From 5598aed16d6bd3564edd901cc3183d5f3c4bb0f0 Mon Sep 17 00:00:00 2001
From: Thomas Wong <thomaskf@gmail.com>
Date: Sun, 10 Mar 2024 22:21:25 +1100
Subject: [PATCH] fixed the progress-display issue for PF

---
 main/phylotesting.cpp | 22 ++++++++++++++--------
 utils/progress.cpp    |  5 +++--
 utils/progress.h      |  2 +-
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/main/phylotesting.cpp b/main/phylotesting.cpp
index 161db2e16..ade799e9e 100644
--- a/main/phylotesting.cpp
+++ b/main/phylotesting.cpp
@@ -2193,6 +2193,8 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
         }
         size_t num_pairs = closest_pairs.size();
         size_t compute_pairs = 0;
+        progress_display progress(num_pairs, "Calculating subsets");
+        progress.setProgressDisplay(true);
 
 #ifdef _OPENMP
 #pragma omp parallel for private(i) schedule(dynamic) if(!params.model_test_and_tree)
@@ -2278,13 +2280,14 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
 //                    cout.width(11);
 //                    cout << cur_pair.tree_len << " " << cur_pair.set_name;
                     if (num_model >= 10) {
-                        double remain_time = max(total_num_model-num_model, (int64_t)0)*(getRealTime()-start_time)/num_model;
-                        if (remain_time < 0.0)
-                            remain_time = 0.0;
-                        double finish_percent = (double) pair * 100.0 / num_pairs;
-                        cout << " Finished subset " << pair << "/" << num_pairs << "     " << finish_percent << "  percent done";
-                        cout << "     " << convert_time(getRealTime()-start_time) << " ("
-                            << convert_time(remain_time) << " left)     \r" << flush;
+//                        double remain_time = max(total_num_model-num_model, (int64_t)0)*(getRealTime()-start_time)/num_model;
+//                        if (remain_time < 0.0)
+//                            remain_time = 0.0;
+//                        double finish_percent = (double) pair * 100.0 / num_pairs;
+//                        cout << " Finished subset " << pair << "/" << num_pairs << "     " << finish_percent << "  percent done";
+//                        cout << "     " << convert_time(getRealTime()-start_time) << " (" << convert_time(remain_time) << " left)     \r" << flush;
+                        progress += 1;
+                        // progress.reportProgress(getRealTime(), getCPUTime(), false);
                     }
 //                    cout << endl;
 
@@ -2296,7 +2299,10 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
         }
 
         // clear the message previous on this line
-        cout << blkStr << "\r" << flush;
+        // cout << blkStr << "\r" << flush;
+        progress.done();
+        progress.hide();
+        progress.setProgressDisplay(false);
 
         if (better_pairs.size() > 0) {
             ModelPairSet compatible_pairs;
diff --git a/utils/progress.cpp b/utils/progress.cpp
index 1d0d2b00b..119223709 100644
--- a/utils/progress.cpp
+++ b/utils/progress.cpp
@@ -172,13 +172,14 @@ void progress_display::reportProgress(double time, double cpu, bool newline) {
     }
 }
 
-progress_display& progress_display::done() {
+progress_display& progress_display::done(bool display) {
     #if _OPENMP
     #pragma omp critical (io)
     #endif
     workDone = totalWorkToDo;
     isDone = true;
-    reportProgress(getRealTime(), getCPUTime(), true);
+    if (display)
+        reportProgress(getRealTime(), getCPUTime(), true);
     return *this;
 }
 
diff --git a/utils/progress.h b/utils/progress.h
index 862131036..15153f8b1 100644
--- a/utils/progress.h
+++ b/utils/progress.h
@@ -33,7 +33,7 @@ class progress_display {
     progress_display& operator =  (double workDoneNow);
     progress_display& hide ();
     progress_display& show ();
-    progress_display& done ();
+    progress_display& done (bool display = false);
     void reportProgress(double time, double cpu, bool newline);
     static void setProgressDisplay(bool displayIt);
     static bool getProgressDisplay();