ove-auto-annotate 0.0.4 → 0.0.8

package/README.md

@@ -1,3 +1,8 @@
+# UI: 
+![image](https://user-images.githubusercontent.com/2730609/125001643-013bf980-e008-11eb-9385-b834b8e9573f.png)
+
+![image](https://user-images.githubusercontent.com/2730609/125001747-38120f80-e008-11eb-9981-292cebba847d.png)
+
 # Usage:
 
 ```js
@@ -43,6 +48,9 @@ window.createVectorEditor(yourDomNodeHere, {
 
 # Passing a custom list of existing annotations to choose from: 
 
+![image](https://user-images.githubusercontent.com/2730609/125001693-14e76000-e008-11eb-903b-e7f074a7747c.png)
+
+
 ```js
 async function getCustomAutoAnnotateList ({ annotationType, sequenceData }) { //annotationType = feature|part|oligo
     const dataToReturn = await fetch("/my/endpoint/here", { ...someParams }); //hit your endpoint here

package/es/index.js

@@ -23,6 +23,7 @@ import { formName } from "./constants";
 import { AutoAnnotateBpMatchingDialog } from "./AutoAnnotateBpMatchingDialog";
 import { parseCsvFile, validateCSVRequiredHeaders, validateCSVRow } from "./fileUtils";
 import downloadjs from "downloadjs";
+import { convertProteinSeqToDNAIupac } from "ve-sequence-utils";
 var _window$addOnGlobals = window.addOnGlobals,
     shortid = _window$addOnGlobals.shortid,
     FileUploadField = _window$addOnGlobals.FileUploadField,
@@ -32,8 +33,8 @@ var _window$addOnGlobals = window.addOnGlobals,
     pluralize = _window$addOnGlobals.pluralize,
     reduxForm = _window$addOnGlobals.reduxForm,
     SubmissionError = _window$addOnGlobals.SubmissionError,
-    featureColors = _window$addOnGlobals.featureColors,
-    FeatureTypes = _window$addOnGlobals.FeatureTypes,
+    getFeatureToColorMap = _window$addOnGlobals.getFeatureToColorMap,
+    getFeatureTypes = _window$addOnGlobals.getFeatureTypes,
     InfoHelper = _window$addOnGlobals.InfoHelper,
     showConfirmationDialog = _window$addOnGlobals.showConfirmationDialog,
     wrapDialog = _window$addOnGlobals.wrapDialog,
@@ -79,6 +80,7 @@ export function autoAnnotatePrimers() {
 }
 export var AutoAnnotateModal = compose(wrapDialog(function (p) {
   return {
+    canEscapeKeyClose: false,
     title: "Auto Annotate " + startCase(pluralize(p.annotationType))
   };
 }), withEditorProps, reduxForm({
@@ -147,8 +149,9 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
           }
         }
       }, _callee, null, [[2, 9, 13, 16]]);
-    }))();
-  }, [getCustomAutoAnnotateList, props]);
+    }))(); // eslint-disable-next-line react-hooks/exhaustive-deps
+
+  }, []);
 
   if (newAnnotations) {
     return /*#__PURE__*/React.createElement(CreateAnnotationsPage, _extends({}, props, {
@@ -163,24 +166,7 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
     onChange: setSelectedImportType,
     selectedTabId: fileType
   }, /*#__PURE__*/React.createElement(Tab, {
-    panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file with the following columns -", /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("div", {
-      style: {
-        display: "flex"
-      }
-    }, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
-      style: {
-        display: "flex"
-      }
-    }, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
-      onClick: function onClick(e) {
-        e.stopPropagation();
-        e.preventDefault();
-        showDialog({
-          ModalComponent: AutoAnnotateBpMatchingDialog
-        });
-      },
-      content: true ? /*#__PURE__*/React.createElement("span", null, "Any valid regexes allowed. Click for more info about regex matching") : "All valid IUPAC bases allowed as well as a couple special characters. Click for more info"
-    }))), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null)), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("a", {
+    panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file (", /*#__PURE__*/React.createElement("a", {
       onClick: function onClick() {
         var rows = [_extends({
           name: "Example " + startCase(annotationType) + " 1",
@@ -189,7 +175,17 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
         }, annotationType === "feature" && {
           type: "cds"
         }, {
-          isRegex: false
+          isRegex: false,
+          matchType: "dna"
+        }), _extends({
+          name: "Example Protein " + startCase(annotationType),
+          description: "I'm a description",
+          sequence: "APGSGTGGGSGSAPG"
+        }, annotationType === "feature" && {
+          type: "cds"
+        }, {
+          isRegex: false,
+          matchType: "protein"
         }), _extends({
           name: "Example " + startCase(annotationType) + " 2",
           description: "I'm another description",
@@ -197,7 +193,8 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
         }, annotationType === "feature" && {
           type: "cds"
         }, {
-          isRegex: true
+          isRegex: true,
+          matchType: "dna"
         })];
         var csv = unparse(rows); // const blob = new Blob([convert(sequenceData)], { type: "text/plain" });
         // const filename = `${sequenceData.name || "Untitled_Sequence"}.${fileExt}`;
@@ -205,7 +202,25 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
 
         downloadjs(csv, "Example CSV Annotation Upload File.csv", "text/plain");
       }
-    }, "download example")), /*#__PURE__*/React.createElement(FileUploadField, {
+    }, "download example"), ") with the following columns:", /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("div", {
+      style: {
+        display: "flex"
+      }
+    }, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
+      style: {
+        display: "flex"
+      }
+    }, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
+      onClick: function onClick(e) {
+        e.stopPropagation();
+        e.preventDefault();
+        showDialog({
+          ModalComponent: AutoAnnotateBpMatchingDialog
+        });
+      },
+      content: true ? /*#__PURE__*/React.createElement("span", null, "Any valid regexes allowed. Click for more info about regex matching") : "All valid IUPAC bases allowed as well as a couple special characters. Click for more info"
+    })), ",matchType"), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null))), /*#__PURE__*/React.createElement(FileUploadField, {
+      validateAgainstSchema: validateAgainstSchema,
       name: "csvFile",
       fileLimit: 1,
       isRequired: true,
@@ -234,10 +249,10 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
   }), getCustomAutoAnnotateList && (loadingCustomAnnList ? /*#__PURE__*/React.createElement(Tab, {
     disabled: true,
     title: "Loading..."
-  }) : customAnnResponse && /*#__PURE__*/React.createElement(Tab, {
+  }) : customAnnResponse && customAnnResponse.list && /*#__PURE__*/React.createElement(Tab, {
     id: "implementerDefined",
-    title: customAnnResponse && customAnnResponse.title || "Custom List",
-    panel: customAnnResponse && customAnnResponse.list && customAnnResponse.list.length ? /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement(DataTable, {
+    title: customAnnResponse.title || "Custom List",
+    panel: customAnnResponse.list.length ? /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement(DataTable, {
       isInfinite: true,
       schema: annotationType === "feature" ? customAnnsSchema : customAnnsSchemaNoType,
       entities: customAnnResponse.list
@@ -247,7 +262,7 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
     disabled: fileType === "implementerDefined" && !(customAnnResponse && customAnnResponse.list && customAnnResponse.list.length),
     onClick: handleSubmit( /*#__PURE__*/function () {
       var _ref3 = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime.mark(function _callee3(_ref2) {
-        var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
+        var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, matchType, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
 
         return _regeneratorRuntime.wrap(function _callee3$(_context3) {
           while (1) {
@@ -273,7 +288,7 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
                               break;
                             }
 
-                            cleanedType = FeatureTypes.find(function (t) {
+                            cleanedType = getFeatureTypes().find(function (t) {
                               return t.toLowerCase() === type.toLowerCase();
                             });
 
@@ -380,11 +395,12 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
                 }
 
                 _step$value = _step.value, // eslint-disable-next-line no-unused-vars
-                i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, type = _step$value$.type, isRegex = _step$value$.isRegex;
+                i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, matchType = _step$value$.matchType, type = _step$value$.type, isRegex = _step$value$.isRegex;
                 _context3.next = 11;
                 return validateRow({
                   name: name,
                   sequence: sequence,
+                  matchType: matchType,
                   type: type,
                   isRegex: isRegex ? "TRUE" : "FALSE"
                 }, "Row " + (i + 1) + " (" + name + ")");
@@ -514,6 +530,10 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
               case 57:
                 annotationsToCheckById = {};
                 annsToCheck.forEach(function (ann) {
+                  if (ann.matchType === "protein") {
+                    ann.sequence = convertProteinSeqToDNAIupac(ann.sequence);
+                  }
+
                   var id = shortid();
                   annotationsToCheckById[id] = _extends({}, ann, {
                     sequence: ann.isRegex ? ann.sequence : convertApELikeRegexToRegex(ann.sequence),
@@ -535,7 +555,7 @@ export var AutoAnnotateModal = compose(wrapDialog(function (p) {
                       id: shortid()
                     });
 
-                    toRet.color = toRet.color || featureColors[toRet.type];
+                    toRet.color = toRet.color || getFeatureToColorMap()[toRet.type];
                     return toRet;
                   }));
                 } else {
@@ -580,4 +600,31 @@ window._ove_addons.autoAnnotateFeatures = autoAnnotateFeatures;
 window._ove_addons.autoAnnotateParts = autoAnnotateParts;
 window._ove_addons.autoAnnotatePrimers = autoAnnotatePrimers;
 var customAnnsSchema = ["name", "sequence", typeField, "isRegex"];
-var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
+var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
+var validateAgainstSchema = {
+  fields: [{
+    path: "name",
+    type: "string",
+    isRequired: true
+  }, {
+    path: "description",
+    type: "string"
+  }, {
+    path: "sequence",
+    type: "string",
+    isRequired: true
+  }, {
+    path: "type",
+    type: "dropdown",
+    values: getFeatureTypes(),
+    defaultValue: "misc_feature"
+  }, {
+    path: "isRegex",
+    type: "boolean"
+  }, {
+    path: "matchType",
+    type: "dropdown",
+    defaultValue: "dna",
+    values: ["dna", "protein"]
+  }]
+};

package/lib/index.js

@@ -20,6 +20,8 @@ var _fileUtils = require("./fileUtils");
 
 var _downloadjs = _interopRequireDefault(require("downloadjs"));
 
+var _veSequenceUtils = require("ve-sequence-utils");
+
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
 
 function _createForOfIteratorHelperLoose(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (it) return (it = it.call(o)).next.bind(it); if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; return function () { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); }
@@ -43,8 +45,8 @@ var _window$addOnGlobals = window.addOnGlobals,
     pluralize = _window$addOnGlobals.pluralize,
     reduxForm = _window$addOnGlobals.reduxForm,
     SubmissionError = _window$addOnGlobals.SubmissionError,
-    featureColors = _window$addOnGlobals.featureColors,
-    FeatureTypes = _window$addOnGlobals.FeatureTypes,
+    getFeatureToColorMap = _window$addOnGlobals.getFeatureToColorMap,
+    getFeatureTypes = _window$addOnGlobals.getFeatureTypes,
     InfoHelper = _window$addOnGlobals.InfoHelper,
     showConfirmationDialog = _window$addOnGlobals.showConfirmationDialog,
     wrapDialog = _window$addOnGlobals.wrapDialog,
@@ -94,6 +96,7 @@ function autoAnnotatePrimers() {
 
 var AutoAnnotateModal = compose(wrapDialog(function (p) {
   return {
+    canEscapeKeyClose: false,
     title: "Auto Annotate " + startCase(pluralize(p.annotationType))
   };
 }), withEditorProps, reduxForm({
@@ -162,8 +165,9 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
           }
         }
       }, _callee, null, [[2, 9, 13, 16]]);
-    }))();
-  }, [getCustomAutoAnnotateList, props]);
+    }))(); // eslint-disable-next-line react-hooks/exhaustive-deps
+
+  }, []);
 
   if (newAnnotations) {
     return /*#__PURE__*/React.createElement(_CreateAnnotationsPage["default"], _extends({}, props, {
@@ -178,24 +182,7 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
     onChange: setSelectedImportType,
     selectedTabId: fileType
   }, /*#__PURE__*/React.createElement(Tab, {
-    panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file with the following columns -", /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("div", {
-      style: {
-        display: "flex"
-      }
-    }, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
-      style: {
-        display: "flex"
-      }
-    }, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
-      onClick: function onClick(e) {
-        e.stopPropagation();
-        e.preventDefault();
-        showDialog({
-          ModalComponent: _AutoAnnotateBpMatchingDialog.AutoAnnotateBpMatchingDialog
-        });
-      },
-      content: true ? /*#__PURE__*/React.createElement("span", null, "Any valid regexes allowed. Click for more info about regex matching") : "All valid IUPAC bases allowed as well as a couple special characters. Click for more info"
-    }))), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null)), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("a", {
+    panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file (", /*#__PURE__*/React.createElement("a", {
       onClick: function onClick() {
         var rows = [_extends({
           name: "Example " + startCase(annotationType) + " 1",
@@ -204,7 +191,17 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
         }, annotationType === "feature" && {
           type: "cds"
         }, {
-          isRegex: false
+          isRegex: false,
+          matchType: "dna"
+        }), _extends({
+          name: "Example Protein " + startCase(annotationType),
+          description: "I'm a description",
+          sequence: "APGSGTGGGSGSAPG"
+        }, annotationType === "feature" && {
+          type: "cds"
+        }, {
+          isRegex: false,
+          matchType: "protein"
         }), _extends({
           name: "Example " + startCase(annotationType) + " 2",
           description: "I'm another description",
@@ -212,7 +209,8 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
         }, annotationType === "feature" && {
           type: "cds"
         }, {
-          isRegex: true
+          isRegex: true,
+          matchType: "dna"
         })];
         var csv = (0, _papaparse.unparse)(rows); // const blob = new Blob([convert(sequenceData)], { type: "text/plain" });
         // const filename = `${sequenceData.name || "Untitled_Sequence"}.${fileExt}`;
@@ -220,7 +218,25 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
 
         (0, _downloadjs["default"])(csv, "Example CSV Annotation Upload File.csv", "text/plain");
       }
-    }, "download example")), /*#__PURE__*/React.createElement(FileUploadField, {
+    }, "download example"), ") with the following columns:", /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("div", {
+      style: {
+        display: "flex"
+      }
+    }, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
+      style: {
+        display: "flex"
+      }
+    }, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
+      onClick: function onClick(e) {
+        e.stopPropagation();
+        e.preventDefault();
+        showDialog({
+          ModalComponent: _AutoAnnotateBpMatchingDialog.AutoAnnotateBpMatchingDialog
+        });
+      },
+      content: true ? /*#__PURE__*/React.createElement("span", null, "Any valid regexes allowed. Click for more info about regex matching") : "All valid IUPAC bases allowed as well as a couple special characters. Click for more info"
+    })), ",matchType"), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null))), /*#__PURE__*/React.createElement(FileUploadField, {
+      validateAgainstSchema: validateAgainstSchema,
       name: "csvFile",
       fileLimit: 1,
       isRequired: true,
@@ -249,10 +265,10 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
   }), getCustomAutoAnnotateList && (loadingCustomAnnList ? /*#__PURE__*/React.createElement(Tab, {
     disabled: true,
     title: "Loading..."
-  }) : customAnnResponse && /*#__PURE__*/React.createElement(Tab, {
+  }) : customAnnResponse && customAnnResponse.list && /*#__PURE__*/React.createElement(Tab, {
     id: "implementerDefined",
-    title: customAnnResponse && customAnnResponse.title || "Custom List",
-    panel: customAnnResponse && customAnnResponse.list && customAnnResponse.list.length ? /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement(DataTable, {
+    title: customAnnResponse.title || "Custom List",
+    panel: customAnnResponse.list.length ? /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement(DataTable, {
       isInfinite: true,
       schema: annotationType === "feature" ? customAnnsSchema : customAnnsSchemaNoType,
       entities: customAnnResponse.list
@@ -262,7 +278,7 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
     disabled: fileType === "implementerDefined" && !(customAnnResponse && customAnnResponse.list && customAnnResponse.list.length),
     onClick: handleSubmit( /*#__PURE__*/function () {
       var _ref3 = _asyncToGenerator( /*#__PURE__*/_regenerator["default"].mark(function _callee3(_ref2) {
-        var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
+        var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, matchType, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
 
         return _regenerator["default"].wrap(function _callee3$(_context3) {
           while (1) {
@@ -288,7 +304,7 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
                               break;
                             }
 
-                            cleanedType = FeatureTypes.find(function (t) {
+                            cleanedType = getFeatureTypes().find(function (t) {
                               return t.toLowerCase() === type.toLowerCase();
                             });
 
@@ -395,11 +411,12 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
                 }
 
                 _step$value = _step.value, // eslint-disable-next-line no-unused-vars
-                i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, type = _step$value$.type, isRegex = _step$value$.isRegex;
+                i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, matchType = _step$value$.matchType, type = _step$value$.type, isRegex = _step$value$.isRegex;
                 _context3.next = 11;
                 return validateRow({
                   name: name,
                   sequence: sequence,
+                  matchType: matchType,
                   type: type,
                   isRegex: isRegex ? "TRUE" : "FALSE"
                 }, "Row " + (i + 1) + " (" + name + ")");
@@ -529,6 +546,10 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
               case 57:
                 annotationsToCheckById = {};
                 annsToCheck.forEach(function (ann) {
+                  if (ann.matchType === "protein") {
+                    ann.sequence = (0, _veSequenceUtils.convertProteinSeqToDNAIupac)(ann.sequence);
+                  }
+
                   var id = shortid();
                   annotationsToCheckById[id] = _extends({}, ann, {
                     sequence: ann.isRegex ? ann.sequence : convertApELikeRegexToRegex(ann.sequence),
@@ -550,7 +571,7 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
                       id: shortid()
                     });
 
-                    toRet.color = toRet.color || featureColors[toRet.type];
+                    toRet.color = toRet.color || getFeatureToColorMap()[toRet.type];
                     return toRet;
                   }));
                 } else {
@@ -596,4 +617,31 @@ window._ove_addons.autoAnnotateFeatures = autoAnnotateFeatures;
 window._ove_addons.autoAnnotateParts = autoAnnotateParts;
 window._ove_addons.autoAnnotatePrimers = autoAnnotatePrimers;
 var customAnnsSchema = ["name", "sequence", typeField, "isRegex"];
-var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
+var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
+var validateAgainstSchema = {
+  fields: [{
+    path: "name",
+    type: "string",
+    isRequired: true
+  }, {
+    path: "description",
+    type: "string"
+  }, {
+    path: "sequence",
+    type: "string",
+    isRequired: true
+  }, {
+    path: "type",
+    type: "dropdown",
+    values: getFeatureTypes(),
+    defaultValue: "misc_feature"
+  }, {
+    path: "isRegex",
+    type: "boolean"
+  }, {
+    path: "matchType",
+    type: "dropdown",
+    defaultValue: "dna",
+    values: ["dna", "protein"]
+  }]
+};

package/package.json

@@ -1,12 +1,11 @@
 {
   "name": "ove-auto-annotate",
-  "version": "0.0.4",
+  "version": "0.0.8",
   "scripts": {
     "build": "nwb build-react-component --copy-files --no-demo",
-    "prepublish": "npm run build"
+    "prepublishOnly": "npm run build"
   },
   "dependencies": {
-    "downloadjs": "^1.4.7",
     "papaparse": "^5.3.1"
   },
   "devDependencies": {