@teselagen/ove 0.8.19 → 0.8.21

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.19",
+  "version": "0.8.21",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -18,8 +18,8 @@
     "@teselagen/file-utils": "0.3.20",
     "@teselagen/range-utils": "0.3.13",
     "@teselagen/react-list": "0.8.18",
-    "@teselagen/sequence-utils": "0.3.35",
-    "@teselagen/ui": "0.10.9",
+    "@teselagen/sequence-utils": "0.3.36",
+    "@teselagen/ui": "0.10.10",
     "@use-gesture/react": "10.3.0",
     "biomsa": "^0.2.4",
     "classnames": "^2.3.2",

package/redux/temporaryAnnotations.d.ts

@@ -0,0 +1,6 @@
+export const updateTemporaryAnnotations: import('redux-act').ComplexActionCreator1<any, any, any>;
+declare const _default: {
+    (newState: {} | undefined, action: any): any;
+    __shouldUseMergedState: boolean;
+};
+export default _default;

package/selectors/featuresSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any) => any, {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/partsSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any) => any, {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/primersSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any) => any, {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/temporaryAnnotationsSelector.d.ts

@@ -0,0 +1,2 @@
+declare function _default(editor: any): any;
+export default _default;

package/src/StatusBar/MeltingTemp.js

@@ -1,7 +1,11 @@
 import React from "react";
 import { Button, Icon, Popover, RadioGroup } from "@blueprintjs/core";
 
-import { calculateTm, calculateNebTm } from "@teselagen/sequence-utils";
+import {
+  calculateTm,
+  calculateNebTm,
+  calculateSantaLuciaTm
+} from "@teselagen/sequence-utils";
 
 import { isNumber, isString } from "lodash-es";
 import { popoverOverflowModifiers } from "@teselagen/ui";
@@ -20,7 +24,13 @@ export default function MeltingTemp({
   const [monovalentCationConc /* , setMonovalentCationConc */] =
     React.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence, {
+  let tm = (
+    tmType === "neb_tm"
+      ? calculateNebTm
+      : tmType === "default"
+        ? calculateSantaLuciaTm
+        : calculateTm
+  )(sequence, {
     monovalentCationConc,
     primerConc
   });
@@ -47,8 +57,9 @@ export default function MeltingTemp({
             <RadioGroup
               label="Choose Tm Type:"
               options={[
-                { value: "default", label: "Default Tm (Breslauer)" },
-                { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+                { value: "default", label: "Santa Lucia (Default)" },
+                { value: "breslauer", label: "Breslauer" },
+                { value: "neb_tm", label: "NEB Tm" }
               ]}
               onChange={e => setTmType(e.target.value)}
               selectedValue={tmType}
@@ -70,7 +81,7 @@ export default function MeltingTemp({
         }
       >
         <React.Fragment>
-          <InnerWrapper>Melting Temp: {Number(tm) || 0} </InnerWrapper>
+          <InnerWrapper>Melting Temp: {Number(tm) || 0}°C</InnerWrapper>
           {hasWarning && (
             <Icon
               style={{ marginLeft: 5, marginRight: 5 }}

package/src/helperComponents/AddOrEditPrimerDialog/index.js

@@ -8,7 +8,9 @@ import {
 } from "@teselagen/ui";
 import {
   filterSequenceString,
-  getReverseComplementSequenceString
+  getReverseComplementSequenceString,
+  calculatePercentGC,
+  calculateEndStability
 } from "@teselagen/sequence-utils";
 
 import AddOrEditAnnotationDialog from "../AddOrEditAnnotationDialog";
@@ -294,15 +296,34 @@ const RenderBases = props => {
           </AdvancedOptions>
 
           <MeltingTemp
-            InnerWrapper={InnerWrapperMeltingTemp}
+            InnerWrapper={TextInnerWrapper}
             sequence={bases}
           ></MeltingTemp>
+          <TextInnerWrapper>
+            GC content: {bases && calculatePercentGC(bases).toFixed(1)}%
+          </TextInnerWrapper>
+          <TextInnerWrapper>
+            3' Stability: {bases && calculateEndStability(bases)} kcal/mol
+          </TextInnerWrapper>
         </div>
       )}
     </div>
   );
 };
 
+const TextInnerWrapper = p => (
+  <div
+    className="bp3-text-muted bp3-text-small"
+    style={{
+      marginBottom: 15,
+      marginTop: -5,
+      fontStyle: "italic"
+    }}
+  >
+    {p.children}
+  </div>
+);
+
 export default AddOrEditAnnotationDialog({
   formName: "AddOrEditPrimerDialog",
   getProps: props => ({
@@ -311,12 +332,3 @@ export default AddOrEditAnnotationDialog({
     RenderBases
   })
 });
-
-const InnerWrapperMeltingTemp = p => (
-  <div
-    className="bp3-text-muted bp3-text-small"
-    style={{ marginBottom: 15, marginTop: -5, fontStyle: "italic" }}
-  >
-    {p.children}
-  </div>
-);

package/src/redux/index.js

@@ -34,6 +34,7 @@ import * as featureLengthsToHide from "./featureLengthsToHide";
 import * as primerLengthsToHide from "./primerLengthsToHide";
 import * as partLengthsToHide from "./partLengthsToHide";
 import * as selectedPartTags from "./selectedPartTags";
+import * as temporaryAnnotations from "./temporaryAnnotations";
 import { combineReducers } from "redux";
 import createAction from "./utils/createMetaAction";
 export { default as vectorEditorMiddleware } from "./middleware";
@@ -72,7 +73,8 @@ const subReducers = {
   partLengthsToHide,
   primerLengthsToHide,
   featureLengthsToHide,
-  selectedPartTags
+  selectedPartTags,
+  temporaryAnnotations
 };
 
 const vectorEditorInitialize = createAction("VECTOR_EDITOR_UPDATE");

package/src/redux/temporaryAnnotations.js

@@ -0,0 +1,23 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+export const updateTemporaryAnnotations = createAction(
+  "TEMPORARY_ANNOTATIONS_UPDATE"
+);
+
+export default createMergedDefaultStateReducer(
+  {
+    TEMPORARY_ANNOTATIONS_UPDATE: (state, payload) => {
+      return { ...state, ...payload };
+    },
+    VECTOR_EDITOR_UPDATE: (state, payload) => {
+      return { ...state, ...payload.temporaryAnnotations };
+    }
+  },
+  {
+    features: {},
+    primers: {},
+    parts: {},
+    selectionLayer: {}
+  }
+);

package/src/selectors/featuresSelector.js

@@ -1,8 +1,13 @@
 import { createSelector } from "reselect";
 import sequenceDataSelector from "./sequenceDataSelector";
+import temporaryAnnotationsSelector from "./temporaryAnnotationsSelector";
 
-function featuresRawSelector(sequenceData) {
-  return sequenceData.features;
+function featuresRawSelector(sequenceData, temporaryAnnotations) {
+  return { ...sequenceData.features, ...temporaryAnnotations?.features };
 }
 
-export default createSelector(sequenceDataSelector, featuresRawSelector);
+export default createSelector(
+  sequenceDataSelector,
+  temporaryAnnotationsSelector,
+  featuresRawSelector
+);

package/src/selectors/partsSelector.js

@@ -1,8 +1,14 @@
 import { createSelector } from "reselect";
 import sequenceDataSelector from "./sequenceDataSelector";
 
-function partsRawSelector(sequenceData) {
-  return sequenceData.parts;
+import temporaryAnnotationsSelector from "./temporaryAnnotationsSelector";
+
+function partsRawSelector(sequenceData, temporaryAnnotations) {
+  return { ...sequenceData.parts, ...temporaryAnnotations?.parts };
 }
 
-export default createSelector(sequenceDataSelector, partsRawSelector);
+export default createSelector(
+  sequenceDataSelector,
+  temporaryAnnotationsSelector,
+  partsRawSelector
+);

package/src/selectors/primersSelector.js

@@ -1,8 +1,14 @@
 import { createSelector } from "reselect";
 import sequenceDataSelector from "./sequenceDataSelector";
 
-function primersRawSelector(sequenceData) {
-  return sequenceData.primers;
+import temporaryAnnotationsSelector from "./temporaryAnnotationsSelector";
+
+function primersRawSelector(sequenceData, temporaryAnnotations) {
+  return { ...sequenceData.primers, ...temporaryAnnotations?.primers };
 }
 
-export default createSelector(sequenceDataSelector, primersRawSelector);
+export default createSelector(
+  sequenceDataSelector,
+  temporaryAnnotationsSelector,
+  primersRawSelector
+);

package/src/selectors/temporaryAnnotationsSelector.js

@@ -0,0 +1 @@
+export default editor => editor.temporaryAnnotations;

package/src/updateEditor.js

@@ -14,7 +14,8 @@ export default function updateEditor(
     annotationVisibility,
     annotationsToSupport,
     findTool,
-    justPassingPartialSeqData
+    justPassingPartialSeqData,
+    temporaryAnnotations
   } = initialValues;
   const currentEditor = store.getState().VectorEditor[editorName] || {};
   const isAlreadyProteinEditor =
@@ -174,6 +175,9 @@ export default function updateEditor(
           //if we have sequence data coming in make sure to tidy it up for the user :)
           annotationsAsObjects: true
         })
+      }),
+      ...(temporaryAnnotations && {
+        temporaryAnnotations
       })
     };
   }