@teselagen/ove 0.0.13 → 0.0.15

package/src/helperComponents/AddOrEditPrimerDialog/index.js

@@ -0,0 +1,329 @@
+import React, { useEffect, useRef, useState, useMemo } from "react";
+import {
+  AdvancedOptions,
+  CheckboxField,
+  DropdownButton,
+  generateField,
+  RadioGroupField
+} from "@teselagen/ui";
+import { getReverseComplementSequenceString } from "@teselagen/sequence-utils";
+
+import AddOrEditAnnotationDialog from "../AddOrEditAnnotationDialog";
+import { convertRangeTo0Based } from "@teselagen/range-utils";
+import { getAcceptedChars } from "../../utils/editorUtils";
+import classNames from "classnames";
+import "./style.css";
+import { getSequenceWithinRange } from "@teselagen/range-utils";
+import { flatMap } from "lodash";
+import CaretPositioning, {
+  selectionSaveCaretPosition
+} from "./EditCaretPosition";
+import { Menu, MenuItem } from "@blueprintjs/core";
+
+import MeltingTemp from "../../StatusBar/MeltingTemp";
+import { getStructuredBases } from "../../RowItem/StackedAnnotations/getStructuredBases";
+
+const CustomContentEditable = generateField(function CustomContentEditable({
+  input,
+  disabled,
+  sequenceData,
+  sequenceLength,
+  start,
+  end,
+  primerBindsOn,
+  bases,
+  forward
+}) {
+  const [hasTempError, setTempError] = useState(false);
+  const inputRef = useRef(null);
+  const [caretPosition, setCaretPosition] = useState({ start: 0, end: 0 });
+
+  const emitChange = (e) => {
+    const newVal = e.target.innerText;
+    const savedCaretPosition = CaretPositioning.saveSelection(e.currentTarget);
+    setCaretPosition(savedCaretPosition);
+    const acceptedChars = getAcceptedChars(sequenceData);
+    let newBases = "";
+    newVal.split("").forEach((letter) => {
+      if (acceptedChars.includes(letter.toLowerCase())) {
+        newBases += letter;
+      }
+    });
+    if (newVal.length !== newBases.length) {
+      setTempError(true);
+      setTimeout(() => {
+        setTempError(false);
+      }, 200);
+    }
+    const restore = selectionSaveCaretPosition(inputRef.current);
+
+    input.onChange(newBases || "");
+    setTimeout(() => {
+      restore();
+    }, 0);
+  };
+
+  useEffect(() => {
+    CaretPositioning.restoreSelection(inputRef.current, caretPosition);
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [bases]);
+
+  const basesToUse = bases || "";
+  const { allBasesWithMetaData } = getStructuredBases({
+    annotationRange: { start: start - 1, end: end - 1 },
+    forward,
+    bases: basesToUse,
+    start: start - 1,
+    end: end - 1,
+    fullSequence: sequenceData.sequence,
+    primerBindsOn,
+    sequenceLength
+  });
+  let html = flatMap(
+    allBasesWithMetaData,
+    ({ b, isMatch, isAmbiguousMatch }) => {
+      if (b === "&") return [];
+      return `<span class="${
+        isMatch
+          ? ""
+          : isAmbiguousMatch
+          ? "tg-ambiguous-match-seq"
+          : "tg-no-match-seq"
+      }">${b}</span>`;
+    }
+  );
+  html = html.join("");
+
+  return (
+    <div
+      style={{
+        display: "flex",
+        ...(disabled ? { pointerEvents: "none" } : {})
+      }}
+    >
+      <span
+        style={{
+          verticalAlign: "top",
+          marginTop: 9,
+          marginRight: 3,
+          fontSize: 12,
+          color: "grey"
+        }}
+      >
+        5'
+      </span>
+      <span
+        ref={inputRef}
+        spellCheck="false"
+        contentEditable={!disabled}
+        className={classNames("bp3-input tg-custom-sequence-editable", {
+          hasTempError
+        })}
+        onInput={emitChange}
+        dangerouslySetInnerHTML={{ __html: html }} // innerHTML of the editable div
+      />
+      <span
+        style={{
+          alignSelf: "end",
+          marginBottom: 9,
+          marginLeft: 3,
+          fontSize: 12,
+          color: "grey"
+        }}
+      >
+        3'
+      </span>
+    </div>
+  );
+});
+
+const RenderBases = (props) => {
+  const {
+    sequenceData,
+    readOnly,
+    start,
+    end,
+    linkedOligo,
+    getLinkedOligoLink,
+    useLinkedOligo,
+    sequenceLength,
+    primerBindsOn,
+    bases,
+    forward,
+    defaultLinkedOligoMessage,
+    change
+  } = props;
+  let defaultValue;
+  const seqLen = sequenceData.sequence.length;
+  const validate = useMemo(() => {
+    return (val /* vals, props */) => {
+      if (!val) return;
+      if (val.length > seqLen) {
+        return "Primer cannot be longer than sequence";
+      }
+      return;
+    };
+  }, [seqLen]);
+  const normalizedSelection = convertRangeTo0Based({
+    start,
+    end
+  });
+  if (!bases) {
+    let bps = getSequenceWithinRange(
+      normalizedSelection,
+      sequenceData.sequence
+    );
+    if (!forward) {
+      bps = getReverseComplementSequenceString(bps);
+    }
+    defaultValue = bps;
+  }
+  return (
+    <div
+      style={{
+        borderTop: "1px solid #A7B6C2",
+        borderBottom: "1px solid #A7B6C2"
+      }}
+    >
+      <div
+        style={{
+          display: "flex",
+          alignItems: "center",
+          justifyContent: "space-between"
+        }}
+      >
+        <CheckboxField
+          name="useLinkedOligo"
+          label="Linked Oligo?"
+          tooltipInfo={`Check this box to link this primer to an oligo in your Oligo Library. If the primer bases match exactly the bases of an existing oligo, it will be linked to that existing oligo. If the bases don't match, a new oligo will be created in the library.`}
+          noMarginBottom
+          defaultValue={true}
+          disabled={readOnly}
+        ></CheckboxField>
+        {useLinkedOligo && (
+          <div
+            className="tg-linked-oligo-holder"
+            style={{ marginTop: -5, fontStyle: "italic", fontSize: 11 }}
+          >
+            {(getLinkedOligoLink && getLinkedOligoLink(props)) ||
+              linkedOligo ||
+              (defaultLinkedOligoMessage !== undefined
+                ? defaultLinkedOligoMessage
+                : "Will Be Created On Save")}
+          </div>
+        )}
+      </div>
+      {useLinkedOligo && (
+        <div>
+          <CustomContentEditable
+            // inlineLabel
+            showErrorIfUntouched
+            tooltipError
+            primerBindsOn={primerBindsOn}
+            validate={validate}
+            sequenceLength={sequenceLength}
+            disabled={readOnly}
+            {...props}
+            {...(defaultValue
+              ? {
+                  defaultValue
+                }
+              : {})}
+            name="bases"
+            label={
+              <div className="tg-bases-label">
+                <div style={{ display: "flex" }}>
+                  Bases{" "}
+                  <div style={{ fontSize: 10 }}>
+                    {" "}
+                    &nbsp; (Length: {bases ? bases.length : 0})
+                  </div>
+                </div>
+                <div style={{ width: "fit-content" }}>
+                  <DropdownButton
+                    disabled={readOnly}
+                    intent="primary"
+                    small
+                    menu={
+                      <Menu>
+                        <MenuItem
+                          onClick={() => {
+                            change("forward", true);
+                            change(
+                              "bases",
+                              getSequenceWithinRange(
+                                normalizedSelection,
+                                sequenceData.sequence
+                              )
+                            );
+                          }}
+                          key="forward"
+                          text="Forward"
+                        ></MenuItem>
+                        <MenuItem
+                          onClick={() => {
+                            change("forward", false);
+                            change(
+                              "bases",
+                              getReverseComplementSequenceString(
+                                getSequenceWithinRange(
+                                  normalizedSelection,
+                                  sequenceData.sequence
+                                )
+                              )
+                            );
+                          }}
+                          key="reverse"
+                          text="Reverse"
+                        ></MenuItem>
+                      </Menu>
+                    }
+                  >
+                    Set From Selection
+                  </DropdownButton>
+                </div>
+              </div>
+            }
+          />
+          <AdvancedOptions style={{ marginBottom: 10 }}>
+            <RadioGroupField
+              name="primerBindsOn"
+              inline
+              inlineLabel
+              disabled={readOnly}
+              label="Oligo Binds On"
+              tooltipError
+              options={[
+                { label: "5' End", value: "5prime" },
+                { label: "3' End", value: "3prime" }
+              ]}
+            ></RadioGroupField>
+          </AdvancedOptions>
+
+          <MeltingTemp
+            InnerWrapper={InnerWrapperMeltingTemp}
+            sequence={bases}
+          ></MeltingTemp>
+        </div>
+      )}
+    </div>
+  );
+};
+
+export default AddOrEditAnnotationDialog({
+  formName: "AddOrEditPrimerDialog",
+  getProps: (props) => ({
+    upsertAnnotation: props.upsertPrimer,
+    annotationTypePlural: "primers",
+    RenderBases
+  })
+});
+
+const InnerWrapperMeltingTemp = (p) => (
+  <div
+    className="bp3-text-muted bp3-text-small"
+    style={{ marginBottom: 15, marginTop: -5, fontStyle: "italic" }}
+  >
+    {p.children}
+  </div>
+);

package/src/helperComponents/AddOrEditPrimerDialog/style.css

@@ -0,0 +1,41 @@
+.tg-custom-sequence-editable {
+  height: auto;
+  line-height: inherit;
+  max-width: 100%;
+  padding: 10px;
+  flex: 1 1 auto;
+  width: 100%;
+  word-break: break-all;
+  max-height: 300px;
+  overflow-y: auto;
+  /* min-width: 190px; */
+}
+.tg-custom-sequence-editable.hasTempError {
+  box-shadow: inset 0 0 3px 1px red;
+}
+.tg-has-error .tg-custom-sequence-editable {
+  box-shadow: inset 0 0 3px 1px red;
+}
+
+/* .tg-match-seq {
+  background-color: aquamarine;
+} */
+.tg-no-match-seq {
+  color: red;
+  fill: red;
+  text-decoration: underline;
+}
+.tg-ambiguous-match-seq {
+  color: blue;
+  fill: blue;
+}
+.tg-no-show-seq {
+  opacity: 0;
+}
+
+.tg-bases-label {
+  width: 100%;
+  display: flex;
+  justify-content: space-between;
+  align-items: baseline;
+}