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now using name decenttree.cpp #9

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merged 7 commits into from
May 7, 2024
Merged

now using name decenttree.cpp #9

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f4ce694
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NicolaDM Sep 7, 2020
957241e
file needed for compilation
NicolaDM Sep 7, 2020
25e8b83
deleted DecentTree.cpp
NicolaDM Sep 7, 2020
e375f23
renamed decenttree as currently in master
NicolaDM Sep 11, 2020
ca82c1e
Delete decentTree.cpp
NicolaDM Sep 11, 2020
c294549
Merge branch 'master' into master
bqminh May 7, 2024
ca6f98b
revert initialisation in modelunrest.cpp
bqminh May 7, 2024
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22 changes: 22 additions & 0 deletions model/modelunrest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
*/

#include "modelunrest.h"
#include <stdlib.h>
#include <string.h>

ModelUnrest::ModelUnrest(PhyloTree *tree, string model_params, StateFreqType freq_type, string freq_params)
: ModelMarkov(tree, false)
Expand All @@ -16,6 +18,7 @@ ModelUnrest::ModelUnrest(PhyloTree *tree, string model_params, StateFreqType fre
for (int i=0; i <= num_params; i++) {
rates[i] = 1.0;
}

if (model_params != "") {
//cout << "WARNING: Supplying model params to constructor not yet properly implemented -- ignored" << endl;
// TODO: parse model_params into model_parameters, then call setRates().
Expand Down Expand Up @@ -54,6 +57,23 @@ ModelUnrest::ModelUnrest(PhyloTree *tree, string model_params, StateFreqType fre
ModelMarkov::init(FREQ_ESTIMATE);
}

void ModelUnrest::writeInfo(ostream &out) {
out << "UNREST rate values:";
out << " A-C: " << rates[0];
out << " A-G: " << rates[1];
out << " A-T: " << rates[2];
out << " C-A: " << rates[3];
out << " C-G: " << rates[4];
out << " C-T: " << rates[5];
out << " G-A: " << rates[6];
out << " G-C: " << rates[7];
out << " G-T: " << rates[8];
out << " T-A: " << rates[9];
out << " T-C: " << rates[10];
out << " T-G: " << rates[11];
out << endl;
}

/* static */ bool ModelUnrest::validModelName(string model_name) {
return (model_name == "UNREST");
}
Expand All @@ -68,6 +88,8 @@ void ModelUnrest::setBounds(double *lower_bound, double *upper_bound, bool *boun
}
}



/*
void ModelUnrest::setRates() {
// For UNREST, parameters are simply the off-diagonal rate matrix entries
Expand Down
1 change: 1 addition & 0 deletions model/modelunrest.h
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Expand Up @@ -48,6 +48,7 @@ class ModelUnrest: public ModelMarkov {
virtual void restoreCheckpoint();

protected:
void writeInfo(ostream &out);
virtual void setRates();
};

Expand Down