From df26fd054b7e99644cfd28f2168ac63da72ca1e0 Mon Sep 17 00:00:00 2001
From: Benjamin Redelings <benjamin.redelings@gmail.com>
Date: Sat, 22 Jun 2024 10:13:02 -0400
Subject: [PATCH] Stop including the values -- they are all 1.0

---
 src/substitution/cache.H          | 2 --
 src/substitution/cache.cc         | 2 +-
 src/substitution/likelihoodSEV.cc | 2 --
 3 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/substitution/cache.H b/src/substitution/cache.H
index bacbe9961..1187017ad 100644
--- a/src/substitution/cache.H
+++ b/src/substitution/cache.H
@@ -203,7 +203,6 @@ class SparseLikelihoods: public Object
     mutable object_ptr<Likelihood_Cache_Branch> DenseLikelihoods_;
 
 public:
-    std::vector<double> values;
     std::vector<int> states;
     std::vector<int> column_offsets;
 
@@ -216,7 +215,6 @@ public:
     bool away_from_root() const {return false;}
 
     int num_non_zeros() const {
-	assert(values.size() == states.size());
 	return states.size();
     }
 
diff --git a/src/substitution/cache.cc b/src/substitution/cache.cc
index f664422a8..9a6353c62 100644
--- a/src/substitution/cache.cc
+++ b/src/substitution/cache.cc
@@ -22,7 +22,7 @@ object_ptr<Likelihood_Cache_Branch> SparseLikelihoods::DenseLikelihoods() const
 
 	    for(int m=0;m<n_models();m++)
 		for(int j=column_offsets[i];j<column_offsets[i+1];j++)
-		    S[m*n_states() + states[j]] = values[j];
+		    S[m*n_states() + states[j]] = 1;
 
 	    i++;
 	}
diff --git a/src/substitution/likelihoodSEV.cc b/src/substitution/likelihoodSEV.cc
index 0f2c9037b..d37ea490e 100644
--- a/src/substitution/likelihoodSEV.cc
+++ b/src/substitution/likelihoodSEV.cc
@@ -1049,7 +1049,6 @@ namespace substitution
 		    int l = smap[s1].as_int();
 		    if (ok[l])
 		    {
-			LCB->values.push_back(1.0);
 			LCB->states.push_back(s1);
 		    }
 		}
@@ -1058,7 +1057,6 @@ namespace substitution
 	    {
 		for(int s1=0;s1<n_states;s1++)
 		{
-		    LCB->values.push_back(1.0);
 		    LCB->states.push_back(s1);
 		}
 	    }