improving passing of alignmentAnnotationVisibility to keep the defaul…

…t values unless explicitly overridden
TeselaGen · Jun 4, 2021 · 9110008 · 9110008
1 parent ce25936
commit 9110008
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 6 deletions.
diff --git a/cypress/integration/standaloneAlignment.spec.js b/cypress/integration/standaloneAlignment.spec.js
@@ -0,0 +1,8 @@
+describe("StandaloneAlignment", function () {
+  it("it should have both parts and features shown by default (via passed in alignmentAnnotationVisibility) and still show the sequence", function () {
+    cy.visit("#/StandaloneAlignment");
+    cy.get(".veRowViewPart").should("exist");
+    cy.get(".veRowViewFeature").should("exist");
+    cy.get(".rowViewTextContainer").should("exist");
+  });
+});
diff --git a/demo/src/StandaloneAlignmentDemo.js b/demo/src/StandaloneAlignmentDemo.js
@@ -28,6 +28,10 @@ export default class StandaloneAlignmentDemo extends React.Component {
       handleAlignmentRename: () => {
         console.info("alignment being renamed!");
       }, //this does nothing right now
+      alignmentAnnotationVisibility: {
+        features: true,
+        parts: true
+      },
       linearViewOptions: () => {
         return {
           selectionLayerRightClicked: ({ event }) => {

diff --git a/src/redux/alignments.js b/src/redux/alignments.js
@@ -23,7 +23,7 @@ const alignmentAnnotationSettings = {
   primers: false
 };
 
-let defaultVisibilities = {
+const defaultVisibilities = {
   alignmentAnnotationVisibility: alignmentAnnotationSettings,
   pairwise_alignmentAnnotationVisibility: alignmentAnnotationSettings,
   alignmentAnnotationLabelVisibility: {
@@ -138,18 +138,21 @@ export default (state = {}, { payload = {}, type }) => {
   }
 
   if (type === "UPSERT_ALIGNMENT_RUN") {
-    let payloadToUse = {
+    const payloadToUse = {
+      ...payload,
       //assign default visibilities
       ...defaultVisibilityTypes.reduce((acc, type) => {
         if (
           (type.startsWith("pairwise_") && payload.pairwiseAlignments) ||
           (!type.startsWith("pairwise_") && !payload.pairwiseAlignments)
         ) {
-          acc[type.replace("pairwise_", "")] = defaultVisibilities[type];
+          acc[type.replace("pairwise_", "")] = {
+            ...defaultVisibilities[type],
+            ...payload[type.replace("pairwise_", "")]
+          };
         }
         return acc;
-      }, {}),
-      ...payload
+      }, {})
     };
     if (payloadToUse.pairwiseAlignments) {
       if (
@@ -287,7 +290,7 @@ function checkForIssues(alignmentTracks, alignmentType) {
     return;
   }
 
-  let alignmentTrackLength = alignmentTracks[0].alignmentData.sequence.length;
+  const alignmentTrackLength = alignmentTracks[0].alignmentData.sequence.length;
   let hasError;
   alignmentTracks.some((track) => {
     if (track.alignmentData.sequence.length !== alignmentTrackLength) {