changing annotation flag doesOverlapSelf -> overlapsSelf for consistency

cypress/integration/partTypes.spec.js

@@ -4,16 +4,16 @@ describe("partTypes", function () {
   });
   it(`parts that overlap with themselves should be supported`, () => {
     cy.tgToggle("allowPartsToOverlapSelf");
-    cy.get(".veRowViewPart.doesOverlapSelf").should("not.exist");
-    cy.get(".veCircularViewPart.doesOverlapSelf").should("not.exist");
+    cy.get(".veRowViewPart.overlapsSelf").should("not.exist");
+    cy.get(".veCircularViewPart.overlapsSelf").should("not.exist");
     cy.contains(".veLabelText", "Part 0").trigger("contextmenu");
     cy.contains(".bp3-menu-item", "Edit Part").click();
     cy.contains(".bp3-dialog div", "Advanced").click();
     cy.contains(".bp3-dialog div", "Overlaps Self").click();
     cy.contains(".bp3-dialog button", "Save").click();
 
-    cy.get(".veRowViewPart.doesOverlapSelf").should("exist");
-    cy.get(".veCircularViewPart.doesOverlapSelf").should("exist");
+    cy.get(".veRowViewPart.overlapsSelf").should("exist");
+    cy.get(".veCircularViewPart.overlapsSelf").should("exist");
     cy.contains(".veLabelText", "Part 0").trigger("contextmenu");
     cy.contains(".bp3-menu-item", "Edit Part").click();
     //this should already be open!
@@ -46,10 +46,10 @@ describe("partTypes", function () {
     cy.get(".tg-select").click();
     cy.contains(".tg-select-option", "misc_RNA").click();
     cy.get(".bp3-dialog-body").contains("Save").click();
-    cy.contains(
-      ".veRowViewFeaturesContainer text",
-      "test feature"
-    ).trigger("contextmenu", { force: true });
+    cy.contains(".veRowViewFeaturesContainer text", "test feature").trigger(
+      "contextmenu",
+      { force: true }
+    );
     cy.contains(".bp3-menu-item", "Make a Part from Feature").click();
     cy.get(".bp3-menu").should("not.exist");
     cy.contains(".veRowViewPart title", "test feature").trigger("contextmenu", {

demo/src/EditorDemo/index.js

@@ -1105,7 +1105,7 @@ sequenceData: {
                 then a new option will appear in the 
                 Edit/Create Part Dialog that a user can use to create a 
                 part that "wraps around the whole sequence and back over itself". 
-                This will cause part.doesOverlapSelf = true
+                This will cause part.overlapsSelf = true
                 `
               })}
               {renderToggle({

src/CircularView/Part.js

@@ -8,12 +8,12 @@ export default function Part({
   annotationHeight,
   totalAngle,
   color,
-  doesOverlapSelf,
+  overlapsSelf,
   className
 }) {
-  let path = drawDirectedPiePiece({
+  const path = drawDirectedPiePiece({
     radius,
-    doesOverlapSelf,
+    overlapsSelf,
     annotationHeight,
     totalAngle,
     arrowheadLength,

src/CircularView/drawAnnotations.js

@@ -46,19 +46,14 @@ function drawAnnotations({
     return -getRangeLength(a, sequenceLength);
   })
     .map((annotation) => {
-      let {
-        startAngle,
-        endAngle,
-        totalAngle,
-        centerAngle,
-        locationAngles
-      } = getRangeAngles(
-        positionBy ? positionBy(annotation) : annotation,
-        sequenceLength
-      );
+      const { startAngle, endAngle, totalAngle, centerAngle, locationAngles } =
+        getRangeAngles(
+          positionBy ? positionBy(annotation) : annotation,
+          sequenceLength
+        );
 
-      let spansOrigin = startAngle > endAngle;
-      let annotationCopy = {
+      const spansOrigin = startAngle > endAngle;
+      const annotationCopy = {
         ...annotation,
         startAngle,
         endAngle,
@@ -69,7 +64,9 @@ function drawAnnotations({
       };
       if (!allOnSameLevel) {
         //expand the end angle if annotation spans the origin
-        let expandedEndAngle = spansOrigin ? endAngle + 2 * Math.PI : endAngle;
+        const expandedEndAngle = spansOrigin
+          ? endAngle + 2 * Math.PI
+          : endAngle;
         let yOffset1;
         let yOffset2;
         if (spansOrigin) {
@@ -188,7 +185,7 @@ function drawAnnotations({
         };
       }
 
-      let annotationColor = getColor
+      const annotationColor = getColor
         ? getColor(annotation)
         : annotation.color || "purple";
 
@@ -204,7 +201,7 @@ function drawAnnotations({
             annotationType,
             showLabels,
             Annotation,
-            doesOverlapSelf: annotation.doesOverlapSelf,
+            overlapsSelf: annotation.overlapsSelf,
             labelCenter: centerAngle,
             startAngle,
             endAngle,

src/CircularView/drawDirectedPiePiece.js

@@ -13,16 +13,16 @@ export default function drawDirectedPiePiece({
   tailThickness = 0.6,
   arrowheadLength = 1,
   radius,
-  doesOverlapSelf,
+  overlapsSelf,
   annotationHeight,
   totalAngle
 }) {
-  let tailHeight = annotationHeight * tailThickness;
+  const tailHeight = annotationHeight * tailThickness;
 
-  let arrowheadOuterRadius = radius + annotationHeight / 2;
-  let arrowheadInnerRadius = radius - annotationHeight / 2;
-  let tailOuterRadius = radius + tailHeight / 2;
-  let tailInnerRadius = radius - tailHeight / 2;
+  const arrowheadOuterRadius = radius + annotationHeight / 2;
+  const arrowheadInnerRadius = radius - annotationHeight / 2;
+  const tailOuterRadius = radius + tailHeight / 2;
+  const tailInnerRadius = radius - tailHeight / 2;
 
   // var arrowheadAngle = totalAngle / 2
   let arrowheadAngle = arrowheadLength / (Math.PI * 2);
@@ -31,35 +31,41 @@ export default function drawDirectedPiePiece({
     //set arrowhead length to the angle in radians length
     arrowheadAngle = totalAngle;
   }
-  let arcAngle = totalAngle - arrowheadAngle;
+  const arcAngle = totalAngle - arrowheadAngle;
 
   //the main points we need to draw the arrow and in the order we draw them in:
-  let arrowheadPoint = polarToSpecialCartesian(radius, 0);
+  const arrowheadPoint = polarToSpecialCartesian(radius, 0);
 
-  let arrowheadPointInner = polarToSpecialCartesian(radius, -stickOutThisMuch);
+  const arrowheadPointInner = polarToSpecialCartesian(
+    radius,
+    -stickOutThisMuch
+  );
 
-  let arrowheadBottom = polarToSpecialCartesian(
+  const arrowheadBottom = polarToSpecialCartesian(
     arrowheadInnerRadius,
     arrowheadAngle
   );
-  let arcLeftBottom = polarToSpecialCartesian(tailInnerRadius, arrowheadAngle);
-  let arcRightBottom = polarToSpecialCartesian(tailInnerRadius, totalAngle);
-  let arcRightTop = polarToSpecialCartesian(tailOuterRadius, totalAngle);
-  let arcRightMiddle = polarToSpecialCartesian(radius, totalAngle);
-  let arcRightMiddleOuter = polarToSpecialCartesian(
+  const arcLeftBottom = polarToSpecialCartesian(
+    tailInnerRadius,
+    arrowheadAngle
+  );
+  const arcRightBottom = polarToSpecialCartesian(tailInnerRadius, totalAngle);
+  const arcRightTop = polarToSpecialCartesian(tailOuterRadius, totalAngle);
+  const arcRightMiddle = polarToSpecialCartesian(radius, totalAngle);
+  const arcRightMiddleOuter = polarToSpecialCartesian(
     radius,
     totalAngle + stickOutThisMuch
   );
-  let arcLeftTop = polarToSpecialCartesian(tailOuterRadius, arrowheadAngle);
-  let arrowheadTop = polarToSpecialCartesian(
+  const arcLeftTop = polarToSpecialCartesian(tailOuterRadius, arrowheadAngle);
+  const arrowheadTop = polarToSpecialCartesian(
     arrowheadOuterRadius,
     arrowheadAngle
   );
 
-  let largeArcFlag = arcAngle > Math.PI ? 1 : 0;
+  const largeArcFlag = arcAngle > Math.PI ? 1 : 0;
   let path = Path().moveto(arrowheadPoint.x, arrowheadPoint.y);
 
-  if (doesOverlapSelf) {
+  if (overlapsSelf) {
     path = path
       .lineto(arrowheadPointInner.x, arrowheadPointInner.y)
       .lineto(arrowheadPoint.x, arrowheadPoint.y);
@@ -78,7 +84,7 @@ export default function drawDirectedPiePiece({
       y: arcRightBottom.y
     });
 
-  if (doesOverlapSelf) {
+  if (overlapsSelf) {
     path = path
       .lineto(arcRightMiddle.x, arcRightMiddle.y)
       .lineto(arcRightMiddleOuter.x, arcRightMiddleOuter.y)

src/RowItem/StackedAnnotations/PointedAnnotation.js

@@ -59,12 +59,12 @@ class PointedAnnotation extends React.PureComponent {
     const widthMinusOne = width - charWN;
     let path;
     let hasAPoint = false;
-    const endLine = annotation.doesOverlapSelf
+    const endLine = annotation.overlapsSelf
       ? `L 0,${height / 2} 
     L -10,${height / 2} 
     L 0,${height / 2} `
       : "";
-    const arrowLine = annotation.doesOverlapSelf
+    const arrowLine = annotation.overlapsSelf
       ? `L ${width + 10},${height / 2} 
     L ${width},${height / 2} `
       : "";

src/helperComponents/AddOrEditAnnotationDialog/index.js

@@ -183,7 +183,7 @@ class AddOrEditAnnotationDialog extends React.Component {
       annotationVisibilityShow,
       renderLocations,
       locations,
-      doesOverlapSelf,
+      overlapsSelf,
       start,
       end,
       advancedOptions,
@@ -226,7 +226,7 @@ class AddOrEditAnnotationDialog extends React.Component {
 
           const newAnnotation = tidyUpAnnotation(
             convertRangeTo0Based({
-              doesOverlapSelf: data.doesOverlapSelf,
+              overlapsSelf: data.overlapsSelf,
               ...updatedData,
               ...(annotationTypePlural === "primers" //if we're making a primer it should automatically have a type of primer
                 ? { type: "primer_bind" }
@@ -235,8 +235,8 @@ class AddOrEditAnnotationDialog extends React.Component {
               ...(hasJoinedLocations && {
                 //only add locations if there are locations
                 start: updatedData.locations[0].start, //override the start and end to use the start and end of the joined locations
-                end:
-                  updatedData.locations[updatedData.locations.length - 1].end,
+                end: updatedData.locations[updatedData.locations.length - 1]
+                  .end,
                 locations: updatedData.locations.map(convertRangeTo0Based)
               })
             }),
@@ -348,9 +348,7 @@ class AddOrEditAnnotationDialog extends React.Component {
           style={{ marginBottom: 15, marginTop: -5, fontStyle: "italic" }}
         >
           Length:{" "}
-          {doesOverlapSelf
-            ? sequenceLength + annotationLength
-            : annotationLength}
+          {overlapsSelf ? sequenceLength + annotationLength : annotationLength}
         </div>
         <Notes readOnly={this.props.readOnly} notes={this.notes}></Notes>
         <Advanced
@@ -429,8 +427,7 @@ export default ({ formName, getProps, dialogProps }) => {
                 "In a non-circular sequence, joined spans must be in ascending order"
             };
             errors.locations[values.locations.length - 1] = {
-              end:
-                "In a non-circular sequence, joined spans must be in ascending order"
+              end: "In a non-circular sequence, joined spans must be in ascending order"
             };
           }
           values.locations.forEach((loc, index) => {
@@ -473,7 +470,7 @@ export default ({ formName, getProps, dialogProps }) => {
         return errors;
       }
     }),
-    formValues("start", "end", "doesOverlapSelf", "locations")
+    formValues("start", "end", "overlapsSelf", "locations")
   )(AddOrEditAnnotationDialog);
 };
 

src/helperComponents/AddOrEditPartDialog/index.js

@@ -49,7 +49,7 @@ const renderAdvancedOptions = ({ readOnly }) => (
     inlineLabel
     tooltipError
     disabled={readOnly}
-    name="doesOverlapSelf"
+    name="overlapsSelf"
     label={
       <div style={{ display: "flex", alignItems: "center" }}>
         Part Overlaps Self
@@ -85,7 +85,7 @@ export default AddOrEditAnnotationDialog({
   },
   getProps: (props) => ({
     upsertAnnotation: props.upsertPart,
-    advancedDefaultOpen: get(props, "initialValues.doesOverlapSelf"),
+    advancedDefaultOpen: get(props, "initialValues.overlapsSelf"),
     advancedOptions: props.allowPartsToOverlapSelf
       ? renderAdvancedOptions({ readOnly: props.readOnly })
       : undefined,

src/utils/getAnnotationClassnames.js

@@ -2,11 +2,11 @@ import classnames from "classnames";
 import { startCase } from "lodash";
 
 export default function getAnnotationClassnames(
-  { doesOverlapSelf },
+  { overlapsSelf },
   { viewName, type }
 ) {
   const Type = startCase(type);
   return classnames(`ve${Type}`, `ve${viewName}${Type}`, {
-    doesOverlapSelf
+    overlapsSelf
   });
 }