download: use the node.shell.inView property

The `node.inView` property is a temporary hold for the node's inView
property to be able to zoom in on specific branches before the
D3 PhyloTree has been constructed.

Once the D3 PhyloTree has been constructed, the inView property is
available through `node.shell.inView`. This is the property that gets
updated by `applyInViewNodesToTree` whenever the user interacts with
any zooming functionality on the tree. The temporary `node.inView`
property will never be updated and thus only represents the initial
state of the node when the tree was first loaded.

Therefore, any downstream uses of the inView property should be using
the `node.shell.inView` property.

src/components/download/downloadButtons.js

@@ -135,7 +135,7 @@ function Button({name, description, icon, onClick}) {
 
 function getNumUniqueAuthors(nodes, nodeVisibilities) {
   const authors = new Set(nodes
-    .filter((n, i) => nodeVisibilities[i] === NODE_VISIBLE && n.inView)
+    .filter((n, i) => nodeVisibilities[i] === NODE_VISIBLE && n.shell.inView)
     .map((n) => getFullAuthorInfoFromNode(n))
     .filter((a) => a && a.value)
     .map((a) => a.value)

src/components/download/helperFunctions.js

@@ -22,7 +22,7 @@ const treeToNewick = (tree, temporal, internalNodeNames=false, nodeAnnotation=()
   const getXVal = temporal ? (n) => getTraitFromNode(n, "num_date") : getDivFromNode;
 
   function recurse(node, parentX) {
-    if (!node.inView || tree.visibility[node.arrayIdx]!==NODE_VISIBLE) {
+    if (!node.shell.inView || tree.visibility[node.arrayIdx]!==NODE_VISIBLE) {
       return "";
     }
     if (node.hasChildren) {
@@ -176,7 +176,7 @@ export const authorTSV = (dispatch, filePrefix, tree) => {
   const UNKNOWN = "unknown";
   const info = {};
   tree.nodes
-    .filter((n, i) => tree.visibility[i] === NODE_VISIBLE && n.inView)
+    .filter((n, i) => tree.visibility[i] === NODE_VISIBLE && n.shell.inView)
     .filter((n) => !n.hasChildren).forEach((n) => {
       const author = getFullAuthorInfoFromNode(n);
       if (!author) return;
@@ -221,7 +221,7 @@ export const strainTSV = (dispatch, filePrefix, nodes, nodeVisibilities) => {
   for (const [i, node] of nodes.entries()) {
     if (node.hasChildren) continue; /* we only consider tips */
 
-    if (nodeVisibilities[i] !== NODE_VISIBLE || !node.inView) {
+    if (nodeVisibilities[i] !== NODE_VISIBLE || !node.shell.inView) {
       continue;
     }
 
@@ -313,7 +313,7 @@ export const acknowledgmentsTSV = (dispatch, filePrefix, nodes, nodeVisibilities
   for (const [i, node] of nodes.entries()) {
     if (node.hasChildren) continue; /* we only consider tips */
 
-    if (nodeVisibilities[i] !== NODE_VISIBLE || !node.inView) {
+    if (nodeVisibilities[i] !== NODE_VISIBLE || !node.shell.inView) {
       continue;
     }