@teselagen/ove 0.7.26 → 0.7.28

package/orfTool.js

@@ -0,0 +1,136 @@
+import { Icon } from "@blueprintjs/core";
+import React from "react";
+import { orfIcon, CmdCheckbox, CmdDiv, InfoHelper } from "@teselagen/ui";
+import ToolbarItem from "./ToolbarItem";
+import { connectToEditor } from "../withEditorProps";
+import withEditorProps from "../withEditorProps";
+import getCommands from "../commands";
+
+export default connectToEditor(
+  ({ annotationVisibility = {}, toolBar = {} }) => {
+    return {
+      toggled: annotationVisibility.orfs,
+      isOpen: toolBar.openItem === "orfTool"
+    };
+  }
+)(({ toolbarItemProps, toggled, annotationVisibilityToggle, isOpen }) => {
+  return (
+    <ToolbarItem
+      {...{
+        Icon: <Icon data-test="orfTool" icon={orfIcon} />,
+        onIconClick: function () {
+          annotationVisibilityToggle("orfs");
+        },
+        toggled,
+        tooltip: "Show Open Reading Frames",
+        tooltipToggled: "Hide Open Reading Frames",
+        Dropdown: OrfToolDropdown,
+        dropdowntooltip:
+          (!isOpen ? "Show" : "Hide") + " Open Reading Frame Options",
+        ...toolbarItemProps
+      }}
+    />
+  );
+});
+
+const OrfToolDropdown = withEditorProps(
+  class OrfDropdown extends React.Component {
+    constructor(props) {
+      super(props);
+      this.commands = getCommands(this);
+    }
+    render() {
+      return (
+        <div className="veToolbarOrfOptionsHolder">
+          <CmdCheckbox
+            prefix="Show "
+            cmd={this.commands.toggleOrfTranslations}
+          />
+          <CmdCheckbox
+            prefix="Show "
+            cmd={this.commands.useGtgAndCtgAsStartCodons}
+          />
+          <CmdDiv cmd={this.commands.minOrfSizeCmd} />
+          <div className="vespacer" />
+
+          <InfoHelper
+            displayToSide
+            content="To translate an arbitrary area, right click a selection."
+          />
+        </div>
+      );
+    }
+  }
+);
+// const OrfToolDropdown = withEditorProps(function({
+//   useAdditionalOrfStartCodons,
+//   useAdditionalOrfStartCodonsToggle,
+//   annotationVisibility,
+//   annotationVisibilityToggle,
+//   editorName
+// }) {
+//   return (
+//     <div className="veToolbarOrfOptionsHolder">
+//       {/* <div className="vespacer" />
+//       <MinOrfSize editorName={editorName} />
+//       <Checkbox
+//         onChange={function() {
+//           annotationVisibilityToggle("orfTranslations");
+//         }}
+//         disabled={!annotationVisibility.orfs}
+//         checked={annotationVisibility.orfTranslations}
+//         label="Show translations for ORFs"
+//       />
+//       <Checkbox
+//         onChange={function() {
+//           annotationVisibilityToggle("cdsFeatureTranslations");
+//         }}
+//         checked={annotationVisibility.cdsFeatureTranslations}
+//         label="Show translations for CDS features"
+//       />
+//       <Checkbox
+//         onChange={useAdditionalOrfStartCodonsToggle}
+//         checked={useAdditionalOrfStartCodons}
+//         label="Use GTG and CTG as start codons"
+//       /> */}
+//       <div className="vespacer" />
+
+//       <InfoHelper
+//         displayToSide
+//         content="To translate an arbitrary area, right click a selection."
+//       />
+//     </div>
+//   );
+// });
+
+// export const MinOrfSize = connectToEditor(editorState => {
+//   return {
+//     sequenceLength: selectors.sequenceLengthSelector(editorState),
+//     minimumOrfSize: editorState.minimumOrfSize
+//   };
+// })(
+//   ({
+//     minimumOrfSizeUpdate,
+//     sequenceLength,
+//     annotationVisibilityShow,
+//     minimumOrfSize
+//   }) => {
+//     return (
+//       <div data-test="min-orf-size" style={{ display: "flex" }}>
+//         Minimum ORF Size:
+//         <input
+//           type="number"
+//           className={classNames(Classes.INPUT, "minOrfSizeInput")}
+//           onChange={function(event) {
+//             let minimumOrfSize = parseInt(event.target.value, 10);
+//             if (!(minimumOrfSize > -1)) return;
+//             if (minimumOrfSize > sequenceLength) return;
+//             annotationVisibilityShow("orfs");
+//             minimumOrfSizeUpdate(minimumOrfSize);
+//           }}
+//           value={minimumOrfSize}
+//         />
+//       </div>
+//     );
+//   }
+// );

package/orfsSelector.js

@@ -0,0 +1,15 @@
+import circularSelector from "./circularSelector";
+import sequenceSelector from "./sequenceSelector";
+import minimumOrfSizeSelector from "./minimumOrfSizeSelector";
+import { findOrfsInPlasmid } from "@teselagen/sequence-utils";
+import { createSelector } from "reselect";
+
+export default createSelector(
+  sequenceSelector,
+  circularSelector,
+  minimumOrfSizeSelector,
+  state => state.useAdditionalOrfStartCodons,
+  findOrfsInPlasmid
+);
+
+//tiny