FONT_WIDTH);
-      const numLetters = Math.floor(fractionToDisplay * name.length);
-      nameToDisplay = name.slice(0, numLetters);
-      if (nameToDisplay.length > 3) {
-        if (nameToDisplay.length !== name.length) {
-          nameToDisplay += "..";
-        }
-
-        textOffset =
-          width / 2 -
-          (nameToDisplay.length * 5) / 2 -
-          (hasAPoint ? (pointiness / 2) * (forward ? 1 : -1) : 0);
-      } else {
-        textOffset = 0;
-        nameToDisplay = "";
-      }
-    } else {
-      textOffset = 0;
-      nameToDisplay = "";
-    }
-  }
-  let _textColor = textColor;
-  if (!textColor) {
-    try {
-      _textColor = Color(color).isDark() ? "white" : "black";
-    } catch (error) {
-      _textColor = "white";
-    }
-  }
-
-  return (
-    <g
-      {...{ onMouseLeave, onMouseOver }}
-      className={` clickable ${className} ${classNames} ${
-        forward ? "ann-forward" : `ann-reverse`
-      }`}
-      data-id={id}
-      onClick={function (event) {
-        onClick({ annotation, event, gapsBefore, gapsInside });
-      }}
-      onDoubleClick={function (event) {
-        onDoubleClick &&
-          onDoubleClick({ annotation, event, gapsBefore, gapsInside });
-      }}
-      onContextMenu={function (event) {
-        onRightClick({ annotation, event, gapsBefore, gapsInside });
-      }}
-    >
-      {!(isOpen || isOpen2) && (
-        <title>
-          {getAnnotationNameAndStartStopString(annotation, {
-            isProtein,
-            readOnly
-          })}
-        </title>
-      )}
-      {isStriped && getStripedPattern({ color, id })}
-
-      <path
-        strokeWidth="1"
-        stroke={stroke || "black"}
-        opacity={opacity}
-        fill={isStriped ? `url(#diagonalHatch-${id})` : fill || color}
-        transform={
-          forward
-            ? null
-            : "translate(" +
-              width +
-              `,${flipAnnotation ? -extraHeight + 10 : 0}) scale(-1,${
-                flipAnnotation ? "-" : ""
-              }1) `
-        }
-        d={path}
-      />
-      {partOverhangStart &&
-        (rangeType === (forward ? "start" : "end") ||
-          rangeType === "beginningAndEnd") && (
-          <Tooltip
-            onInteraction={isOpen => {
-              setOpen(isOpen);
-            }}
-            isOpen={isOpen}
-            wrapperTagName="g"
-            targetTagName="g"
-            content={partOverhangStart}
-          >
-            <circle
-              className="partWithOverhangsIndicator"
-              style={{ fillOpacity: 1 }}
-              fill="#ac68cc"
-              cx={(forward ? -7 : 0) + 15}
-              cy={7}
-              r={4}
-            ></circle>
-          </Tooltip>
-        )}
-      {partOverhangEnd &&
-        (rangeType === (forward ? "end" : "start") ||
-          rangeType === "beginningAndEnd") && (
-          <Tooltip
-            onInteraction={isOpen => {
-              setOpen2(isOpen);
-            }}
-            isOpen={isOpen2}
-            wrapperTagName="g"
-            targetTagName="g"
-            content={partOverhangEnd}
-          >
-            <circle
-              className="partWithOverhangsIndicator"
-              style={{ fillOpacity: 1 }}
-              fill="#ac68cc"
-              cx={(forward ? -7 : 0) + width - 10}
-              cy={7}
-              r={4}
-            ></circle>
-          </Tooltip>
-        )}
-      {!hideName && nameToDisplay && (
-        <text
-          className={classnames(
-            "veLabelText ve-monospace-font",
-            annotation.labelClassName
-          )}
-          style={{
-            // fontSize: ".8em",
-            fill: _textColor
-          }}
-          transform={`translate(${textOffset},${height - 2})`}
-        >
-          {nameToDisplay}
-        </text>
-      )}
-    </g>
-  );
-}
-
-export default withHover(PointedAnnotation);
-
-//  {/* <Tooltip
-//               wrapperTagName="g"
-//               targetTagName="g"
-//               content={"asdfasdfasdfasfdp"}
-//             >
-//               <rect
-//                 style={{ fillOpacity: 1 }}
-//                 stroke="#ac68cc"
-//                 fill="none"
-//                 x={-10}
-//                 width={10}
-//                 height={5}
-//               ></rect>
-//             </Tooltip>
-//             <Tooltip
-//               wrapperTagName="g"
-//               targetTagName="g"
-//               content={"asdfasdfasdfasfdp"}
-//             >
-//               <rect
-//                 style={{ fillOpacity: 1 }}
-//                 stroke="#ac68cc"
-//                 fill="none"
-//                 x={ width + 2 }
-//                 y={7}
-//                 width={10}
-//                 height={5}
-//               ></rect>
-//             </Tooltip> */}

package/PositionAnnotationOnCircle.js

@@ -1,26 +0,0 @@
-import React from "react";
-export default function PositionAnnotationOnCircle({
-  children,
-  height = 0,
-  sAngle = 0,
-  eAngle = 0,
-  forward = true,
-  ...rest
-}) {
-  const sAngleDegs = (sAngle * 360) / Math.PI / 2;
-  const eAngleDegs = (eAngle * 360) / Math.PI / 2;
-  let transform;
-  let revTransform;
-  if (forward) {
-    transform = `translate(0,${-height}) rotate(${sAngleDegs},0,${height})`;
-  } else {
-    transform = `scale(-1,1) translate(0,${-height}) rotate(${-eAngleDegs},0,${height}) `;
-    revTransform = ` rotate(${eAngleDegs},0,${height}) scale(-1,1) rotate(${sAngleDegs}, 0,${height})`;
-  }
-  const props = { transform, ...rest };
-  /* eslint-disable */
-  if (!children) return { transform, revTransform };
-  /* eslint-enable */
-
-  return React.cloneElement(children, props);
-}

package/Primer.js

@@ -1,41 +0,0 @@
-import React from "react";
-import { getStripedPattern } from "../utils/editorUtils";
-import drawDirectedPiePiece from "./drawDirectedPiePiece";
-import { getInternalLabel } from "./getInternalLabel";
-
-export default function CircularPrimer(props) {
-  const {
-    color = "orange",
-    radius,
-    arrowheadLength = 0.5,
-    annotationHeight,
-    totalAngle,
-    id,
-    labelNeedsFlip,
-    ellipsizedName
-  } = props;
-  const [path, textPath] = drawDirectedPiePiece({
-    radius,
-    annotationHeight,
-    totalAngle,
-    arrowheadLength,
-    tailThickness: 1, //feature specific
-    returnTextPath: true,
-    hasLabel: ellipsizedName,
-    labelNeedsFlip
-  });
-  return (
-    <React.Fragment>
-      {getStripedPattern({ color, id })}
-      <path
-        className="vePrimer veCircularViewPrimer"
-        id={id}
-        strokeWidth=".5"
-        stroke="black"
-        fill={`url(#diagonalHatch-${id})`}
-        d={path.print()}
-      />
-      {getInternalLabel({ ...props, colorToUse: color, textPath })}
-    </React.Fragment>
-  );
-}

package/PrimerProperties.js

@@ -1,19 +0,0 @@
-import { Button } from "@blueprintjs/core";
-import React from "react";
-import { primersSubmenu } from "../../MenuBar/viewSubmenu";
-
-import genericAnnotationProperties from "./GenericAnnotationProperties";
-export default genericAnnotationProperties({
-  annotationType: "primer",
-  noColor: true,
-  visSubmenu: primersSubmenu,
-  noType: true,
-  withBases: true,
-  additionalFooterEls: props => {
-    return (
-      <Button onClick={props.createNewPCR} intent="success">
-        Simulate PCR
-      </Button>
-    );
-  }
-});