From 82a5c35aa0d5b8a2580005425e04c92711390499 Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Sat, 3 Jun 2023 20:25:18 +0100
Subject: [PATCH] UPDATE

---
 taxonium_component/public/taxonium.proto | 59 ------------------------
 taxonium_component/src/README.md         | 22 +++++++++
 2 files changed, 22 insertions(+), 59 deletions(-)
 delete mode 100644 taxonium_component/public/taxonium.proto
 create mode 100644 taxonium_component/src/README.md

diff --git a/taxonium_component/public/taxonium.proto b/taxonium_component/public/taxonium.proto
deleted file mode 100644
index 2f18d51e..00000000
--- a/taxonium_component/public/taxonium.proto
+++ /dev/null
@@ -1,59 +0,0 @@
-syntax = "proto3";
-
-message ColourMapping{
-  string key = 1;
-  repeated int32 colour = 2;
-}
-
-
-message MutationList{
-  repeated int32 mutation = 1;
-}
-
-message MetadataUniqueStringPerNode{
-  string metadata_name = 1;
-  string metadata_title = 2;
-  repeated string node_values = 3;
-}
-
-message MetadataSingleValuePerNode{
-  string metadata_name = 1;
-  string metadata_title = 2;
-  repeated string mapping = 3;
-  repeated int32 node_values = 4;
-}
-
-message AllNodeData {
-  repeated string names = 1; // Deprecated: DO NOT USE (use metadata_unique_strings)
- repeated float x = 2;
- repeated float y = 3;
- repeated int32 countries = 4;//Deprecated: DO NOT USE (use metadata_singles)
- repeated int32 dates = 7;  // Deprecated: DO NOT USE (use metadata_singles)
- repeated int32 lineages = 5;//Deprecated: DO NOT USE (use metadata_singles)
-
-
- repeated MutationList mutations = 6;
- repeated int32 parents = 8;
- repeated string genbanks = 9; // Deprecated: DO NOT USE
-repeated int32 epi_isl_numbers = 10;  // Deprecated: DO NOT USE
-repeated int32 num_tips = 11;
-repeated MetadataSingleValuePerNode metadata_singles = 12;
-repeated MetadataUniqueStringPerNode metadata_unique_strings=13;
-repeated float time_x = 14; // Temporary
-
-}
-
-
-message AllData{
-  AllNodeData node_data= 1;
-  repeated string country_mapping = 2;//Deprecated: DO NOT USE (use metadata_singles above)
-  repeated string lineage_mapping = 3; //Deprecated: DO NOT USE (use metadata_singles above)
-  repeated string mutation_mapping = 4;
-  repeated string date_mapping = 5; //Deprecated: DO NOT USE (use metadata_singles above)
-  string tree_description = 6;
-  string tree_title = 7;
-  string default_search = 8;
-  string default_seq_name_field = 9;
-  string default_colourby = 10;
-  repeated ColourMapping colour_mapping = 11;
-}
diff --git a/taxonium_component/src/README.md b/taxonium_component/src/README.md
new file mode 100644
index 00000000..740e23bf
--- /dev/null
+++ b/taxonium_component/src/README.md
@@ -0,0 +1,22 @@
+src/Taxonium.jsx: This is the main entry point for the Taxonium component. It brings together all the hooks and components to render the interactive phylogenetic tree.
+
+src/Deck.jsx: This component renders the actual DeckGL canvas and handles interactions with it. It contains the layers for nodes, lines, labels, etc.
+
+src/hooks: This folder contains all the React hooks used in the project. Some of the main hooks are:
+
+- useBackend: This hook is used to interface with either a local or server backend to get data and search 
+- useColor, useColorBy: These hooks handle the node coloring logic
+- useConfig: This hook is used to get configuration information (title, source, etc)
+- useGetDynamicData: This hook is used to get data from the backend within the current viewport
+- useLayers: This hook generates the DeckGL layers 
+- useNodeDetails: This hook is used to get details for selected nodes
+- useSearch: This hook handles searching the tree
+- useView: This hook manages the view state and zooming/panning
+- useHoverDetails: This hook manages hovered node details
+
+src/utils: This folder contains various utility functions, including:
+
+- processNewick.js: For converting Newick/Nexus into Taxonium JSON format
+- processNextstrain.js: For converting Nextstrain JSON into Taxonium JSON format 
+- searchUtil.js: Contains utility functions for searching 
+- formatNumber.js: Used to format large numbers with commas
\ No newline at end of file