@teselagen/ove 0.5.20 → 0.5.22

package/index.cjs.js

@@ -72086,7 +72086,6 @@ const _ResizableDraggableDialog = class _ResizableDraggableDialog extends React$
 __name(_ResizableDraggableDialog, "ResizableDraggableDialog");
 let ResizableDraggableDialog = _ResizableDraggableDialog;
 function MenuItemLink({ text: text2, onClick, icon, navTo, active: active3, disabled }) {
-  console.log(`navTo:`, navTo);
   if (disabled) {
     return /* @__PURE__ */ React$2.createElement("li", { className: core.Classes.POPOVER_DISMISS }, /* @__PURE__ */ React$2.createElement(core.MenuItem, { icon, disabled: true, text: text2 }));
   }
@@ -72138,7 +72137,6 @@ const EnhancedMenuItem = compose(
   if (navTo) {
     MenuItemComp = MenuItemLink;
   }
-  console.log(`navTo:`, navTo);
   return /* @__PURE__ */ React$2.createElement(
     MenuItemComp,
     __spreadProps(__spreadValues(__spreadValues({
@@ -105755,11 +105753,11 @@ function getSelFromWrappedAddon(selectionLayer2, sequenceLength) {
   return selToUse;
 }
 __name(getSelFromWrappedAddon, "getSelFromWrappedAddon");
-function getStripedPattern({ color: color2 }) {
+function getStripedPattern({ color: color2, id: id2 }) {
   return /* @__PURE__ */ React$2.createElement(
     "pattern",
     {
-      id: "diagonalHatch",
+      id: `diagonalHatch-${id2}`,
       patternUnits: "userSpaceOnUse",
       width: "4",
       height: "4"
@@ -119232,7 +119230,7 @@ function PointedAnnotation(props) {
         strokeWidth: "1",
         stroke: stroke || "black",
         opacity,
-        fill: isStriped ? "url(#diagonalHatch)" : fill || color2,
+        fill: isStriped ? `url(#diagonalHatch-${id2})` : fill || color2,
         transform: forward ? null : "translate(" + width + `,${flipAnnotation ? -extraHeight + 10 : 0}) scale(-1,${flipAnnotation ? "-" : ""}1) `,
         d: path2
       }
@@ -122383,7 +122381,7 @@ function oveCommandFactory(instance, commandDefs2) {
       return args;
     },
     handleReturn: noop$6,
-    commandDefs: commandDefs2
+    commandDefs: instance.props.massageCmds ? instance.props.massageCmds(commandDefs2) : commandDefs2
   });
 }
 __name(oveCommandFactory, "oveCommandFactory");
@@ -122411,7 +122409,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.5.19";
+const version = "0.5.21";
 const main = "./src/index.js";
 const type = "module";
 const exports$1 = {
@@ -133088,14 +133086,14 @@ function CircularPrimer(props) {
     hasLabel: ellipsizedName,
     labelNeedsFlip
   });
-  return /* @__PURE__ */ React$2.createElement(React$2.Fragment, null, getStripedPattern({ color: color2 }), /* @__PURE__ */ React$2.createElement(
+  return /* @__PURE__ */ React$2.createElement(React$2.Fragment, null, getStripedPattern({ color: color2, id: id2 }), /* @__PURE__ */ React$2.createElement(
     "path",
     {
       className: "vePrimer veCircularViewPrimer",
       id: id2,
       strokeWidth: ".5",
       stroke: "black",
-      fill: "url(#diagonalHatch)",
+      fill: `url(#diagonalHatch-${id2})`,
       d: path2.print()
     }
   ), getInternalLabel(__spreadProps(__spreadValues({}, props), { colorToUse: color2, textPath })));
@@ -143196,6 +143194,7 @@ const userDefinedHandlersAndOpts = [
   "disableSetReadOnly",
   "allowAnnotationEditLocking",
   "disableBpEditing",
+  "massageCmds",
   "showReadOnly",
   "showCircularity",
   "onHiddenEnzymeAdd",
@@ -148976,6 +148975,7 @@ exports.connectToEditor = connectToEditor;
 exports.createVectorEditor = createVectorEditor;
 exports.getOveHotkeyDefs = getOveHotkeyDefs;
 exports.getRangeAnglesSpecial = getRangeAnglesSpecial;
+exports.getStructuredBases = getStructuredBases;
 exports.getUserGroupLabel = getUserGroupLabel;
 exports.specialCutsiteFilterOptions = specialCutsiteFilterOptions;
 exports.updateEditor = updateEditor;

package/index.d.ts

@@ -16,6 +16,7 @@ export { default as PositionAnnotationOnCircle } from './CircularView/PositionAn
 export { default as EnzymeViewer } from './EnzymeViewer';
 export { default as AlignmentView } from './AlignmentView';
 export { default as getOveHotkeyDefs } from './commands/getOveHotkeyDefs';
+export { getStructuredBases } from './RowItem/StackedAnnotations/getStructuredBases';
 export { default as withEditorProps, connectToEditor } from './withEditorProps';
 export { default as Editor, Editor as EditorUnconnected } from './Editor';
 export { default as CutsiteFilter, CutsiteFilter as CutsiteFilterUnconnected } from './CutsiteFilter';

package/index.es.js

@@ -72068,7 +72068,6 @@ const _ResizableDraggableDialog = class _ResizableDraggableDialog extends React_
 __name(_ResizableDraggableDialog, "ResizableDraggableDialog");
 let ResizableDraggableDialog = _ResizableDraggableDialog;
 function MenuItemLink({ text: text2, onClick, icon, navTo, active: active3, disabled }) {
-  console.log(`navTo:`, navTo);
   if (disabled) {
     return /* @__PURE__ */ React__default$1.createElement("li", { className: Classes.POPOVER_DISMISS }, /* @__PURE__ */ React__default$1.createElement(MenuItem, { icon, disabled: true, text: text2 }));
   }
@@ -72120,7 +72119,6 @@ const EnhancedMenuItem = compose(
   if (navTo) {
     MenuItemComp = MenuItemLink;
   }
-  console.log(`navTo:`, navTo);
   return /* @__PURE__ */ React__default$1.createElement(
     MenuItemComp,
     __spreadProps(__spreadValues(__spreadValues({
@@ -105737,11 +105735,11 @@ function getSelFromWrappedAddon(selectionLayer2, sequenceLength) {
   return selToUse;
 }
 __name(getSelFromWrappedAddon, "getSelFromWrappedAddon");
-function getStripedPattern({ color: color2 }) {
+function getStripedPattern({ color: color2, id: id2 }) {
   return /* @__PURE__ */ React__default$1.createElement(
     "pattern",
     {
-      id: "diagonalHatch",
+      id: `diagonalHatch-${id2}`,
       patternUnits: "userSpaceOnUse",
       width: "4",
       height: "4"
@@ -119214,7 +119212,7 @@ function PointedAnnotation(props) {
         strokeWidth: "1",
         stroke: stroke || "black",
         opacity,
-        fill: isStriped ? "url(#diagonalHatch)" : fill || color2,
+        fill: isStriped ? `url(#diagonalHatch-${id2})` : fill || color2,
         transform: forward ? null : "translate(" + width + `,${flipAnnotation ? -extraHeight + 10 : 0}) scale(-1,${flipAnnotation ? "-" : ""}1) `,
         d: path2
       }
@@ -122365,7 +122363,7 @@ function oveCommandFactory(instance, commandDefs2) {
       return args;
     },
     handleReturn: noop$6,
-    commandDefs: commandDefs2
+    commandDefs: instance.props.massageCmds ? instance.props.massageCmds(commandDefs2) : commandDefs2
   });
 }
 __name(oveCommandFactory, "oveCommandFactory");
@@ -122393,7 +122391,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.5.19";
+const version = "0.5.21";
 const main = "./src/index.js";
 const type = "module";
 const exports$1 = {
@@ -133070,14 +133068,14 @@ function CircularPrimer(props) {
     hasLabel: ellipsizedName,
     labelNeedsFlip
   });
-  return /* @__PURE__ */ React__default$1.createElement(React__default$1.Fragment, null, getStripedPattern({ color: color2 }), /* @__PURE__ */ React__default$1.createElement(
+  return /* @__PURE__ */ React__default$1.createElement(React__default$1.Fragment, null, getStripedPattern({ color: color2, id: id2 }), /* @__PURE__ */ React__default$1.createElement(
     "path",
     {
       className: "vePrimer veCircularViewPrimer",
       id: id2,
       strokeWidth: ".5",
       stroke: "black",
-      fill: "url(#diagonalHatch)",
+      fill: `url(#diagonalHatch-${id2})`,
       d: path2.print()
     }
   ), getInternalLabel(__spreadProps(__spreadValues({}, props), { colorToUse: color2, textPath })));
@@ -143178,6 +143176,7 @@ const userDefinedHandlersAndOpts = [
   "disableSetReadOnly",
   "allowAnnotationEditLocking",
   "disableBpEditing",
+  "massageCmds",
   "showReadOnly",
   "showCircularity",
   "onHiddenEnzymeAdd",
@@ -148960,6 +148959,7 @@ export {
   getGaps,
   getOveHotkeyDefs,
   getRangeAnglesSpecial,
+  getStructuredBases,
   getUserGroupLabel,
   specialCutsiteFilterOptions,
   updateEditor,

package/index.umd.js

@@ -101256,7 +101256,6 @@ ${latestSubscriptionCallbackError.current.stack}
   __name(_ResizableDraggableDialog, "ResizableDraggableDialog");
   let ResizableDraggableDialog = _ResizableDraggableDialog;
   function MenuItemLink({ text: text2, onClick, icon, navTo, active: active2, disabled }) {
-    console.log(`navTo:`, navTo);
     if (disabled) {
       return /* @__PURE__ */ React$2.createElement("li", { className: POPOVER_DISMISS }, /* @__PURE__ */ React$2.createElement(MenuItem, { icon, disabled: true, text: text2 }));
     }
@@ -101308,7 +101307,6 @@ ${latestSubscriptionCallbackError.current.stack}
     if (navTo) {
       MenuItemComp = MenuItemLink;
     }
-    console.log(`navTo:`, navTo);
     return /* @__PURE__ */ React$2.createElement(
       MenuItemComp,
       __spreadProps(__spreadValues(__spreadValues({
@@ -134256,11 +134254,11 @@ ${seq.sequence}
     return selToUse;
   }
   __name(getSelFromWrappedAddon, "getSelFromWrappedAddon");
-  function getStripedPattern({ color: color2 }) {
+  function getStripedPattern({ color: color2, id: id2 }) {
     return /* @__PURE__ */ React$2.createElement(
       "pattern",
       {
-        id: "diagonalHatch",
+        id: `diagonalHatch-${id2}`,
         patternUnits: "userSpaceOnUse",
         width: "4",
         height: "4"
@@ -147733,7 +147731,7 @@ double click --> edit`}`;
           strokeWidth: "1",
           stroke: stroke || "black",
           opacity: opacity2,
-          fill: isStriped ? "url(#diagonalHatch)" : fill || color2,
+          fill: isStriped ? `url(#diagonalHatch-${id2})` : fill || color2,
           transform: forward ? null : "translate(" + width + `,${flipAnnotation ? -extraHeight + 10 : 0}) scale(-1,${flipAnnotation ? "-" : ""}1) `,
           d: path2
         }
@@ -150850,7 +150848,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         return args;
       },
       handleReturn: noop$6,
-      commandDefs: commandDefs2
+      commandDefs: instance.props.massageCmds ? instance.props.massageCmds(commandDefs2) : commandDefs2
     });
   }
   __name(oveCommandFactory, "oveCommandFactory");
@@ -150878,7 +150876,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __name(showFileDialog, "showFileDialog");
   const name = "@teselagen/ove";
-  const version = "0.5.19";
+  const version = "0.5.21";
   const main = "./src/index.js";
   const type = "module";
   const exports$1 = {
@@ -159950,14 +159948,14 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       hasLabel: ellipsizedName,
       labelNeedsFlip
     });
-    return /* @__PURE__ */ React$2.createElement(React$2.Fragment, null, getStripedPattern({ color: color2 }), /* @__PURE__ */ React$2.createElement(
+    return /* @__PURE__ */ React$2.createElement(React$2.Fragment, null, getStripedPattern({ color: color2, id: id2 }), /* @__PURE__ */ React$2.createElement(
       "path",
       {
         className: "vePrimer veCircularViewPrimer",
         id: id2,
         strokeWidth: ".5",
         stroke: "black",
-        fill: "url(#diagonalHatch)",
+        fill: `url(#diagonalHatch-${id2})`,
         d: path2.print()
       }
     ), getInternalLabel(__spreadProps(__spreadValues({}, props), { colorToUse: color2, textPath })));
@@ -169546,6 +169544,7 @@ ${seqDataToCopy}\r
     "disableSetReadOnly",
     "allowAnnotationEditLocking",
     "disableBpEditing",
+    "massageCmds",
     "showReadOnly",
     "showCircularity",
     "onHiddenEnzymeAdd",
@@ -183216,6 +183215,7 @@ ${seqDataToCopy}\r
   exports2.createVectorEditor = createVectorEditor;
   exports2.getOveHotkeyDefs = getOveHotkeyDefs;
   exports2.getRangeAnglesSpecial = getRangeAnglesSpecial;
+  exports2.getStructuredBases = getStructuredBases;
   exports2.getUserGroupLabel = getUserGroupLabel;
   exports2.specialCutsiteFilterOptions = specialCutsiteFilterOptions;
   exports2.updateEditor = updateEditor;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.5.20",
+  "version": "0.5.22",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -12,7 +12,7 @@
   "dependencies": {
     "@teselagen/sequence-utils": "0.3.25",
     "@teselagen/range-utils": "0.3.7",
-    "@teselagen/ui": "0.4.17",
+    "@teselagen/ui": "0.4.18",
     "@teselagen/file-utils": "0.3.16",
     "@teselagen/bounce-loader": "0.3.11",
     "@teselagen/bio-parsers": "0.4.19",

package/src/CircularView/Primer.js

@@ -26,13 +26,13 @@ export default function CircularPrimer(props) {
   });
   return (
     <React.Fragment>
-      {getStripedPattern({ color })}
+      {getStripedPattern({ color, id })}
       <path
         className="vePrimer veCircularViewPrimer"
         id={id}
         strokeWidth=".5"
         stroke="black"
-        fill="url(#diagonalHatch)"
+        fill={`url(#diagonalHatch-${id})`}
         d={path.print()}
       />
       {getInternalLabel({ ...props, colorToUse: color, textPath })}

package/src/Editor/userDefinedHandlersAndOpts.js

@@ -22,6 +22,7 @@ export const userDefinedHandlersAndOpts = [
   "disableSetReadOnly",
   "allowAnnotationEditLocking",
   "disableBpEditing",
+  "massageCmds",
   "showReadOnly",
   "showCircularity",
   "onHiddenEnzymeAdd",

package/src/RowItem/StackedAnnotations/PointedAnnotation.js

@@ -239,7 +239,7 @@ function PointedAnnotation(props) {
         strokeWidth="1"
         stroke={stroke || "black"}
         opacity={opacity}
-        fill={isStriped ? "url(#diagonalHatch)" : fill || color}
+        fill={isStriped ? `url(#diagonalHatch-${id})` : fill || color}
         transform={
           forward
             ? null

package/src/StatusBar/MeltingTemp.js

@@ -16,8 +16,9 @@ export default function MeltingTemp({
     </Button>
   )
 }) {
-  const [primerConc/* , setPrimerConcentration */] = React.useState(0.0000005);
-  const [monovalentCationConc/* , setMonovalentCationConc */] = React.useState(0.05);
+  const [primerConc /* , setPrimerConcentration */] = React.useState(0.0000005);
+  const [monovalentCationConc /* , setMonovalentCationConc */] =
+    React.useState(0.05);
   const [tmType, setTmType] = useTmType();
   let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence, {
     monovalentCationConc,

package/src/index.js

@@ -51,3 +51,4 @@ export { default as PositionAnnotationOnCircle } from "./CircularView/PositionAn
 export { default as EnzymeViewer } from "./EnzymeViewer";
 export { default as AlignmentView } from "./AlignmentView";
 export { default as getOveHotkeyDefs } from "./commands/getOveHotkeyDefs";
+export { getStructuredBases } from "./RowItem/StackedAnnotations/getStructuredBases";

package/src/utils/commandUtils.js

@@ -13,6 +13,8 @@ export function oveCommandFactory(instance, commandDefs) {
       return args;
     },
     handleReturn: noop,
-    commandDefs
+    commandDefs: instance.props.massageCmds
+      ? instance.props.massageCmds(commandDefs)
+      : commandDefs
   });
 }

package/src/utils/editorUtils.js

@@ -171,10 +171,10 @@ export function getSelFromWrappedAddon(selectionLayer, sequenceLength) {
   return selToUse;
 }
 
-export function getStripedPattern({ color }) {
+export function getStripedPattern({ color, id }) {
   return (
     <pattern
-      id="diagonalHatch"
+      id={`diagonalHatch-${id}`}
       patternUnits="userSpaceOnUse"
       width="4"
       height="4"

package/style.css

@@ -9042,6 +9042,9 @@ button:not(:disabled):active {
 .bp3-tabs.bp3-vertical > .bp3-tab-panel {
   min-width: 0px;
 }
+.bp3-toast[class*="bp3-intent-"] .bp3-button.tg-clear-all-toasts {
+  border: 1px solid white !important;
+}
 .bp3-toast[class*="bp3-intent-"] .bp3-button.tg-clear-all-toasts:hover {
   /* background: blue !important; */
   /* background: unset !important; */

package/utils/editorUtils.d.ts

@@ -30,7 +30,8 @@ export function getClientX(event: any): any;
 export function getClientY(event: any): any;
 export function hideAnnByLengthFilter(hideOpts: any, ann: any, seqLen: any): any;
 export function getSelFromWrappedAddon(selectionLayer: any, sequenceLength: any): any;
-export function getStripedPattern({ color }: {
+export function getStripedPattern({ color, id }: {
     color: any;
+    id: any;
 }): import("react/jsx-runtime").JSX.Element;
 export function getEnzymeAliases(enzyme: any): any[];