@teselagen/ove 0.7.26 → 0.7.28

package/Ladder.js

@@ -0,0 +1,303 @@
+/* eslint-disable react/jsx-no-bind */
+import React, { useState } from "react";
+import { showConfirmationDialog, TgSelect } from "@teselagen/ui";
+
+import "./Ladder.css";
+import { Button, Tooltip } from "@blueprintjs/core";
+import { showDialog } from "../GlobalDialogUtils";
+import { AddLaddersDialog } from "./AddLaddersDialog";
+import { ladderDefaults } from "./ladderDefaults";
+import useLadders from "../utils/useLadders";
+import { map } from "lodash-es";
+import { filter } from "lodash-es";
+
+export default function Ladder({
+  // gelDigestEnzymes = [],
+  boxHeight = 550,
+  lanes = [],
+  digestLaneRightClicked,
+  selectedFragment,
+  ladders = ladderDefaults
+}) {
+  const [additionalLadders, setLadders] = useLadders();
+  const laddersToUse = [
+    ...ladders,
+    ...map(additionalLadders, (l, i) => ({
+      ...l,
+      label: (
+        <div
+          key={i}
+          style={{
+            display: "flex",
+            alignItems: "center",
+            justifyContent: "space-between",
+            width: "100%"
+          }}
+        >
+          {l.label}{" "}
+          <Button
+            onClick={async e => {
+              e.preventDefault();
+              e.stopPropagation();
+              const confirm = await showConfirmationDialog({
+                text: "Are you sure you want to delete this custom ladder? You cannot undo this action",
+                intent: "danger",
+                confirmButtonText: "Delete",
+                cancelButtonText: "Cancel",
+                canEscapeKeyCancel: true
+              });
+              if (!confirm) {
+                return;
+              }
+              setSelectedLadder(ladders[0].value);
+              setLadders(
+                filter(additionalLadders, lad => lad.value !== l.value)
+              );
+            }}
+            intent="danger"
+            small
+            minimal
+            icon="trash"
+          ></Button>
+        </div>
+      )
+    }))
+  ];
+  const [highlightedFragment, setHighlightedFragment] = useState();
+  const [selectedLadder, setSelectedLadder] = useState(ladders[0].value);
+  let ladderInfo;
+  laddersToUse.forEach(ladder => {
+    if (ladder.value === selectedLadder)
+      ladderInfo = {
+        ...ladder,
+        markings: ladder.markings.sort((a, b) => {
+          return b - a;
+        })
+      };
+  });
+  if (!ladderInfo) {
+    return console.error("Uh oh there needs to be ladder info here!");
+  }
+  const sharedStyle = { color: "white", background: "black" }; //use a shared style to get the copy image to look nice
+  const upperBoundary = ladderInfo.markings[0];
+  return (
+    <div>
+      Ladder:
+      <div style={{ display: "flex" }}>
+        <TgSelect
+          className="tg-ladder-selector"
+          value={selectedLadder}
+          onChange={val => setSelectedLadder(val.value)}
+          options={laddersToUse}
+        />
+        <Button
+          onClick={() => {
+            showDialog({
+              ModalComponent: AddLaddersDialog,
+              props: {
+                setSelectedLadder
+              }
+            });
+          }}
+          style={{ minWidth: 150 }}
+          minimal
+          small
+          icon="plus"
+          intent="primary"
+        >
+          Add Ladder
+        </Button>
+      </div>
+      <br />
+      <div
+        className="ve-digest-outer-container"
+        style={{
+          position: "relative",
+          width: "fit-content",
+          ...sharedStyle
+        }}
+      >
+        {navigator.clipboard && window.isSecureContext && (
+          <Button
+            icon="duplicate"
+            minimal
+            style={{ position: "absolute", top: 5, right: 5, color: "white" }}
+            onClick={async () => {
+              try {
+                const canvas = await import("html2canvas");
+                canvas
+                  .default(document.querySelector(".ve-digest-container"))
+                  .then(canvas => {
+                    canvas.toBlob(blob =>
+                      navigator.clipboard.write([
+                        new window.ClipboardItem({ "image/png": blob })
+                      ])
+                    );
+                    window.toastr.success("Image copied to clipboard!");
+                  });
+              } catch (e) {
+                window.toastr.error(
+                  "Error copying the image, try just taking a screenshot instead ;)"
+                );
+              }
+            }}
+          ></Button>
+        )}
+        <div style={{ padding: 3, paddingLeft: 7, width: 290 }}>
+          Highlighted Fragment:{" "}
+          {highlightedFragment ? highlightedFragment.size : "--"}{" "}
+        </div>
+        <div
+          style={{ height: boxHeight, ...sharedStyle }}
+          className="ve-digest-container"
+        >
+          <div
+            style={{ width: 100 }}
+            className="ve-digest-column ve-digest-ladder"
+          >
+            <div className="ve-digest-header"> </div>
+            {ladderInfo.markings.map((val, index) => {
+              return (
+                <div
+                  key={index}
+                  style={{
+                    fontSize: 12,
+                    position: "absolute",
+                    width: "100%",
+                    display: "flex",
+                    alignItems: "center",
+                    color: "white",
+                    bottom: calculateOffset(boxHeight, val, upperBoundary) - 3 //subtract 3 to get the labels to align better
+                  }}
+                >
+                  <span
+                    style={{
+                      color: "white",
+                      paddingLeft: 6,
+                      paddingRight: 4
+                    }}
+                  >
+                    {val}{" "}
+                  </span>
+                  <span style={{ color: "white", paddingRight: 4 }}> bp </span>
+                </div>
+              );
+            })}
+          </div>
+          <div className="ve-digest-column ve-digest-ladder">
+            <div className="ve-digest-header">Ladder </div>
+            {ladderInfo.markings.map((val, index) => {
+              return (
+                <div
+                  key={index}
+                  style={{
+                    fontSize: 12,
+                    position: "absolute",
+                    width: "100%",
+                    display: "flex",
+                    alignItems: "center",
+                    color: "white",
+                    height: "2px",
+                    background: "white",
+                    bottom: calculateOffset(boxHeight, val, upperBoundary)
+                  }}
+                />
+              );
+            })}
+          </div>
+          {lanes.map((fragments, index) => {
+            return (
+              <Lane
+                key={index}
+                {...{
+                  onMouseOver: fragment => setHighlightedFragment(fragment),
+                  onMouseOut: () => setHighlightedFragment(undefined),
+                  digestLaneRightClicked,
+                  laneNumber: index + 1,
+                  fragments,
+                  highlightedFragment,
+                  selectedFragment,
+                  boxHeight,
+                  upperBoundary
+                }}
+              />
+            );
+          })}
+        </div>
+      </div>
+    </div>
+  );
+}
+
+function Lane({
+  laneNumber,
+  onMouseOver,
+  onMouseOut,
+  digestLaneRightClicked,
+  fragments,
+  highlightedFragment,
+  selectedFragment,
+  boxHeight,
+  upperBoundary
+}) {
+  return (
+    <div
+      style={{ marginLeft: 20, marginRight: 20 }}
+      className="ve-digest-column ve-digest-lane"
+    >
+      <div className="ve-digest-header">Lane {laneNumber} </div>
+      {fragments.map((fragment, index) => {
+        const { size, id, name } = fragment;
+        const isHighlighted =
+          (highlightedFragment && id === highlightedFragment.id) ||
+          (selectedFragment && id === highlightedFragment.id);
+        return (
+          <div
+            key={index}
+            onMouseOver={() => {
+              onMouseOver(fragment);
+            }}
+            onMouseOut={() => {
+              onMouseOut(fragment);
+            }}
+            onClick={() => {
+              fragment.onFragmentSelect();
+            }}
+            onContextMenu={e => {
+              fragment.onFragmentSelect();
+              digestLaneRightClicked(e);
+            }}
+            data-test={name}
+            style={{
+              fontSize: 12,
+              position: "absolute",
+              display: "flex",
+              alignItems: "center",
+              color: isHighlighted ? "#fdffdd" : "white",
+              width: "90%",
+              height: isHighlighted ? "3px" : "2px",
+              background: "white",
+              bottom: calculateOffset(boxHeight, size, upperBoundary)
+            }}
+          >
+            <Tooltip
+              className="ve-digest-fragment-tooltip"
+              content={<div>{name}</div>}
+            >
+              <div
+                style={{
+                  width: "100%",
+                  height: isHighlighted ? "3px" : "2px"
+                }}
+              />
+            </Tooltip>
+          </div>
+        );
+      })}
+    </div>
+  );
+}
+
+function calculateOffset(boxHeight, size, upperBoundary) {
+  return (boxHeight * Math.log(size)) / Math.log(upperBoundary) - 55;
+}

package/MeltingTemp.js

@@ -0,0 +1,85 @@
+import React from "react";
+import { Button, Icon, Popover, RadioGroup } from "@blueprintjs/core";
+
+import { calculateTm, calculateNebTm } from "@teselagen/sequence-utils";
+
+import { isNumber, isString } from "lodash-es";
+import { popoverOverflowModifiers } from "@teselagen/ui";
+import useTmType from "../utils/useTmType";
+
+export default function MeltingTemp({
+  sequence,
+  WrapperToUse = p => <div>{p.children}</div>,
+  InnerWrapper = p => (
+    <Button minimal small>
+      {p.children}
+    </Button>
+  )
+}) {
+  const [primerConc /* , setPrimerConcentration */] = React.useState(0.0000005);
+  const [monovalentCationConc /* , setMonovalentCationConc */] =
+    React.useState(0.05);
+  const [tmType, setTmType] = useTmType();
+  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence, {
+    monovalentCationConc,
+    primerConc
+  });
+  if (isNumber(tm)) {
+    tm = tm.toFixed(1);
+  }
+  const hasWarning = isString(tm) && tm.length > 7 && tm;
+  return (
+    <WrapperToUse dataTest="veStatusBar-selection-tm">
+      <Popover
+        modifiers={popoverOverflowModifiers}
+        content={
+          <div style={{ maxWidth: 300, padding: 20 }}>
+            Using Tm calculations based on these{" "}
+            <a
+              rel="noopener noreferrer"
+              target="_blank"
+              href="https://github.com/TeselaGen/tg-oss/blob/master/packages/sequence-utils/src/calculateNebTm.js"
+            >
+              algorithms
+            </a>
+            <br></br>
+            <br></br>
+            <RadioGroup
+              label="Choose Tm Type:"
+              options={[
+                { value: "default", label: "Default Tm (Breslauer)" },
+                { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+              ]}
+              onChange={e => setTmType(e.target.value)}
+              selectedValue={tmType}
+            ></RadioGroup>
+            {hasWarning && (
+              <div>
+                <Icon
+                  style={{ marginLeft: 5, marginRight: 5 }}
+                  size={10}
+                  icon="warning-sign"
+                ></Icon>
+                {hasWarning}
+                <br></br>
+                <br></br>
+                Try using the Default Tm
+              </div>
+            )}
+          </div>
+        }
+      >
+        <React.Fragment>
+          <InnerWrapper>Melting Temp: {Number(tm) || 0} </InnerWrapper>
+          {hasWarning && (
+            <Icon
+              style={{ marginLeft: 5, marginRight: 5 }}
+              size={10}
+              icon="warning-sign"
+            ></Icon>
+          )}
+        </React.Fragment>
+      </Popover>
+    </WrapperToUse>
+  );
+}