From 1f6b4433c4e95a385aaf8727793f2b43f47bffad Mon Sep 17 00:00:00 2001
From: Iago Bonnici <iago.bonnici@umontpellier.fr>
Date: Thu, 29 Aug 2024 16:18:58 +0200
Subject: [PATCH] =?UTF-8?q?=F0=9F=94=A7=20Small=20proofreading=20of=20the?=
=?UTF-8?q?=20main=20function.?=
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The idea is to get a better idea
what the desired formal output of aphid could be.
---
src/bin/aphid/main.rs | 28 +++++++++++++---------------
src/tree.rs | 3 ++-
2 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/src/bin/aphid/main.rs b/src/bin/aphid/main.rs
index a464b6b..e88d398 100644
--- a/src/bin/aphid/main.rs
+++ b/src/bin/aphid/main.rs
@@ -155,10 +155,10 @@ fn run() -> Result<(), Error> {
//==============================================================================
// Extract various information from the trees,
// and handle data from them with some kind of 'dataframe' pattern:
- // an informal sequence of same-sized columns.
+ // an informal collection of same-sized columns.
let ids = forest.ids();
let raw_trees = forest.trees();
- let raw_nodes = raw_trees.iter().map(GeneTree::len).collect::<Vec<_>>();
+ let raw_n_nodes = raw_trees.iter().map(GeneTree::len).collect::<Vec<_>>();
let sequences_lengths = raw_trees
.iter()
.map(GeneTree::sequence_length)
@@ -166,13 +166,13 @@ fn run() -> Result<(), Error> {
//----------------------------------------------------------------------------------------------
eprintln!("Prune trees so they only contain relevant species.");
- let (pruned_trees, pruned_nodes) = raw_trees.iter().fold(
+ let (pruned_trees, pruned_n_nodes) = raw_trees.iter().fold(
(Vec::new(), Vec::new()),
- |(mut trees, mut nodes), raw_tree| {
+ |(mut trees, mut n_nodes), raw_tree| {
let pruned = raw_tree.pruned(|_, leaf| relevant_species.contains(&leaf.payload));
- nodes.push(pruned.len());
+ n_nodes.push(pruned.len());
trees.push(pruned);
- (trees, nodes)
+ (trees, n_nodes)
},
);
@@ -256,8 +256,7 @@ fn run() -> Result<(), Error> {
//----------------------------------------------------------------------------------------------
// Geometry filter.
- // Is is actually needed?
- let geometry_pass = max_clock_ratio.is_some();
+ let geometry_pass = max_clock_ratio.is_some(); // (TODO: is this flag actually needed?)
if geometry_pass {
separator();
@@ -352,8 +351,8 @@ fn run() -> Result<(), Error> {
for i in 0..ids.len() {
let id = ids[i];
let sl = &sequences_lengths[i];
- let n = &raw_nodes[i];
- let np = &pruned_nodes[i];
+ let n = &raw_n_nodes[i];
+ let np = &pruned_n_nodes[i];
let otrip = &passed_triplets[i];
let out = passed_outgroup[i];
let top = passed_top[i];
@@ -472,7 +471,7 @@ fn run() -> Result<(), Error> {
.map(|pass| u64::from(!pass))
.sum::<u64>();
eprintln!(
- " - {} outroup{} rejected (empty or non-monophyletic).",
+ " - {} outgroup{} rejected (empty or non-monophyletic).",
n,
s(n)
);
@@ -545,10 +544,7 @@ fn run() -> Result<(), Error> {
eprintln!("total: {lnl}");
eprintln!("\nOptimizing ln-likelihood:");
- let (opt, opt_lnl) =
- optimize_likelihood(&triplets, parms, &config.search).unwrap_or_else(|e| {
- panic!("TODO: once learning works, remove all error types in favour of snafu.\n{e}")
- });
+ let (opt, opt_lnl) = optimize_likelihood(&triplets, parms, &config.search)?;
eprintln!("\nOptimized ln-likelihood:");
#[cfg(test)]
@@ -596,4 +592,6 @@ enum Error {
},
#[snafu(display("Inconsistent input:\n{mess}"))]
InputConsistency { mess: String },
+ #[snafu(transparent)]
+ Learn { source: aphid::learn::Error },
}
diff --git a/src/tree.rs b/src/tree.rs
index 4eea031..6978dea 100644
--- a/src/tree.rs
+++ b/src/tree.rs
@@ -22,7 +22,8 @@ pub(crate) mod prune;
#[cfg_attr(test, derive(Debug, PartialEq))]
pub(crate) struct Tree<B, IN, TN> {
- pub(crate) nodes: Vec<Node<B, IN, TN>>, // Stored in order of appearance in original Newick input.
+ // Stored in pre-order corresponding to appearance order in original Newick input.
+ pub(crate) nodes: Vec<Node<B, IN, TN>>,
}
#[cfg_attr(test, derive(Debug, PartialEq))]
--
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