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2024 refactoring rf2 #165

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2024 refactoring rf2 #165

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b5fb814
Fixing playwright bug
spond Feb 25, 2025
63372f3
Caching COI traversal fix
spond Mar 4, 2025
19148dd
v1.2.5-alpha.0
stevenweaver Mar 4, 2025
b099f82
CoI merging indirect revisions and stats updates
spond Mar 10, 2025
c90a5a9
Updating all html templates
spond Mar 10, 2025
fb5c08f
Merge branch '2024-refactoring-RF2' of github.com:veg/hivtrace-viz in…
stevenweaver Mar 10, 2025
b3d0c16
v1.2.5-alpha.1
stevenweaver Mar 10, 2025
e154d38
resolves #358
stevenweaver Mar 11, 2025
1f28c0a
Merge pull request #166 from veg/2024-refactoring-RF2-SW
stevenweaver Mar 12, 2025
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2 changes: 1 addition & 1 deletion html/network.html
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Original file line number Diff line number Diff line change
Expand Up @@ -862,7 +862,7 @@ <h4 class="modal-title">Listing nodes in cluster X</h4>
} else {
d3.select("#app-error").style("display", "none");
hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
hivtrace.graphSummary(graph, graph_summary_tag);
hivtrace.graphSummary(user_graph, graph_summary_tag);

[
"#main-tab",
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2 changes: 1 addition & 1 deletion html/plain.html
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Expand Up @@ -809,7 +809,7 @@ <h4 class="modal-title">Listing nodes in cluster X</h4>
} else {
d3.select("#app-error").style("display", "none");
hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
hivtrace.graphSummary(graph, graph_summary_tag);
hivtrace.graphSummary(user_graph, graph_summary_tag);

[
"#main-tab",
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2 changes: 1 addition & 1 deletion html/priority-sets-args.html
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Expand Up @@ -979,7 +979,7 @@ <h5 class="modal-desc">Select CoI from the list</h5>
} else {
d3.select("#app-error").style("display", "none");
hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
hivtrace.graphSummary(user_graph.json, graph_summary_tag);
hivtrace.graphSummary(user_graph, graph_summary_tag);

[
"#main-tab",
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5 changes: 2 additions & 3 deletions html/social.html
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Original file line number Diff line number Diff line change
Expand Up @@ -836,7 +836,7 @@ <h4 class="modal-title">Listing nodes in cluster X</h4>
} else {
d3.select("#app-error").style("display", "none");
hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
hivtrace.graphSummary(graph, graph_summary_tag);
hivtrace.graphSummary(user_graph, graph_summary_tag);

[
"#main-tab",
Expand Down Expand Up @@ -927,8 +927,7 @@ <h4 class="modal-title">Listing nodes in cluster X</h4>

var initialize_cluster_network_graphs = function () {
//Initialize clusternetworkgraph with json url
url =
"../test/workshop/SocialDemoFiles/SocialNetwork.trace.json";
url = "../test/workshop/SocialDemoFiles/SocialNetwork.trace.json";
//url = "test/LA.json"

d3.json(url, function (error, results) {
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2 changes: 1 addition & 1 deletion index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -874,7 +874,7 @@ <h4 class="modal-title">Listing nodes in cluster X</h4>
} else {
d3.select("#app-error").style("display", "none");
hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
hivtrace.graphSummary(graph, graph_summary_tag);
hivtrace.graphSummary(user_graph, graph_summary_tag);

[
"#main-tab",
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "hivtrace-viz",
"version": "1.2.4-alpha.7",
"version": "1.2.5-alpha.1",
"description": "Visualization for the popular HIV-TRACE package",
"engines": {
"node": ">=18 || >20"
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20 changes: 12 additions & 8 deletions src/clusternetwork.js
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Original file line number Diff line number Diff line change
Expand Up @@ -4482,7 +4482,13 @@ var hivtrace_cluster_network_graph = function (
container
.selectAll("path")
.attr("d", misc.symbol(symbol_type).size(node_size(node)))
.style("fill", (d) => node_color(d));
.style("fill", (d) => node_color(d))
.classed(
"multi_sequence",
(d) =>
_.isArray(d[kGlobals.network.AliasedSequencesID]) &&
d[kGlobals.network.AliasedSequencesID].length > 1
);

if (node.show_label) {
if (container.selectAll("text").empty()) {
Expand Down Expand Up @@ -4514,12 +4520,6 @@ var hivtrace_cluster_network_graph = function (
"selected_object",
(d) => d.match_filter && !self.hide_unselected
)
.classed(
"multi_sequence",
(d) =>
_.isArray(d[kGlobals.network.AliasedSequencesID]) &&
d[kGlobals.network.AliasedSequencesID].length > 1
)
.classed("injected_object", (d) => d.node_class === "injected")
.attr("transform", (d) => "translate(" + d.x + "," + d.y + ")")
.style("opacity", (d) => node_opacity(d))
Expand Down Expand Up @@ -5715,7 +5715,7 @@ var hivtrace_cluster_network_graph = function (
anything_changed = true;
}

if (n.match_filter) {
if (n.match_filter && n.parent) {
n.parent.match_filter += 1;
}
});
Expand Down Expand Up @@ -6318,6 +6318,10 @@ var hivtrace_cluster_network_graph = function (
null,
{ "no-filter": true }
);
} else {
self.draw_extended_node_table([], null, null, {
"no-filter": true,
});
}
});
}
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6 changes: 3 additions & 3 deletions src/clustersOfInterest.js
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Original file line number Diff line number Diff line change
Expand Up @@ -689,9 +689,9 @@ function open_editor(
}

_.each(nodes_to_add, (n) => {
if (!(n in existing_ids) && n in valid_ids) {
panel_object._append_node(valid_ids[n]);
existing_ids[n] = 1;
if (!(n.id in existing_ids) && n.id in valid_ids) {
panel_object._append_node(valid_ids[n.id]);
existing_ids[n.id] = 1;
need_update = true;
} else {
console.log("***", n);
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