From dabaaba208f4af5df56d45d836a42e9a47d60c7c Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 25 Jul 2024 10:57:18 +0100
Subject: [PATCH] Progress bar for `.MaxInfo()`

---
 DESCRIPTION       |  2 +-
 NAMESPACE         |  1 +
 NEWS.md           |  4 +++-
 R/tree_distance.R | 18 +++++++++++-------
 4 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ac860edce..5710565b1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TreeDist
 Type: Package
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.7.1.9003
+Version: 2.7.1.9004
 Authors@R: c(person("Martin R.", "Smith",
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph", "prg"), 
diff --git a/NAMESPACE b/NAMESPACE
index 31ea6fbef..ff9c6bbca 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -164,6 +164,7 @@ importFrom(ape,plot.phylo)
 importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
+importFrom(cli,cli_progress_along)
 importFrom(cli,cli_progress_bar)
 importFrom(cli,cli_progress_update)
 importFrom(colorspace,qualitative_hcl)
diff --git a/NEWS.md b/NEWS.md
index 7eaf32b95..0abf75525 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,9 +1,11 @@
-# TreeDist 2.7.1.9003 (2024-06-28)
+# TreeDist 2.7.1.9004 (2024-07-25)
 
 - `Islands()` allows the identification of islands of trees.
 
 - Internal implementation of path and SPR distances, removing dependency
   on phangorn (and thus R 4.4).
+  
+- Add progress bar within `.MaxValue()`
 
 
 # TreeDist 2.7.1 (2024-06-13)
diff --git a/R/tree_distance.R b/R/tree_distance.R
index 4bdcd7e48..86c88614a 100644
--- a/R/tree_distance.R
+++ b/R/tree_distance.R
@@ -73,6 +73,8 @@ GeneralizedRF <- function(splits1, splits2, nTip, PairScorer,
   ret
 }
 
+
+#' @importFrom cli cli_progress_along
 .MaxValue <- function(tree1, tree2, Value) {
   lab1 <- TipLabels(tree1)
   sameTips <- .AllTipsSame(lab1, TipLabels(tree2))
@@ -95,13 +97,15 @@ GeneralizedRF <- function(splits1, splits2, nTip, PairScorer,
       pairs <- combn(seq_along(tree1), 2)
       nPairs <- dim(pairs)[[2]]
       
-      apply(pairs, 2, function(ij) {
-        i <- ij[[1]]
-        j <- ij[[2]]
-        common <- intersect(lab1[[i]], lab1[[j]])
-        Value(KeepTip(tree1[[i]], common)) +
-          Value(KeepTip(tree1[[j]], common))
-      })
+      vapply(cli_progress_along(seq_len(nPairs), "Calc max value"),
+             function(pair) {
+               i <- pairs[1, pair]
+               j <- pairs[2, pair]
+               common <- intersect(lab1[[i]], lab1[[j]])
+               Value(KeepTip(tree1[[i]], common)) +
+                 Value(KeepTip(tree1[[j]], common))
+             }, double(1))
+      
     }
   } else {
     value1 <- Value(tree1)