diff --git a/cypress.json b/cypress.json index 58b3e7040..b1b8ca966 100644 --- a/cypress.json +++ b/cypress.json @@ -1,4 +1,6 @@ { "projectId": "mp89gp", - "baseUrl": "http://localhost:3344" + "baseUrl": "http://localhost:3344", + "viewportHeight": 800, + "viewportWidth": 1280 } diff --git a/cypress/integration/addYourOwnEnzyme.spec.js b/cypress/integration/addYourOwnEnzyme.spec.js index 679f5094a..d294c3cf0 100644 --- a/cypress/integration/addYourOwnEnzyme.spec.js +++ b/cypress/integration/addYourOwnEnzyme.spec.js @@ -19,13 +19,13 @@ describe("addAdditionalEnzymes", function() { cy.contains("(2 cuts)"); }); - it(`can open the add additional enzymes dialog from the Tools > Add Additional Enzymes + it(`can open the add additional enzymes dialog from the Tools > Manage Enzymes and add a custom user enzyme `, function() { cy.get(".tg-menu-bar") .contains("Tools") .click(); cy.get(".bp3-menu-item") - .contains("Add Additional Enzymes") + .contains("Manage Enzymes") .click(); cy.contains("Create your own enzyme").click(); cy.contains("Cuts 0 times in your Destination Vector"); @@ -37,13 +37,13 @@ describe("addAdditionalEnzymes", function() { cy.contains("Use Enzyme").click(); cy.get(`[data-test="cutsiteToolDropdown"]`).click(); }); - it(`can open the add additional enzymers dialog from the Tools > Add Additional Enzymes + it(`can open the add additional enzymers dialog from the Tools > Manage Enzymes and add an additional enzyme `, function() { cy.get(".tg-menu-bar") .contains("Tools") .click(); cy.get(".bp3-menu-item") - .contains("Add Additional Enzymes") + .contains("Manage Enzymes") .click(); cy.get(`input[placeholder="Select cut sites..."]`).click(); cy.contains("AaaI").click(); @@ -55,8 +55,8 @@ describe("addAdditionalEnzymes", function() { it("can open the create a new enzyme dialog from the cutsite filter dropdown", function() { cy.get(`[data-test="cutsiteToolDropdown"]`).click(); cy.get(`.veToolbarCutsiteFilterHolder .tg-select`).click(); - cy.contains(".bp3-menu-item", `Add additional enzyme`).click(); - cy.contains(".bp3-heading", "Add Additional Enzymes"); + cy.contains(".bp3-menu-item", `Manage Enzymes`).click(); + cy.contains(".bp3-heading", "Manage Enzymes"); // cy.get(`[data-test="veStatusBar-circularity"]`) // .find("select") diff --git a/cypress/integration/enzymeManager.spec.js b/cypress/integration/enzymeManager.spec.js new file mode 100644 index 000000000..1c6e8f523 --- /dev/null +++ b/cypress/integration/enzymeManager.spec.js @@ -0,0 +1,35 @@ +describe("manage enzymes dialog", () => { + it(`should be able to add a new group and add enzymes to it`, () => { + cy.visit(""); + cy.window().then(win => { + win.localStorage.clear(); + }); + cy.triggerFileCmd("Manage Enzymes"); + cy.get(".veEnzymeDialogAddGroupBtn").click(); + cy.get(".veNewEnzymeGroupPopover input").type("newGroup"); + cy.get(".veNewEnzymeGroupPopover .bp3-icon-tick").click(); + cy.contains("Common Enzymes").click(); + cy.contains("AccIII").click(); + cy.contains("Eco52I").click(); + cy.get(".veEnzymeGroupAddEnzymesBtn").click(); + // cy.get('.veEnzymeGroupAddEnzymesBtn').blur() + cy.contains("Copy 2 Enzyme(s)"); + cy.get(".veEnzymeGroupMoveEnzymePopover .bp3-icon-tick").click(); + cy.contains("Deselect 2").click({ force: true }); + cy.contains("Deselect 0").should("exist"); + + cy.contains("newGroup").click(); + cy.contains("AccIII").click(); + cy.get(".veRemoveEnzymeFromGroupBtn").click(); + cy.contains("button", "OK").click(); + cy.contains("AccIII").should("not.exist"); + cy.get(`[data-test="cutsiteToolDropdown"]`).click(); + cy.get(`.veToolbarCutsiteFilterHolder .tg-select`).click(); + cy.contains( + ".veToolbarCutsiteFilterHolder .bp3-menu-item", + "newGroup" + ).click(); + + // cy.get('.veEnzymeGroupAddEnzymesBtn').click() + }); +}); diff --git a/cypress/integration/enzymeViewer.spec.js b/cypress/integration/enzymeViewer.spec.js index fbac1319c..0a6c9e06a 100644 --- a/cypress/integration/enzymeViewer.spec.js +++ b/cypress/integration/enzymeViewer.spec.js @@ -1,4 +1,3 @@ - describe("tabs", function() { beforeEach(() => { cy.visit("#EnzymeViewer"); diff --git a/cypress/integration/simpleCircularOrLinearView.spec.js b/cypress/integration/simpleCircularOrLinearView.spec.js index 4c1df418d..b551f7ac6 100644 --- a/cypress/integration/simpleCircularOrLinearView.spec.js +++ b/cypress/integration/simpleCircularOrLinearView.spec.js @@ -1,4 +1,3 @@ - describe("tabs", function() { beforeEach(() => { cy.visit("/#/SimpleCircularOrLinearView"); diff --git a/cypress/integration/tabs.spec.js b/cypress/integration/tabs.spec.js index caaec9ace..aba2b26ac 100644 --- a/cypress/integration/tabs.spec.js +++ b/cypress/integration/tabs.spec.js @@ -1,4 +1,3 @@ - describe("tabs", function() { beforeEach(() => { cy.visit(""); diff --git a/editorStateExample.js b/editorStateExample.js index 86c20ff67..3176a3132 100644 --- a/editorStateExample.js +++ b/editorStateExample.js @@ -126,31 +126,31 @@ const exampleEditorState = { cutsThisManyTimes: 1 } ], - allRestrictionEnzymes: { - aatii: { - name: "AatII", - site: "gacgtc", - forwardRegex: "gacgtc", - reverseRegex: "gacgtc", - topSnipOffset: 5, - bottomSnipOffset: 1, - usForward: 0, - usReverse: 0, - color: "#059369" - }, - acci: { - name: "AccI", - site: "gtmkac", - forwardRegex: "gt[acm][gkt]ac", - reverseRegex: "gt[acm][gkt]ac", - topSnipOffset: 2, - bottomSnipOffset: 4, - usForward: 0, - usReverse: 0, - color: "#0d994a" - }, - // ...etc - } + // allRestrictionEnzymes: { + // aatii: { + // name: "AatII", + // site: "gacgtc", + // forwardRegex: "gacgtc", + // reverseRegex: "gacgtc", + // topSnipOffset: 5, + // bottomSnipOffset: 1, + // usForward: 0, + // usReverse: 0, + // color: "#059369" + // }, + // acci: { + // name: "AccI", + // site: "gtmkac", + // forwardRegex: "gt[acm][gkt]ac", + // reverseRegex: "gt[acm][gkt]ac", + // topSnipOffset: 2, + // bottomSnipOffset: 4, + // usForward: 0, + // usReverse: 0, + // color: "#0d994a" + // }, + // // ...etc + // } }, selectedAnnotations: { idMap: {}, diff --git a/nwb.config.js b/nwb.config.js index 4b108f655..1e8cdd612 100644 --- a/nwb.config.js +++ b/nwb.config.js @@ -27,6 +27,10 @@ module.exports = { // "teselagen-react-components": // console.log("comment me back out!") || // path.resolve("../teselagen-react-components/src/"), + // "@teselagen/apollo-methods": + // console.log("comment me back out!") || + // path.resolve("../teselagen-common/apollo-methods/src/"), + //don't comment this out! react: path.resolve(__dirname, "node_modules/react"), "react-dom": path.resolve(__dirname, "node_modules/react-dom") diff --git a/src/CutsiteFilter/index.js b/src/CutsiteFilter/index.js index 870a85850..2cf65824a 100644 --- a/src/CutsiteFilter/index.js +++ b/src/CutsiteFilter/index.js @@ -10,17 +10,89 @@ import "./style.css"; import { TgSelect } from "teselagen-react-components"; import map from "lodash/map"; +import { flatMap } from "lodash"; export class CutsiteFilter extends React.Component { static defaultProps = { onChangeHook: () => {}, + closeDropDown: () => {}, filteredRestrictionEnzymes: [], - filteredRestrictionEnzymesUpdate: [], + filteredRestrictionEnzymesUpdate: () => {}, allCutsites: { cutsitesByName: {} }, sequenceData: { sequence: "" - }, - dispatch: () => {} + } + }; + + // getManageEnzymesLink = () => ( + // { + // // e.stopPropagation(); + // const { + // createYourOwnEnzymeReset, + // showManageEnzymesDialog, + // sequenceData, + // closeDropDown + // } = this.props; + // closeDropDown(); + // createYourOwnEnzymeReset(); + // showManageEnzymesDialog({ + // inputSequenceToTestAgainst: sequenceData ? sequenceData.sequence : "" + // }); + // }} + // className={"ta_link " + Classes.POPOVER_DISMISS} + // > + // Manage enzymes   + // + // + // ); + + renderOptions = ({ label, value, canBeHidden }, props) => { + // if (value === "manageEnzymes") { + // return this.getManageEnzymesLink(); + // } + const { + filteredRestrictionEnzymes, + filteredRestrictionEnzymesUpdate + } = props; + + return ( +
+ {label}{" "} + {canBeHidden && ( + { + e.stopPropagation(); + + filteredRestrictionEnzymesUpdate( + flatMap(filteredRestrictionEnzymes, (e) => { + if (e.value === value) return []; + return e; + }).concat({ + label, + className: "veHiddenEnzyme", + value, + // hiddenEnzyme: true, + isHidden: true, + canBeHidden + }) + ); + }} + htmlTitle="Hide this enzyme" + className="veHideEnzymeBtn" + style={{ paddingTop: 5 }} + iconSize={14} + icon="eye-off" + > + )} +
+ ); }; render() { @@ -29,31 +101,45 @@ export class CutsiteFilter extends React.Component { style = {}, filteredRestrictionEnzymes, filteredRestrictionEnzymesUpdate, - allCutsites: { cutsitesByName }, - sequenceData: { sequence: inputSequenceToTestAgainst }, - dispatch + allCutsites: { cutsitesByName } // ...rest } = this.props; + const userEnzymeGroups = window.getExistingEnzymeGroups(); // var {handleOpen, handleClose} = this let options = [ - ...map(specialCutsiteFilterOptions, opt => opt), - ...Object.keys(cutsitesByName).map(function(key) { + ...map(specialCutsiteFilterOptions, (opt) => opt), + ...map(userEnzymeGroups, (g, name) => { + return { + label: ( + +  {name} + + ), + value: "__userCreatedGroup" + name + }; + }), + + ...Object.keys(cutsitesByName).map(function (key) { const label = getLabel(cutsitesByName[key], key); return { + canBeHidden: true, label, + // hiddenEnzyme: false, value: key }; }) ]; - function openAddYourOwn() { - dispatch({ - type: "ADD_ADDITIONAL_ENZYMES_RESET", - payload: { - inputSequenceToTestAgainst, - isOpen: true - } - }); - } + // function openManageEnzymes() { + // dispatch({ + // type: "CREATE_YOUR_OWN_ENZYME_RESET" + // }); + // dispatch({ + // type: "CREATE_YOUR_OWN_ENZYME_RESET", + // payload: { + // inputSequenceToTestAgainst + // } + // }); + // } return (
No matching enzymes found that cut in the sequence.{" "} - {" "} + {/* {this.getManageEnzymesLink()} */}
} - placeholder="Filter cut sites..." + placeholder="Filter cutsites..." options={options} - optionRenderer={renderOptions} - onChange={filteredRestrictionEnzymes => { - if ( - filteredRestrictionEnzymes && - filteredRestrictionEnzymes.some( - enzyme => - enzyme.value === specialCutsiteFilterOptions.addYourOwn.value - ) - ) { - return openAddYourOwn(); - } + filteredRestrictionEnzymes={filteredRestrictionEnzymes} + filteredRestrictionEnzymesUpdate={filteredRestrictionEnzymesUpdate} + optionRenderer={this.renderOptions} + isSimpleSearch + onChange={(filteredRestrictionEnzymes) => { + // if ( + // filteredRestrictionEnzymes && + // filteredRestrictionEnzymes.some( + // enzyme => + // enzyme.value === + // specialCutsiteFilterOptions.manageEnzymes.value + // ) + // ) { + // return; + // } onChangeHook && onChangeHook(filteredRestrictionEnzymes); filteredRestrictionEnzymesUpdate(filteredRestrictionEnzymes); }} - value={filteredRestrictionEnzymes.map(filteredOpt => { + value={filteredRestrictionEnzymes.map((filteredOpt) => { if (filteredOpt.cutsThisManyTimes) { return filteredOpt; } + if (filteredOpt.value.includes("__userCreatedGroup")) { + return filteredOpt; + } const label = getLabel( cutsitesByName[filteredOpt.value], @@ -102,25 +195,7 @@ export class CutsiteFilter extends React.Component { } } -export default compose( - withEditorProps, - connect() -)(CutsiteFilter); -function renderOptions({ label, value }) { - if (value === "addYourOwn") { - return ; - } - - return label; -} - -function AddAdditionalEnzymeLink({ onClick }) { - return ( - - Add additional enzymes - - ); -} +export default compose(withEditorProps, connect())(CutsiteFilter); const getLabel = (maybeCutsites = [], val) => { const cutNumber = maybeCutsites.length; diff --git a/src/CutsiteFilter/style.css b/src/CutsiteFilter/style.css index 2d40f4907..e8a754be3 100644 --- a/src/CutsiteFilter/style.css +++ b/src/CutsiteFilter/style.css @@ -6,6 +6,15 @@ .ta_link:hover { color: lightblue; } - +.veHideEnzymeBtn { + opacity: 0.3; +} +.veHideEnzymeBtn:hover { + opacity: 1; +} +.veHiddenEnzyme { + background-color: #b83211 !important; + color: #f5f8fa !important; +} - /*# sourceMappingURL= style.css.map */ \ No newline at end of file +/*# sourceMappingURL= style.css.map */ diff --git a/src/Dialogs/index.js b/src/Dialogs/index.js index 7cdebea24..9ac2dfde5 100644 --- a/src/Dialogs/index.js +++ b/src/Dialogs/index.js @@ -1,6 +1,4 @@ import React from "react"; -import { connect } from "react-redux"; - import AddOrEditPrimerDialogDefault from "../helperComponents/AddOrEditPrimerDialog"; import AddOrEditFeatureDialogDefault from "../helperComponents/AddOrEditFeatureDialog"; import AddOrEditPartDialogDefault from "../helperComponents/AddOrEditPartDialog"; @@ -9,18 +7,24 @@ import MergeFeaturesDialog from "../helperComponents/MergeFeaturesDialog"; import RenameSequenceDialog from "../helperComponents/RenameSequenceDialog"; import GoToDialog from "../helperComponents/GoToDialog"; import SelectDialog from "../helperComponents/SelectDialog"; -import _AddAdditionalEnzymes from "../AddAdditionalEnzymes"; +// import _ManageEnzymes from "../ManageEnzymes"; import { withDialog } from "teselagen-react-components"; -import { addAdditionalEnzymesClose } from "../redux/addAdditionalEnzymes"; import { AlignmentToolInner } from "../ToolBar/alignmentTool"; import PrintDialog from "../helperComponents/PrintDialog"; import RemoveDuplicatesDialog from "../helperComponents/RemoveDuplicates"; import { userDefinedHandlersAndOpts } from "../Editor/userDefinedHandlersAndOpts"; import { pick } from "lodash"; +import _EnzymesDialog from "../helperComponents/EnzymesDialog"; + +const EnzymesDialog = withDialog({ + title: "Manage Enzymes", + // isOpen: true, + isDraggable: true, + height: 500, + width: 500 +})(_EnzymesDialog); -const AddAdditionalEnzymes = withDialog({ - title: "Add Additional Enzymes" -})(_AddAdditionalEnzymes); +// })(_ManageEnzymes); const CreateAlignmentDialog = withDialog({ title: "Create New Alignment" @@ -32,21 +36,9 @@ export const dialogOverrides = [ "AddOrEditPrimerDialogOverride" ]; -export default connect( - state => { - return { - addAdditionalEnzymesOpen: - state.VectorEditor.__allEditorsOptions.addAdditionalEnzymes.isOpen - }; - }, - { - addAdditionalEnzymesClose - } -)(props => { +export default props => { const { editorName, - addAdditionalEnzymesOpen, - addAdditionalEnzymesClose, AddOrEditFeatureDialogOverride, AddOrEditPartDialogOverride, AddOrEditPrimerDialogOverride @@ -65,13 +57,13 @@ export default connect( AddOrEditPrimerDialogOverride || AddOrEditPrimerDialogDefault; return (
- + /> */} +
); -}); +}; diff --git a/src/DigestTool/DigestTool.js b/src/DigestTool/DigestTool.js index 74c0e41d8..168a4ab9b 100644 --- a/src/DigestTool/DigestTool.js +++ b/src/DigestTool/DigestTool.js @@ -96,7 +96,7 @@ export class DigestTool extends React.Component { )} { + onChange={(id) => { this.setState({ selectedTab: id }); }} > @@ -166,7 +166,7 @@ const schema = { export default compose( withEditorInteractions, - withProps(props => { + withProps((props) => { const { sequenceData, sequenceLength, @@ -238,7 +238,7 @@ export default compose( }); }); - fragments.filter(fragment => { + fragments.filter((fragment) => { if (!fragment.size) { overlappingEnzymes.push(fragment); return false; diff --git a/src/AddAdditionalEnzymes/index.js b/src/ManageEnzymes/index.js similarity index 82% rename from src/AddAdditionalEnzymes/index.js rename to src/ManageEnzymes/index.js index df4d61d7a..3429e2be8 100644 --- a/src/AddAdditionalEnzymes/index.js +++ b/src/ManageEnzymes/index.js @@ -1,4 +1,4 @@ -import map from "lodash/map"; +import { map } from "lodash"; // import enzymeListFull from '../../../enzymeListFull.json'; import { connect } from "react-redux"; @@ -6,37 +6,41 @@ import { connect } from "react-redux"; // import {reduxForm, Field, formValueSelector} from 'redux-form' import React from "react"; import { Button } from "@blueprintjs/core"; -import { InfoHelper, TgSelect } from "teselagen-react-components"; +import { InfoHelper, MultiSelectSideBySide } from "teselagen-react-components"; -import enzymeListFull from "../redux/utils/expandedEnzymeList.json"; -import defaultEnzymeList from "../redux/utils/defaultEnzymeList.json"; +import defaultEnzymeList from "../redux/utils/defaultEnzymeList.js"; // import './style.css'; import { cutSequenceByRestrictionEnzyme } from "ve-sequence-utils"; // import QuestionTooltip from '../../components/QuestionTooltip'; -import "./style.css"; -import { getReverseComplementSequenceString } from "ve-sequence-utils"; +import { + getReverseComplementSequenceString, + enzymeList as enzymeListFull +} from "ve-sequence-utils"; import EnzymeViewer from "../EnzymeViewer"; -import { addAdditionalEnzymesClose } from "../redux/addAdditionalEnzymes"; -let AddAdditionalEnzyme = function(props) { +import { createYourOwnEnzymeClose } from "../redux/createYourOwnEnzyme"; +import s from "../selectors"; +import "./style.css"; + +let CreateYouOwnEnzyme = function(props) { const paddingStart = "-------"; const paddingEnd = "-------"; const { // filteredRestrictionEnzymesAdd, // addRestrictionEnzyme, inputSequenceToTestAgainst = "", //pass this prop in! - addAdditionalEnzymesClose: hideModal, + createYourOwnEnzymeClose: hideModal, seqName = "Destination Vector", - addAdditionalEnzymes, + createYourOwnEnzyme, dispatch, editorName, - stopAddingYourOwnEnzyme + stopCreatingYourOwnEnzyme } = props; - addAdditionalEnzymes.chop_top_index = Number( - addAdditionalEnzymes.chop_top_index + createYourOwnEnzyme.chop_top_index = Number( + createYourOwnEnzyme.chop_top_index ); - addAdditionalEnzymes.chop_bottom_index = Number( - addAdditionalEnzymes.chop_bottom_index + createYourOwnEnzyme.chop_bottom_index = Number( + createYourOwnEnzyme.chop_bottom_index ); const { @@ -44,7 +48,7 @@ let AddAdditionalEnzyme = function(props) { chop_top_index = 0, chop_bottom_index = 0, name = "" - } = addAdditionalEnzymes; + } = createYourOwnEnzyme; const regexString = bpsToRegexString(sequence); const enzyme = { name: name, @@ -80,15 +84,15 @@ let AddAdditionalEnzyme = function(props) { ); } - const errors = validate(addAdditionalEnzymes); + const errors = validate(createYourOwnEnzyme); if (Object.keys(errors || {}).length) { invalid = true; } function onChange(updatedVal) { dispatch({ - type: "ADD_ADDITIONAL_ENZYMES_UPDATE", + type: "CREATE_YOUR_OWN_ENZYME_UPDATE", payload: { - ...addAdditionalEnzymes, + ...createYourOwnEnzyme, ...updatedVal } }); @@ -211,7 +215,7 @@ let AddAdditionalEnzyme = function(props) {
@@ -254,59 +258,80 @@ let AddAdditionalEnzyme = function(props) { ); }; -AddAdditionalEnzyme = connect( +CreateYouOwnEnzyme = connect( function(state) { return { - addAdditionalEnzymes: - state.VectorEditor.__allEditorsOptions.addAdditionalEnzymes + createYourOwnEnzyme: + state.VectorEditor.__allEditorsOptions.createYourOwnEnzyme }; }, - { addAdditionalEnzymesClose } -)(AddAdditionalEnzyme); + { createYourOwnEnzymeClose } +)(CreateYouOwnEnzyme); -class AddAdditionalEnzymes extends React.Component { +class ManageEnzymes extends React.Component { state = { - addAdditionalEnzymes: false, + createYourOwnEnzyme: false, enzymesToAdd: [] }; + handleChange = () => {}; startAddingYourOwnEnzyme = () => { - this.setState({ addAdditionalEnzymes: true }); + this.setState({ createYourOwnEnzyme: true }); }; - stopAddingYourOwnEnzyme = () => { - this.setState({ addAdditionalEnzymes: false }); + stopCreatingYourOwnEnzyme = () => { + this.setState({ createYourOwnEnzyme: false }); }; render() { - if (this.state.addAdditionalEnzymes) { + if (this.state.createYourOwnEnzyme) { return ( - ); } const { dispatch, - addAdditionalEnzymesClose: hideModal, - inputSequenceToTestAgainst = "" + createYourOwnEnzymeClose: hideModal, + // inputSequenceToTestAgainst = "", + selectedEnzymes } = this.props; + + const selectedItems = []; + const allEnzymes = map(enzymeListFull, function(enzyme) { + const inList = selectedEnzymes[enzyme.name.toLowerCase()]; + const o = { + label: enzyme.name, + id: enzyme + }; + if (inList) { + selectedItems.push(o); + } + + return o; + }); + const { enzymesToAdd } = this.state; return (
-

Add additional enzymes

+

Manage enzymes

Our default list contains just the most common enzymes. Search here to add less common ones:
- + {/* { this.setState({ enzymesToAdd: enzymesToAdd.map(function({ value }) { @@ -325,7 +350,7 @@ class AddAdditionalEnzymes extends React.Component { }); }} value={enzymesToAdd} - /> + /> */}
+
+ ); + } +} + +export default compose( + withEditorProps + // reduxForm({ + // form: "EnzymesDialog", + // validate: ({ id1, id2 }) => { + // const errors = {}; + // if (!id1 || Array.isArray(id1)) { + // errors.id1 = "Please select a feature"; + // } + // if (!id2 || Array.isArray(id2)) { + // errors.id2 = "Please select a feature"; + // } + // return errors; + // } + // }), + // formValues("id1", "id2") +)(EnzymesDialog); + +function getEnzymesForNames(names) { + return names.map(n => { + return (n && expandedEnzymeList[n.toLowerCase()]) || { name: "Not Found!" }; + }); +} + +class MoveToInner extends React.Component { + componentDidMount() { + const { + selectedEnzymeGroup, + enzymeGroupToMoveTo, + setStateAbove, + enzymeGroups + } = this.props; + const enzymeOpts = flatMap(enzymeGroups, g => { + if (g.protected || g.name === selectedEnzymeGroup) return []; + return { + value: g.name + }; + }); + if (!enzymeGroupToMoveTo && enzymeOpts.length) { + setStateAbove({ enzymeGroupToMoveTo: enzymeOpts[0].value }); + } + this.setState({ + enzymeOpts + }); + } + state = { enzymeOpts: [] }; + render() { + const { + setStateAbove, + selectedCount, + enzymeGroupToMoveTo, + enzymeGroups, + refreshEnzymeGroups, + selectedEnzymesForGroup + } = this.props; + const { enzymeOpts } = this.state; + return ( +
+ {enzymeOpts && !enzymeOpts.length ? ( +
+ No other custom enzyme groups exist. Please create a new enzyme + group to add enzymes to it. +
+ ) : ( +
+
Copy {selectedCount} Enzyme(s) To:
+ + { + setStateAbove({ + enzymeGroupToMoveTo: e.target.value + }); + }} + value={enzymeGroupToMoveTo} + options={enzymeOpts} + > + { + //tnrtodo + const enzymes = uniq([ + ...map( + enzymeGroups[enzymeGroupToMoveTo].enzymes, + e => e.name + ), + ...flatMap(selectedEnzymesForGroup, (selected, name) => + selected ? name : [] + ) + ]); + window.updateEnzymeGroup(enzymeGroupToMoveTo, enzymes); + refreshEnzymeGroups(); + + window.toastr.success( + `${selectedCount} enzyme(s) moved to ${enzymeGroupToMoveTo}` + ); + // this.set + // debugger; + }} + intent="success" + icon="tick" + > +
+ )} +
+ ); + } +} + +const HoverView = view(() => { + const { hoveredEnzyme } = easyStore; + return ( +
+ {hoveredEnzyme}{" "} + {hoveredEnzyme && ( + + )} +
+ ); +}); diff --git a/src/helperComponents/EnzymesDialog/style.css b/src/helperComponents/EnzymesDialog/style.css new file mode 100644 index 000000000..b8eee65dd --- /dev/null +++ b/src/helperComponents/EnzymesDialog/style.css @@ -0,0 +1,20 @@ +.veSelectedEnzymeGroup { + background-color: #106ba3; +} +.veEnzymeDialogEnzyme { + cursor: pointer; + padding: 1px 5px; + margin: 1px; +} +.veEnzymeDialogEnzymes { + width: 100%; + padding-left: 20px; + /* padding-right: 5px; */ + display: flex; + flex-direction: column; + justify-content: space-between; +} + +.veEnzymeDialogEnzymeAddIcon { + flex: 0 0 auto !important; +} diff --git a/src/helperComponents/MergeFeaturesDialog/index.js b/src/helperComponents/MergeFeaturesDialog/index.js index fd0ec0236..bcb3fefbb 100644 --- a/src/helperComponents/MergeFeaturesDialog/index.js +++ b/src/helperComponents/MergeFeaturesDialog/index.js @@ -37,7 +37,7 @@ export class MergeFeaturesDialog extends React.Component { const feat2 = features[id2]; const [id1default, id2default] = flatMap( selectedAnnotations.idStack, - id => { + (id) => { const ann = selectedAnnotations.idMap[id]; if (ann.annotationTypePlural === "features") { return id; @@ -88,7 +88,7 @@ export class MergeFeaturesDialog extends React.Component {
} - options={flatMap(features, feat => { + options={flatMap(features, (feat) => { if (feat.id === (feat2 && feat2.id)) return []; //filter out other feature as an option return { value: feat.id, @@ -141,7 +141,7 @@ export class MergeFeaturesDialog extends React.Component { } - options={flatMap(features, feat => { + options={flatMap(features, (feat) => { if (feat.id === (feat1 && feat1.id)) return []; //filter out other feature as an option return { value: feat.id, diff --git a/src/helperComponents/PropertiesDialog/CutsiteProperties.js b/src/helperComponents/PropertiesDialog/CutsiteProperties.js index 561a57d2a..930382296 100644 --- a/src/helperComponents/PropertiesDialog/CutsiteProperties.js +++ b/src/helperComponents/PropertiesDialog/CutsiteProperties.js @@ -6,7 +6,7 @@ import { } from "teselagen-react-components"; import { map, get } from "lodash"; import EnzymeViewer from "../../EnzymeViewer"; -import enzymeList from "../../redux/utils/defaultEnzymeList.json"; +import enzymeList from "../../redux/utils/defaultEnzymeList.js"; import CutsiteFilter from "../../CutsiteFilter"; import { Button } from "@blueprintjs/core"; import { connectToEditor } from "../../withEditorProps"; diff --git a/src/helperComponents/PropertiesDialog/OrfProperties.js b/src/helperComponents/PropertiesDialog/OrfProperties.js index ac24a1e06..80a41a60a 100644 --- a/src/helperComponents/PropertiesDialog/OrfProperties.js +++ b/src/helperComponents/PropertiesDialog/OrfProperties.js @@ -50,7 +50,7 @@ class OrfProperties extends React.Component { + } annotationVisibility={annotationVisibility} //we need to pass this in order to force the DT to rerender noPadding diff --git a/src/index.js b/src/index.js index ca9fcf3c7..36357a85c 100644 --- a/src/index.js +++ b/src/index.js @@ -19,9 +19,7 @@ export { default as CircularView, CircularView as CircularViewUnconnected } from "./CircularView"; -export { - default as SimpleCircularOrLinearView -} from "./SimpleCircularOrLinearView"; +export { default as SimpleCircularOrLinearView } from "./SimpleCircularOrLinearView"; export { default as RowView, RowView as RowViewUnconnected } from "./RowView"; export { default as RowItem, RowItem as RowItemUnconnected } from "./RowItem"; export { default as Editor, Editor as EditorUnconnected } from "./Editor"; @@ -52,12 +50,8 @@ export { export { default as updateEditor } from "./updateEditor"; export { default as addAlignment } from "./addAlignment"; -export { - default as getRangeAnglesSpecial -} from "./CircularView/getRangeAnglesSpecial"; -export { - default as PositionAnnotationOnCircle -} from "./CircularView/PositionAnnotationOnCircle"; +export { default as getRangeAnglesSpecial } from "./CircularView/getRangeAnglesSpecial"; +export { default as PositionAnnotationOnCircle } from "./CircularView/PositionAnnotationOnCircle"; export { default as EnzymeViewer } from "./EnzymeViewer"; export { default as AlignmentView } from "./AlignmentView"; export { default as getOveHotkeyDefs } from "./commands/getOveHotkeyDefs"; diff --git a/src/redux/addAdditionalEnzymes.js b/src/redux/createYourOwnEnzyme.js similarity index 51% rename from src/redux/addAdditionalEnzymes.js rename to src/redux/createYourOwnEnzyme.js index 3d1ec3859..ffd8cd1ff 100644 --- a/src/redux/addAdditionalEnzymes.js +++ b/src/redux/createYourOwnEnzyme.js @@ -3,15 +3,14 @@ import { createReducer, createAction } from "redux-act"; // ------------------------------------ // Actions // ------------------------------------ -export const addAdditionalEnzymesUpdate = createAction( - "ADD_ADDITIONAL_ENZYMES_UPDATE" +export const createYourOwnEnzymeUpdate = createAction( + "CREATE_YOUR_OWN_ENZYME_UPDATE" ); -export const addAdditionalEnzymesReset = createAction( - "ADD_ADDITIONAL_ENZYMES_RESET" +export const createYourOwnEnzymeReset = createAction( + "CREATE_YOUR_OWN_ENZYME_RESET" ); -export const addAdditionalEnzymesClose = createAction( - "ADD_ADDITIONAL_ENZYMES_CLOSE", - () => {} +export const createYourOwnEnzymeClose = createAction( + "CREATE_YOUR_OWN_ENZYME_CLOSE" ); // ------------------------------------ @@ -22,18 +21,17 @@ const initialValues = { sequence: "ggatcc", chop_top_index: 1, chop_bottom_index: 5, - inputSequenceToTestAgainst: "", isOpen: false }; export default createReducer( { - [addAdditionalEnzymesClose]: state => { - return { ...state, isOpen: false }; + [createYourOwnEnzymeClose]: (state, payload = {}) => { + return { ...initialValues, isOpen: false }; }, - [addAdditionalEnzymesReset]: (state, payload = {}) => { + [createYourOwnEnzymeReset]: (state, payload = {}) => { return { ...initialValues, ...payload }; }, - [addAdditionalEnzymesUpdate]: (state, payload) => { + [createYourOwnEnzymeUpdate]: (state, payload) => { return payload; } }, diff --git a/src/redux/index.js b/src/redux/index.js index 62e37f8f7..bef3bb718 100644 --- a/src/redux/index.js +++ b/src/redux/index.js @@ -1,5 +1,5 @@ import { merge } from "lodash"; -import * as addAdditionalEnzymes from "./addAdditionalEnzymes"; +import * as createYourOwnEnzyme from "./createYourOwnEnzyme"; import * as annotationLabelVisibility from "./annotationLabelVisibility"; import * as annotationsToSupport from "./annotationsToSupport"; import * as annotationVisibility from "./annotationVisibility"; @@ -38,7 +38,7 @@ import createAction from "./utils/createMetaAction"; export { default as vectorEditorMiddleware } from "./middleware"; const subReducers = { - addAdditionalEnzymes, + createYourOwnEnzyme, annotationLabelVisibility, annotationsToSupport, annotationVisibility, @@ -164,10 +164,10 @@ export default function reducerFactory(initialState = {}) { ...stateToReturn, //these are reducers that are not editor specific (aka shared across editor instances) __allEditorsOptions: { - addAdditionalEnzymes: addAdditionalEnzymes.default( + createYourOwnEnzyme: createYourOwnEnzyme.default( !state.__allEditorsOptions ? undefined - : state.__allEditorsOptions.addAdditionalEnzymes, + : state.__allEditorsOptions.createYourOwnEnzyme, action ), uppercaseSequenceMapFont: uppercaseSequenceMapFont.default( diff --git a/src/redux/modalActions.js b/src/redux/modalActions.js index f7f026312..cead94241 100644 --- a/src/redux/modalActions.js +++ b/src/redux/modalActions.js @@ -57,6 +57,12 @@ export function hidePrintDialog(props) { props }; } +export function showManageEnzymesDialog() { + return { + type: "TG_SHOW_MODAL", + name: "ManageEnzymesDialog" //you'll need to pass a unique dialogName prop to the compoennt + }; +} export function showRemoveDuplicatesDialog(props) { return { type: "TG_SHOW_MODAL", diff --git a/src/redux/restrictionEnzymes.js b/src/redux/restrictionEnzymes.js index 516428d27..b31bb92f8 100644 --- a/src/redux/restrictionEnzymes.js +++ b/src/redux/restrictionEnzymes.js @@ -2,7 +2,7 @@ import { combineReducers } from "redux"; import { createReducer } from "redux-act"; import createAction from "./utils/createMetaAction"; import specialCutsiteFilterOptions from "../constants/specialCutsiteFilterOptions"; -import defaultEnzymeList from "./utils/defaultEnzymeList.json"; +// import defaultEnzymeList from "./utils/defaultEnzymeList.js"; // ------------------------------------ // Actions // ------------------------------------ @@ -23,6 +23,8 @@ export const allRestrictionEnzymesUpdate = createAction( // Reducer // ------------------------------------ let initialState = [specialCutsiteFilterOptions.single]; +// const userEnzymeGroups = window.localStorage.getItem("restrictionEnzymeGroups") || [] + export default combineReducers({ //filteredRestrictionEnzymes refer to the enzymes actively included in the react-select filter component filteredRestrictionEnzymes: createReducer( @@ -34,18 +36,5 @@ export default combineReducers({ } }, initialState - ), - - allRestrictionEnzymes: createReducer( - { - [addRestrictionEnzyme]: function(state, payload) { - return { - ...state, - [payload.name]: payload - }; - }, - [allRestrictionEnzymesUpdate]: (state, payload) => payload - }, - defaultEnzymeList ) }); diff --git a/src/redux/sequenceData/index.js b/src/redux/sequenceData/index.js index 73559c18f..3da8b4bea 100644 --- a/src/redux/sequenceData/index.js +++ b/src/redux/sequenceData/index.js @@ -32,7 +32,7 @@ export * from "./translations"; // ------------------------------------ const _updateSequenceData = createAction("SEQUENCE_DATA_UPDATE"); -export const updateSequenceData = function(seqData, ...rest) { +export const updateSequenceData = function (seqData, ...rest) { //tnrtodo: currently we're not using that type variable for anything return _updateSequenceData( tidyUpSequenceData(seqData, { annotationsAsObjects: true }), @@ -58,7 +58,7 @@ const coreReducer = combineReducersDontIgnoreKeys({ fromFileUpload: createReducer({}, false) }); -export default function(state, action) { +export default function (state, action) { let stateToPass = state; if (action.type === "SEQUENCE_DATA_UPDATE") { stateToPass = action.payload; diff --git a/src/redux/sequenceData/upsertDeleteActionGenerator.js b/src/redux/sequenceData/upsertDeleteActionGenerator.js index 83cb0930a..d99d025ec 100644 --- a/src/redux/sequenceData/upsertDeleteActionGenerator.js +++ b/src/redux/sequenceData/upsertDeleteActionGenerator.js @@ -19,7 +19,7 @@ export default function upsertDeleteActionGenerator( [deleteAction]: (state, payload) => { let ids; if (Array.isArray(payload)) { - ids = payload.map(val => { + ids = payload.map((val) => { return val.id || val; }); } else { diff --git a/src/redux/utils/defaultEnzymeList.js b/src/redux/utils/defaultEnzymeList.js new file mode 100644 index 000000000..69d253e4a --- /dev/null +++ b/src/redux/utils/defaultEnzymeList.js @@ -0,0 +1,4 @@ +import { enzymeList } from "ve-sequence-utils"; +import defaultEnzymeListJson from "./defaultEnzymeListJson.json"; + +export default defaultEnzymeListJson.map(e => enzymeList[e]); diff --git a/src/redux/utils/defaultEnzymeList.json b/src/redux/utils/defaultEnzymeList.json deleted file mode 100644 index f1ab4a690..000000000 --- a/src/redux/utils/defaultEnzymeList.json +++ /dev/null @@ -1,1236 +0,0 @@ - -{ - "aatii": { - "name": "AatII", - "site": "gacgtc", - "forwardRegex": "gacgtc", - "reverseRegex": "gacgtc", - "topSnipOffset": 5, - "bottomSnipOffset": 1, - "usForward": 0, - "usReverse": 0, - "color": "#059369" - }, - "acci": { - "name": "AccI", - "site": "gtmkac", - "forwardRegex": "gt[acm][gkt]ac", - "reverseRegex": "gt[acm][gkt]ac", - "topSnipOffset": 2, - "bottomSnipOffset": 4, - "usForward": 0, - "usReverse": 0, - "color": "#0d994a" - }, - "accii": { - "name": "AccII", - "site": "cgcg", - "forwardRegex": "cgcg", - "reverseRegex": "cgcg", - "topSnipOffset": 2, - "bottomSnipOffset": 2, - "usForward": 0, - "usReverse": 0, - "color": "#487a03" - }, - "acciii": { - "name": "AccIII", - "site": "tccgga", - "forwardRegex": "tc{2}g{2}a", - "reverseRegex": "tc{2}g{2}a", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#168709" - }, - "afai": { - "name": "AfaI", - "site": "gtac", - "forwardRegex": "gtac", - "reverseRegex": "gtac", - "topSnipOffset": 2, - "bottomSnipOffset": 2, - "usForward": 0, - "usReverse": 0, - "color": "#4e0b82" - }, - "aflii": { - "name": "AflII", - "site": "cttaag", - "forwardRegex": "ct{2}a{2}g", - "reverseRegex": "ct{2}a{2}g", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#96000f" - }, - "alui": { - "name": "AluI", - "site": "agct", - "forwardRegex": "agct", - "reverseRegex": "agct", - "topSnipOffset": 2, - "bottomSnipOffset": 2, - "usForward": 0, - "usReverse": 0, - "color": "#035877" - }, - "aor13hi": { - "name": "Aor13HI", - "site": "tccgga", - "forwardRegex": "tc{2}g{2}a", - "reverseRegex": "tc{2}g{2}a", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#88990c" - }, - "aor51hi": { - "name": "Aor51HI", - "site": "agcgct", - "forwardRegex": "agcgct", - "reverseRegex": "agcgct", - "topSnipOffset": 3, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#e51677" - }, - "apai": { - "name": "ApaI", - "site": "gggccc", - "forwardRegex": "g{3}c{3}", - "reverseRegex": "g{3}c{3}", - "topSnipOffset": 5, - "bottomSnipOffset": 1, - "usForward": 0, - "usReverse": 0, - "color": "#53047a" - }, - "apali": { - "name": "ApaLI", - "site": "gtgcac", - "forwardRegex": "gtgcac", - "reverseRegex": "gtgcac", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#049b16" - }, - "asci": { - "name": "AscI", - "site": "ggcgcgcc", - "forwardRegex": "g{2}cgcgc{2}", - "reverseRegex": "g{2}cgcgc{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 6, - "usForward": 0, - "usReverse": 0, - "color": "#110463" - }, - "asisi": { - "name": "AsiSI", - "site": "gcgatcgc", - "forwardRegex": "gcgatcgc", - "reverseRegex": "gcgatcgc", - "topSnipOffset": 5, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#820330" - }, - "avrii": { - "name": "AvrII", - "site": "cctagg", - "forwardRegex": "c{2}tag{2}", - "reverseRegex": "c{2}tag{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "bali": { - "name": "BalI", - "site": "tggcca", - "forwardRegex": "tg{2}c{2}a", - "reverseRegex": "tg{2}c{2}a", - "topSnipOffset": 3, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#e006dc" - }, - "bamhi": { - "name": "BamHI", - "site": "ggatcc", - "forwardRegex": "g{2}atc{2}", - "reverseRegex": "g{2}atc{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#500c7a" - }, - "banii": { - "name": "BanII", - "site": "grgcyc", - "forwardRegex": "g[agr]gc[cty]c", - "reverseRegex": "g[agr]gc[cty]c", - "topSnipOffset": 5, - "bottomSnipOffset": 1, - "usForward": 0, - "usReverse": 0, - "color": "#026d05" - }, - "bcni": { - "name": "BcnI", - "site": "ccsgg", - "forwardRegex": "c{2}[cgs]g{2}", - "reverseRegex": "c{2}[cgs]g{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#058405" - }, - "bgli": { - "name": "BglI", - "site": "gccnnnnnggc", - "forwardRegex": "gc{2}[abcdghkmnrstvwy]{5}g{2}c", - "reverseRegex": "gc{2}[abcdghkmnrstvwy]{5}g{2}c", - "topSnipOffset": 7, - "bottomSnipOffset": 4, - "usForward": 0, - "usReverse": 0, - "color": "#00275e" - }, - "bglii": { - "name": "BglII", - "site": "agatct", - "forwardRegex": "agatct", - "reverseRegex": "agatct", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#008e39" - }, - "blni": { - "name": "BlnI", - "site": "cctagg", - "forwardRegex": "c{2}tag{2}", - "reverseRegex": "c{2}tag{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#457503" - }, - "bmet110i": { - "name": "BmeT110I", - "site": "cycgrg", - "forwardRegex": "c[cty]cg[agr]g", - "reverseRegex": "c[cty]cg[agr]g", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#03277a" - }, - "bmgt120i": { - "name": "BmgT120I", - "site": "ggncc", - "forwardRegex": "g{2}[abcdghkmnrstvwy]c{2}", - "reverseRegex": "g{2}[abcdghkmnrstvwy]c{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#51a010" - }, - "bpu1102i": { - "name": "Bpu1102I", - "site": "gctnagc", - "forwardRegex": "gct[abcdghkmnrstvwy]agc", - "reverseRegex": "gct[abcdghkmnrstvwy]agc", - "topSnipOffset": 2, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#859b07" - }, - "bsai": { - "name": "BsaI", - "site": "ggtctc", - "forwardRegex": "g{2}tctc", - "reverseRegex": "gagac{2}", - "topSnipOffset": 7, - "bottomSnipOffset": 11 - }, - "bsgi": { - "name": "BsgI", - "site": "gtgcag", - "forwardRegex": "gtgcag", - "reverseRegex": "ctgcac", - "topSnipOffset": 22, - "bottomSnipOffset": 20 - }, - "bsmbi": { - "name": "BsmBI", - "site": "cgtctc", - "forwardRegex": "cgtctc", - "reverseRegex": "gagacg", - "topSnipOffset": 7, - "bottomSnipOffset": 11 - }, - "bsp1286i": { - "name": "Bsp1286I", - "site": "gdgchc", - "forwardRegex": "g[adgkrtw]gc[achmtwy]c", - "reverseRegex": "g[adgkrtw]gc[achmtwy]c", - "topSnipOffset": 5, - "bottomSnipOffset": 1, - "usForward": 0, - "usReverse": 0, - "color": "#033166" - }, - "bsp1407i": { - "name": "Bsp1407I", - "site": "tgtaca", - "forwardRegex": "tgtaca", - "reverseRegex": "tgtaca", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#e25600" - }, - "bspt104i": { - "name": "BspT104I", - "site": "ttcgaa", - "forwardRegex": "t{2}cga{2}", - "reverseRegex": "t{2}cga{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 4, - "usForward": 0, - "usReverse": 0, - "color": "#010387" - }, - "bspt107i": { - "name": "BspT107I", - "site": "ggyrcc", - "forwardRegex": "g{2}[cty][agr]c{2}", - "reverseRegex": "g{2}[cty][agr]c{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#47087a" - }, - "bsshii": { - "name": "BssHII", - "site": "gcgcgc", - "forwardRegex": "gcgcgc", - "reverseRegex": "gcgcgc", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#0e8908" - }, - "bst1107i": { - "name": "Bst1107I", - "site": "gtatac", - "forwardRegex": "gtatac", - "reverseRegex": "gtatac", - "topSnipOffset": 3, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#c1790d" - }, - "bstpi": { - "name": "BstPI", - "site": "ggtnacc", - "forwardRegex": "g{2}t[abcdghkmnrstvwy]ac{2}", - "reverseRegex": "g{2}t[abcdghkmnrstvwy]ac{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 6, - "usForward": 0, - "usReverse": 0, - "color": "#0c6887" - }, - "bstxi": { - "name": "BstXI", - "site": "ccannnnnntgg", - "forwardRegex": "c{2}a[abcdghkmnrstvwy]{6}tg{2}", - "reverseRegex": "c{2}a[abcdghkmnrstvwy]{6}tg{2}", - "topSnipOffset": 8, - "bottomSnipOffset": 4, - "usForward": 0, - "usReverse": 0, - "color": "#09666d" - }, - "cfr10i": { - "name": "Cfr10I", - "site": "rccggy", - "forwardRegex": "[agr]c{2}g{2}[cty]", - "reverseRegex": "[agr]c{2}g{2}[cty]", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#f9cb11" - }, - "clai": { - "name": "ClaI", - "site": "atcgat", - "forwardRegex": "atcgat", - "reverseRegex": "atcgat", - "topSnipOffset": 2, - "bottomSnipOffset": 4, - "usForward": 0, - "usReverse": 0, - "color": "#bf03b9" - }, - "cpoi": { - "name": "CpoI", - "site": "cggwccg", - "forwardRegex": "cg{2}[atw]c{2}g", - "reverseRegex": "cg{2}[atw]c{2}g", - 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"site": "ggwcc", - "forwardRegex": "g{2}[atw]c{2}", - "reverseRegex": "g{2}[atw]c{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 4, - "usForward": 0, - "usReverse": 0, - "color": "#097f01" - }, - "xbai": { - "name": "XbaI", - "site": "tctaga", - "forwardRegex": "tctaga", - "reverseRegex": "tctaga", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#0a586d" - }, - "xhoi": { - "name": "XhoI", - "site": "ctcgag", - "forwardRegex": "ctcgag", - "reverseRegex": "ctcgag", - "topSnipOffset": 1, - "bottomSnipOffset": 5, - "usForward": 0, - "usReverse": 0, - "color": "#240975" - }, - "xmai": { - "name": "XmaI", - "site": "cccggg", - "forwardRegex": "c{3}g{3}", - "reverseRegex": "c{3}g{3}", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "xspi": { - "name": "XspI", - "site": "ctag", - "forwardRegex": "ctag", - "reverseRegex": "ctag", - "topSnipOffset": 1, - "bottomSnipOffset": 3, - "usForward": 0, - "usReverse": 0, - "color": "#0b6a84" - } -} \ No newline at end of file diff --git a/src/redux/utils/defaultEnzymeListJson.json b/src/redux/utils/defaultEnzymeListJson.json new file mode 100644 index 000000000..0db4bbda7 --- /dev/null +++ b/src/redux/utils/defaultEnzymeListJson.json @@ -0,0 +1,116 @@ +[ + "aatii", + "acci", + "accii", + "acciii", + "afai", + "aflii", + "alui", + "aor13hi", + "aor51hi", + "apai", + "apali", + "asci", + "asisi", + "avrii", + "bali", + "bamhi", + "banii", + "bcni", + "bgli", + "bglii", + "blni", + "bmet110i", + "bmgt120i", + "bpu1102i", + "bsai", + "bsgi", + "bsmbi", + "bsp1286i", + "bsp1407i", + "bspt104i", + "bspt107i", + "bsshii", + "bst1107i", + "bstpi", + "bstxi", + "cfr10i", + "clai", + "cpoi", + "ddei", + "dpni", + "drai", + "eaei", + "eagi", + "eam1105i", + "eco52i", + "eco81i", + "ecoo109i", + "ecoo65i", + "ecori", + "ecorv", + "ecot14i", + "ecot22i", + "fbai", + "foki", + "fsei", + "haeii", + "haeiii", + "hapii", + "hhai", + "hin1i", + "hincii", + "hindiii", + "hinfi", + "hpai", + "kpni", + "mboi", + "mboii", + "mfli", + "mlui", + "msei", + "mspi", + "muni", + "naei", + "ncoi", + "ndei", + "nhei", + "noti", + "nrui", + "nsbi", + "paci", + "pmaci", + "pmei", + "pshai", + "pshbi", + "psp1406i", + "psti", + "pvui", + "pvuii", + "saci", + "sacii", + "sali", + "sapi", + "sau3ai", + "sbfi", + "scai", + "sfii", + "smai", + "smii", + "snabi", + "spei", + "sphi", + "srfi", + "sse8387i", + "sspi", + "stui", + "swai", + "taqi", + "tth111i", + "van91i", + "vpak11bi", + "xbai", + "xhoi", + "xmai", + "xspi" +] diff --git a/src/redux/utils/expandedEnzymeList.json b/src/redux/utils/expandedEnzymeList.json deleted file mode 100644 index 242c627b1..000000000 --- a/src/redux/utils/expandedEnzymeList.json +++ /dev/null @@ -1,29927 +0,0 @@ -{ - "aaai": { - "name": "AaaI", - "site": "cggccg", - "forwardRegex": "cg{2}c{2}g", - "reverseRegex": "cg{2}c{2}g", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "aacli": { - "name": "AacLI", - "site": "ggatcc", - "forwardRegex": "g{2}atc{2}", - "reverseRegex": "g{2}atc{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "aaei": { - "name": "AaeI", - "site": "ggatcc", - "forwardRegex": "g{2}atc{2}", - "reverseRegex": "g{2}atc{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "aagi": { - "name": "AagI", - "site": "atcgat", - "forwardRegex": "atcgat", - "reverseRegex": "atcgat", - "topSnipOffset": 2, - "bottomSnipOffset": 4 - }, - "aani": { - "name": "AanI", - "site": "ttataa", - "forwardRegex": "t{2}ata{2}", - "reverseRegex": "t{2}ata{2}", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "aaqi": { - "name": "AaqI", - "site": "gtgcac", - "forwardRegex": "gtgcac", - "reverseRegex": "gtgcac", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "aari": { - "name": "AarI", - "site": "cacctgc", - "forwardRegex": "cac{2}tgc", - "reverseRegex": "gcag{2}tg", - "topSnipOffset": 11, - "bottomSnipOffset": 15 - }, - "aasi": { - "name": "AasI", - "site": "gacnnnnnngtc", - "forwardRegex": "gac[abcdghkmnrstvwy]{6}gtc", - "reverseRegex": "gac[abcdghkmnrstvwy]{6}gtc", - "topSnipOffset": 7, - "bottomSnipOffset": 5 - }, - "aati": { - "name": "AatI", - "site": "aggcct", - "forwardRegex": "ag{2}c{2}t", - "reverseRegex": "ag{2}c{2}t", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "aatii": { - "name": "AatII", - "site": "gacgtc", - "forwardRegex": "gacgtc", - "reverseRegex": "gacgtc", - "topSnipOffset": 5, - "bottomSnipOffset": 1 - }, - "aaui": { - "name": "AauI", - "site": "tgtaca", - "forwardRegex": "tgtaca", - "reverseRegex": "tgtaca", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "abai": { - "name": "AbaI", - "site": "tgatca", - "forwardRegex": "tgatca", - "reverseRegex": "tgatca", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "abei": { - "name": "AbeI", - "site": "cctcagc", - "forwardRegex": "c{2}tcagc", - "reverseRegex": "gctgag{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 5 - }, - "abri": { - "name": "AbrI", - "site": "ctcgag", - "forwardRegex": "ctcgag", - "reverseRegex": "ctcgag", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "absi": { - "name": "AbsI", - "site": "cctcgagg", - "forwardRegex": "c{2}tcgag{2}", - "reverseRegex": "c{2}tcgag{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 6 - }, - "acai": { - "name": "AcaI", - "site": "ttcgaa", - "forwardRegex": "t{2}cga{2}", - "reverseRegex": "t{2}cga{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acaii": { - "name": "AcaII", - "site": "ggatcc", - "forwardRegex": "g{2}atc{2}", - "reverseRegex": "g{2}atc{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acaiii": { - "name": "AcaIII", - "site": "tgcgca", - "forwardRegex": "tgcgca", - "reverseRegex": "tgcgca", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acaiv": { - "name": "AcaIV", - "site": "ggcc", - "forwardRegex": "g{2}c{2}", - "reverseRegex": "g{2}c{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acc113i": { - "name": "Acc113I", - "site": "agtact", - "forwardRegex": "agtact", - "reverseRegex": "agtact", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "acc16i": { - "name": "Acc16I", - "site": "tgcgca", - "forwardRegex": "tgcgca", - "reverseRegex": "tgcgca", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "acc36i": { - "name": "Acc36I", - "site": "acctgc", - "forwardRegex": "ac{2}tgc", - "reverseRegex": "gcag{2}t", - "topSnipOffset": 10, - "bottomSnipOffset": 14 - }, - "acc38i": { - "name": "Acc38I", - "site": "ccwgg", - "forwardRegex": "c{2}[atw]g{2}", - "reverseRegex": "c{2}[atw]g{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acc65i": { - "name": "Acc65I", - "site": "ggtacc", - "forwardRegex": "g{2}tac{2}", - "reverseRegex": "g{2}tac{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "accb1i": { - "name": "AccB1I", - "site": "ggyrcc", - "forwardRegex": "g{2}[cty][agr]c{2}", - "reverseRegex": "g{2}[cty][agr]c{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "accb2i": { - "name": "AccB2I", - "site": "rgcgcy", - "forwardRegex": "[agr]gcgc[cty]", - "reverseRegex": "[agr]gcgc[cty]", - "topSnipOffset": 5, - "bottomSnipOffset": 1 - }, - "accb7i": { - "name": "AccB7I", - "site": "ccannnnntgg", - "forwardRegex": "c{2}a[abcdghkmnrstvwy]{5}tg{2}", - "reverseRegex": "c{2}a[abcdghkmnrstvwy]{5}tg{2}", - "topSnipOffset": 7, - "bottomSnipOffset": 4 - }, - "accbsi": { - "name": "AccBSI", - "site": "ccgctc", - "forwardRegex": "c{2}gctc", - "reverseRegex": "gagcg{2}", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "accebi": { - "name": "AccEBI", - "site": "ggatcc", - "forwardRegex": "g{2}atc{2}", - "reverseRegex": "g{2}atc{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "acci": { - "name": "AccI", - "site": "gtmkac", - "forwardRegex": "gt[acm][gkt]ac", - "reverseRegex": "gt[acm][gkt]ac", - "topSnipOffset": 2, - "bottomSnipOffset": 4 - }, - "accii": { - "name": "AccII", - "site": "cgcg", - "forwardRegex": "cgcg", - "reverseRegex": "cgcg", - "topSnipOffset": 2, - "bottomSnipOffset": 2 - }, - "acciii": { - "name": "AccIII", - "site": "tccgga", - "forwardRegex": "tc{2}g{2}a", - "reverseRegex": "tc{2}g{2}a", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "acei": { - "name": "AceI", - "site": "gcwgc", - "forwardRegex": "gc[atw]gc", - "reverseRegex": "gc[atw]gc", - "topSnipOffset": 1, - "bottomSnipOffset": 4 - }, - "aceii": { - "name": "AceII", - "site": "gctagc", - "forwardRegex": "gctagc", - "reverseRegex": "gctagc", - "topSnipOffset": 5, - "bottomSnipOffset": 1 - }, - "aceiii": { - "name": "AceIII", - "site": "cagctc", - "forwardRegex": "cagctc", - "reverseRegex": "gagctg", - "topSnipOffset": 13, - "bottomSnipOffset": 17 - }, - "acii": { - "name": "AciI", - "site": "ccgc", - "forwardRegex": "c{2}gc", - "reverseRegex": "gcg{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 3 - }, - "acli": { - "name": "AclI", - "site": "aacgtt", - "forwardRegex": "a{2}cgt{2}", - "reverseRegex": "a{2}cgt{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 4 - }, - "aclni": { - "name": "AclNI", - "site": "actagt", - "forwardRegex": "actagt", - "reverseRegex": "actagt", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "aclwi": { - "name": "AclWI", - "site": "ggatc", - "forwardRegex": "g{2}atc", - "reverseRegex": "gatc{2}", - "topSnipOffset": 9, - "bottomSnipOffset": 10 - }, - "acoi": { - "name": "AcoI", - "site": "yggccr", - "forwardRegex": "[cty]g{2}c{2}[agr]", - "reverseRegex": "[cty]g{2}c{2}[agr]", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "acpi": { - "name": "AcpI", - "site": "ttcgaa", - "forwardRegex": "t{2}cga{2}", - "reverseRegex": "t{2}cga{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 4 - }, - "acpii": { - "name": "AcpII", - "site": "ccannnnntgg", - "forwardRegex": "c{2}a[abcdghkmnrstvwy]{5}tg{2}", - "reverseRegex": "c{2}a[abcdghkmnrstvwy]{5}tg{2}", - "topSnipOffset": 7, - "bottomSnipOffset": 4 - }, - "acri": { - "name": "AcrI", - "site": "cycgrg", - "forwardRegex": "c[cty]cg[agr]g", - "reverseRegex": "c[cty]cg[agr]g", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acrii": { - "name": "AcrII", - "site": "ggtnacc", - "forwardRegex": "g{2}t[abcdghkmnrstvwy]ac{2}", - "reverseRegex": "g{2}t[abcdghkmnrstvwy]ac{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 6 - }, - "acs1371i": { - "name": "Acs1371I", - "site": "gtcgac", - "forwardRegex": "gtcgac", - "reverseRegex": "gtcgac", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acs1372i": { - "name": "Acs1372I", - "site": "gtcgac", - "forwardRegex": "gtcgac", - "reverseRegex": "gtcgac", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acs1373i": { - "name": "Acs1373I", - "site": "gtcgac", - "forwardRegex": "gtcgac", - "reverseRegex": "gtcgac", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acs1421i": { - "name": "Acs1421I", - "site": "gtcgac", - "forwardRegex": "gtcgac", - "reverseRegex": "gtcgac", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acs1422i": { - "name": "Acs1422I", - "site": "gtcgac", - "forwardRegex": "gtcgac", - "reverseRegex": "gtcgac", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acsi": { - "name": "AcsI", - "site": "raatty", - "forwardRegex": "[agr]a{2}t{2}[cty]", - "reverseRegex": "[agr]a{2}t{2}[cty]", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "acui": { - "name": "AcuI", - "site": "ctgaag", - "forwardRegex": "ctga{2}g", - "reverseRegex": "ct{2}cag", - "topSnipOffset": 22, - "bottomSnipOffset": 20 - }, - "acuii": { - "name": "AcuII", - "site": "ccwgg", - "forwardRegex": "c{2}[atw]g{2}", - "reverseRegex": "c{2}[atw]g{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "acvi": { - "name": "AcvI", - "site": "cacgtg", - "forwardRegex": "cacgtg", - "reverseRegex": "cacgtg", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "acyi": { - "name": "AcyI", - "site": "grcgyc", - "forwardRegex": "g[agr]cg[cty]c", - "reverseRegex": "g[agr]cg[cty]c", - "topSnipOffset": 2, - "bottomSnipOffset": 4 - }, - "adei": { - "name": "AdeI", - "site": "cacnnngtg", - "forwardRegex": "cac[abcdghkmnrstvwy]{3}gtg", - "reverseRegex": "cac[abcdghkmnrstvwy]{3}gtg", - "topSnipOffset": 6, - "bottomSnipOffset": 3 - }, - "aerai": { - "name": "AerAI", - "site": "ctcgag", - "forwardRegex": "ctcgag", - "reverseRegex": "ctcgag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "aeui": { - "name": "AeuI", - "site": "ccwgg", - "forwardRegex": "c{2}[atw]g{2}", - "reverseRegex": "c{2}[atw]g{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 3 - }, - "afa16ri": { - "name": "Afa16RI", - "site": "cgatcg", - "forwardRegex": "cgatcg", - "reverseRegex": "cgatcg", - "topSnipOffset": 4, - "bottomSnipOffset": 2 - }, - "afa22mi": { - "name": "Afa22MI", - "site": "cgatcg", - "forwardRegex": "cgatcg", - "reverseRegex": "cgatcg", - "topSnipOffset": 4, - "bottomSnipOffset": 2 - }, - "afa24ri": { - "name": "Afa24RI", - "site": "gccggc", - "forwardRegex": "gc{2}g{2}c", - "reverseRegex": "gc{2}g{2}c", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "afai": { - "name": "AfaI", - "site": "gtac", - "forwardRegex": "gtac", - "reverseRegex": "gtac", - "topSnipOffset": 2, - "bottomSnipOffset": 2 - }, - "afei": { - "name": "AfeI", - "site": "agcgct", - "forwardRegex": "agcgct", - "reverseRegex": "agcgct", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "afii": { - "name": "AfiI", - "site": "ccnnnnnnngg", - "forwardRegex": "c{2}[abcdghkmnrstvwy]{7}g{2}", - "reverseRegex": "c{2}[abcdghkmnrstvwy]{7}g{2}", - "topSnipOffset": 7, - "bottomSnipOffset": 4 - }, - "afl83i": { - "name": "Afl83I", - "site": "ttcgaa", - "forwardRegex": "t{2}cga{2}", - "reverseRegex": "t{2}cga{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "afl83ii": { - "name": "Afl83II", - "site": "ggcc", - "forwardRegex": "g{2}c{2}", - "reverseRegex": "g{2}c{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "afli": { - "name": "AflI", - "site": "ggwcc", - "forwardRegex": "g{2}[atw]c{2}", - "reverseRegex": "g{2}[atw]c{2}", - "topSnipOffset": 1, - "bottomSnipOffset": 4 - 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"forwardRegex": "cgatcg", - "reverseRegex": "cgatcg", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "xorkii": { - "name": "XorKII", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "xpai": { - "name": "XpaI", - "site": "ctcgag", - "forwardRegex": "ctcgag", - "reverseRegex": "ctcgag", - "topSnipOffset": 1, - "bottomSnipOffset": 5 - }, - "xphi": { - "name": "XphI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "xspi": { - "name": "XspI", - "site": "ctag", - "forwardRegex": "ctag", - "reverseRegex": "ctag", - "topSnipOffset": 1, - "bottomSnipOffset": 3 - }, - "xvei": { - "name": "XveI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "yenai": { - "name": "YenAI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "yenbi": { - "name": "YenBI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "yenci": { - "name": "YenCI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "yendi": { - "name": "YenDI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "yenei": { - "name": "YenEI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 1, - "bottomSnipOffset": 1 - }, - "yeni": { - "name": "YenI", - "site": "ctgcag", - "forwardRegex": "ctgcag", - "reverseRegex": "ctgcag", - "topSnipOffset": 5, - "bottomSnipOffset": 1 - }, - "zani": { - "name": "ZanI", - "site": "ccwgg", - "forwardRegex": "c{2}[atw]g{2}", - "reverseRegex": "c{2}[atw]g{2}", - "topSnipOffset": 2, - "bottomSnipOffset": 3 - }, - "zhoi": { - "name": "ZhoI", - "site": "atcgat", - "forwardRegex": "atcgat", - "reverseRegex": "atcgat", - "topSnipOffset": 2, - "bottomSnipOffset": 4 - }, - "zrai": { - "name": "ZraI", - "site": "gacgtc", - "forwardRegex": "gacgtc", - "reverseRegex": "gacgtc", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "zrmi": { - "name": "ZrmI", - "site": "agtact", - "forwardRegex": "agtact", - "reverseRegex": "agtact", - "topSnipOffset": 3, - "bottomSnipOffset": 3 - }, - "zsp2i": { - "name": "Zsp2I", - "site": "atgcat", - "forwardRegex": "atgcat", - "reverseRegex": "atgcat", - "topSnipOffset": 5, - "bottomSnipOffset": 1 - } -} diff --git a/src/selectors/cutsiteLabelColorSelector.js b/src/selectors/cutsiteLabelColorSelector.js index b28a5aa2c..a0ee24a27 100644 --- a/src/selectors/cutsiteLabelColorSelector.js +++ b/src/selectors/cutsiteLabelColorSelector.js @@ -1,4 +1,6 @@ +import { createSelector } from "reselect"; import sequenceDataSelector from "./sequenceDataSelector"; -export default function(state) { - return sequenceDataSelector(state).cutsiteLabelColors; -} + +export default createSelector(sequenceDataSelector, function(sequenceData) { + return sequenceData.cutsiteLabelColors; +}); diff --git a/src/selectors/cutsitesSelector.js b/src/selectors/cutsitesSelector.js index e3cc4038a..41b3a3a32 100644 --- a/src/selectors/cutsitesSelector.js +++ b/src/selectors/cutsitesSelector.js @@ -4,7 +4,7 @@ import restrictionEnzymesSelector from "./restrictionEnzymesSelector"; import cutsiteLabelColorSelector from "./cutsiteLabelColorSelector"; import { createSelector } from "reselect"; import bsonObjectid from "bson-objectid"; -import { flatMap as flatmap } from "lodash"; +import { flatMap as flatmap, map } from "lodash"; import { getCutsitesFromSequence } from "ve-sequence-utils"; function cutsitesSelector(sequence, circular, enzymeList, cutsiteLabelColors) { @@ -12,9 +12,7 @@ function cutsitesSelector(sequence, circular, enzymeList, cutsiteLabelColors) { let cutsitesByName = getCutsitesFromSequence( sequence, circular, - Object.keys(enzymeList).map(function(enzymeName) { - return enzymeList[enzymeName]; - }) + map(enzymeList) ); //tag each cutsite with a unique id let cutsitesById = {}; @@ -60,9 +58,7 @@ export default createSelector( circularSelector, restrictionEnzymesSelector, cutsiteLabelColorSelector, - function() { - return cutsitesSelector(...arguments); - } + cutsitesSelector ); // // diff --git a/src/selectors/filteredCutsitesSelector.js b/src/selectors/filteredCutsitesSelector.js index 2df0ff09b..f9315b1c9 100644 --- a/src/selectors/filteredCutsitesSelector.js +++ b/src/selectors/filteredCutsitesSelector.js @@ -11,20 +11,37 @@ export default createSelector( let returnVal = { cutsitesByName: {} }; - if ( - !filteredRestrictionEnzymes || - filteredRestrictionEnzymes.length === 0 - ) { + + const hiddenEnzymesByName = {}; + let filteredEnzymes = []; + //handle adding enzymes that are included in user created groups + filteredRestrictionEnzymes.forEach(e => { + if (e.value.includes("__userCreatedGroup")) { + const groupName = e.value.replace("__userCreatedGroup", ""); + + const enzymes = window.getExistingEnzymeGroups()[groupName] || []; + + filteredEnzymes = filteredEnzymes.concat( + enzymes.map(e => ({ value: e })) + ); + } else if (e.isHidden) { + hiddenEnzymesByName[e.value] = e; + } else { + filteredEnzymes.push(e); + } + }); + if (!filteredEnzymes || filteredEnzymes.length === 0) { returnVal.cutsitesByName = cutsitesByName; } else { //loop through each filter option ('Single Cutters', 'BamHI') - filteredRestrictionEnzymes.forEach(function({ value }) { + filteredEnzymes.forEach(function({ value }) { let cutsThisManyTimes = specialCutsiteFilterOptions[value] && specialCutsiteFilterOptions[value].cutsThisManyTimes; if (cutsThisManyTimes > 0) { //the cutter type is either 1,2,3 for single, double or triple cutters Object.keys(cutsitesByName).forEach(function(key) { + if (hiddenEnzymesByName[key]) return; //don't show that cutsite if (cutsitesByName[key].length === cutsThisManyTimes) { returnVal.cutsitesByName[key] = cutsitesByName[key]; } diff --git a/src/selectors/restrictionEnzymesSelector.js b/src/selectors/restrictionEnzymesSelector.js index 69e055593..1fe6b3b13 100644 --- a/src/selectors/restrictionEnzymesSelector.js +++ b/src/selectors/restrictionEnzymesSelector.js @@ -1 +1,26 @@ -export default state => state.restrictionEnzymes.allRestrictionEnzymes; +import { createSelector } from "reselect"; +import defaultEnzymeList from "../redux/utils/defaultEnzymeList.js"; +import { reduce } from "lodash"; + +export default createSelector( + () => defaultEnzymeList, + () => localStorage.getItem("enzymeGroups"), //it should recompute if the enzyme groups change in localstorage + () => { + const userEnzymeGroups = window.getExistingEnzymeGroupsWithEnzymeData(); + return { + ...defaultEnzymeList, + ...reduce( + userEnzymeGroups, + (acc, group) => { + // tnrtodo: more work needed here to return user created enzymes + default enzymes + // const group = userEnzymeGroups[key]; + (group || []).forEach(enzyme => { + acc[enzyme.name.toLowerCase()] = enzyme; + }); + return acc; + }, + {} + ) + }; + } +); diff --git a/src/selectors/translationsSelector.js b/src/selectors/translationsSelector.js index 4e405e6f5..ad21a95c7 100644 --- a/src/selectors/translationsSelector.js +++ b/src/selectors/translationsSelector.js @@ -95,7 +95,7 @@ function translationsSelector( {} ) }; - each(translationsToPass, function(translation) { + each(translationsToPass, function (translation) { translation.aminoAcids = getAminoAcidDataForEachBaseOfDna( sequence, translation.forward, @@ -109,14 +109,14 @@ export default createSelector( translationSearchMatchesSelector, sequenceSelector, orfsSelector, - state => state.annotationVisibility.orfTranslations, - state => state.annotationVisibility.orfs, + (state) => state.annotationVisibility.orfTranslations, + (state) => state.annotationVisibility.orfs, cdsFeaturesSelector, - state => state.annotationVisibility.cdsFeatureTranslations, - state => state.annotationVisibility.features, + (state) => state.annotationVisibility.cdsFeatureTranslations, + (state) => state.annotationVisibility.features, translationsRawSelector, - state => state.frameTranslations, - state => state.sequenceData.isProtein, - state => state.sequenceData.proteinSequence, + (state) => state.frameTranslations, + (state) => state.sequenceData.isProtein, + (state) => state.sequenceData.proteinSequence, translationsSelector );