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Commit 21f826b2 authored by Stephen Smith's avatar Stephen Smith
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more memory fixes

parent e1d78225
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BioGeoTree.cpp
View file @ 21f826b2
......@@ -52,20 +52,13 @@ namespace {
*/
BioGeoTree::BioGeoTree(Tree * tr, vector<double> ps):tree(tr),periods(ps),
seg("segments"),age("age"),dc("dist_conditionals"),en("excluded_dists"),
age("age"),dc("dist_conditionals"),en("excluded_dists"),
andc("anc_dist_conditionals"),columns(NULL),whichcolumns(NULL),rootratemodel(NULL),
distmap(NULL),store_p_matrices(false),use_stored_matrices(false),revB("revB"),
rev(false),rev_exp_number("rev_exp_number"),rev_exp_time("rev_exp_time"),
stochastic(false),stored_EN_matrices(map<int,map<double, mat > >()),
stored_ER_matrices(map<int,map<double, mat > >()),scale(1.),totalscale(0),
limit(1e-200),run_with_scale(true){
stored_ER_matrices(map<int,map<double, mat > >()){
//testing the scaling ability
scale = 1e+49;
limit = 1e-50;
#ifdef BIGTREE
run_with_scale = false;
#endif
/*
* initialize each node with segments
*/
......@@ -74,13 +67,13 @@ BioGeoTree::BioGeoTree(Tree * tr, vector<double> ps):tree(tr),periods(ps),
if(tree->getNode(i)->getBL()<0.000001)
tree->getNode(i)->setBL(0.000001);
//VectorNodeObject<BranchSegment> * segs = new VectorNodeObject<BranchSegment>();
vector<BranchSegment> segs;
//tree->getNode(i)->assocObject(seg,*segs);
tree->getNode(i)->assocSegVector(segs);
tree->getNode(i)->initSegVector();
//delete segs;
VectorNodeObject<vector<int> > * ens = new VectorNodeObject<vector<int> >();
tree->getNode(i)->assocObject(en,*ens);
delete ens;
//VectorNodeObject<vector<int> > * ens = new VectorNodeObject<vector<int> >();
//tree->getNode(i)->assocObject(en,*ens);
//delete ens;
tree->getNode(i)->initExclDistVector();
}
/*
* initialize the actual branch segments for each node
......@@ -199,25 +192,9 @@ void BioGeoTree::set_tip_conditionals(map<string,vector<int> > distrib_data){
}
}
// testing scale
// this is testing scaling internal nodes when they get too small
void BioGeoTree::scale_node(VectorNodeObject<double> * conds){
bool min = false;
double num = *max_element(conds->begin(), conds->end());
//cout << "first: "<< num << endl;
if (num <= limit){
for(unsigned int i=0;i<conds->size();i++){
conds->at(i) = conds->at(i)*scale;
}
totalscale += 1;
}
//num = *max_element(conds->begin(), conds->end());
//cout << "second: "<< num << endl;
}
void BioGeoTree::set_excluded_dist(vector<int> ind,Node * node){
((VectorNodeObject<vector<int> >*) node->getObject(en))->push_back(ind);
//((VectorNodeObject<vector<int> >*) node->getObject(en))->push_back(ind);
node->getExclDistVector()->push_back(ind);
}
/*
......@@ -239,8 +216,6 @@ mpfr_class calculate_vector_mpfr_class_sum(vector<mpfr_class> & in){
#endif
double BioGeoTree::eval_likelihood(bool marginal){
//testing scale
totalscale = 0;
if( rootratemodel->sparse == true){
columns = new vector<int>(rootratemodel->getDists()->size());
whichcolumns = new vector<int>();
......@@ -266,18 +241,6 @@ double BioGeoTree::eval_likelihood(bool marginal){
}
double BioGeoTree::get_scale(){
return (log(scale)*totalscale);
}
void BioGeoTree::set_scale(double sc, double tsc){
}
void BioGeoTree::set_run_with_scale(bool bl){
run_with_scale = bl;
}
#ifdef BIGTREE
VectorNodeObject<mpfr_class> BioGeoTree::conditionals(Node & node, bool marginal,bool sparse){
#else
......@@ -300,7 +263,8 @@ vector<double> BioGeoTree::conditionals(Node & node, bool marginal,bool sparse){
#ifdef BIGTREE
VectorNodeObject<mpfr_class> * v = new VectorNodeObject<mpfr_class> (rootratemodel->getDists()->size(), 0);
#else
VectorNodeObject<double> * v = new VectorNodeObject<double> (rootratemodel->getDists()->size(), 0);
//VectorNodeObject<double> * v = new VectorNodeObject<double> (rootratemodel->getDists()->size(), 0);
vector<double> *v = new vector<double> (rootratemodel->getDists()->size(),0);
#endif
vector<int> distrange;
if(tsegs->at(i).get_start_dist_int() != -666){
......@@ -486,7 +450,8 @@ void BioGeoTree::ancdist_conditional_lh(Node & node, bool marginal){
#else
double lh = 0.0;
#endif
VectorNodeObject<vector<int> >* exdist = ((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist = ((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(),exdist->end(),dists->at(i));
if(cou == 0){
iter_ancsplits_just_int(rootratemodel,dists->at(i),leftdists,rightdists,weight);
......@@ -547,7 +512,8 @@ void BioGeoTree::setFossilatNodeByMRCA(vector<string> nodeNames, int fossilarea)
vector<vector<int> > * dists = rootratemodel->getDists();
for(unsigned int i=0;i<dists->size();i++){
if(dists->at(i).at(fossilarea) == 0){
VectorNodeObject<vector<int> > * exd = ((VectorNodeObject<vector<int> > *) mrca->getObject(en));
//VectorNodeObject<vector<int> > * exd = ((VectorNodeObject<vector<int> > *) mrca->getObject(en));
vector<vector<int> > * exd = mrca->getExclDistVector();
exd->push_back(dists->at(i));
}
}
......@@ -556,7 +522,8 @@ void BioGeoTree::setFossilatNodeByMRCA_id(Node * id, int fossilarea){
vector<vector<int> > * dists = rootratemodel->getDists();
for(unsigned int i=0;i<dists->size();i++){
if(dists->at(i).at(fossilarea) == 0){
VectorNodeObject<vector<int> > * exd = ((VectorNodeObject<vector<int> > *) id->getObject(en));
//VectorNodeObject<vector<int> > * exd = ((VectorNodeObject<vector<int> > *) id->getObject(en));
vector<vector<int> > * exd = id->getExclDistVector();
exd->push_back(dists->at(i));
}
}
......@@ -652,7 +619,8 @@ void BioGeoTree::reverse(Node & node){
#endif
for (unsigned int i = 0; i < dists->size(); i++) {
if (accumulate(dists->at(i).begin(), dists->at(i).end(), 0) > 0) {
VectorNodeObject<vector<int> >* exdist = ((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist = ((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), dists->at(i));
if (cou == 0) {
iter_ancsplits_just_int(rootratemodel, dists->at(i), leftdists, rightdists, weight);
......@@ -750,8 +718,9 @@ map<vector<int>,vector<AncSplit> > BioGeoTree::calculate_ancsplit_reverse(Node &
//VectorNodeObject<BranchSegment>* tsegs2 = ((VectorNodeObject<BranchSegment>*) c2->getObject(seg));
vector<BranchSegment> * tsegs2 = c2->getSegVector();
for (unsigned int i=0;i<ans.size();i++){
VectorNodeObject<vector<int> >* exdist =
((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist =
// ((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), (*rootratemodel->get_int_dists_map())[ans[i].ancdistint]);
if (cou == 0) {
#ifdef BIGTREE
......@@ -815,8 +784,9 @@ vector<double> BioGeoTree::calculate_ancstate_reverse(Node & node,bool marg)
#endif
for (unsigned int i = 0; i < dists->size(); i++) {
if (accumulate(dists->at(i).begin(), dists->at(i).end(), 0) > 0) {
VectorNodeObject<vector<int> >* exdist =
((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist =
//((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), dists->at(i));
if (cou == 0) {
iter_ancsplits_just_int(rootratemodel, dists->at(i),
......@@ -948,8 +918,9 @@ vector<double> BioGeoTree::calculate_reverse_stochmap(Node & node,bool time)
#endif
for (unsigned int i = 0; i < dists->size(); i++) {
if (accumulate(dists->at(i).begin(), dists->at(i).end(), 0) > 0) {
VectorNodeObject<vector<int> >* exdist =
((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist =
//((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), dists->at(i));
if (cou == 0) {
iter_ancsplits_just_int(rootratemodel, dists->at(i),
......@@ -986,8 +957,9 @@ vector<double> BioGeoTree::calculate_reverse_stochmap(Node & node,bool time)
#endif
for (unsigned int i = 0; i < dists->size(); i++) {
if (accumulate(dists->at(i).begin(), dists->at(i).end(), 0) > 0) {
VectorNodeObject<vector<int> >* exdist =
((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist =
//((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), dists->at(i));
if (cou == 0) {
LHOODS[i] = Bs.at(i) * (alphs[i] );//do i do this or do i do from i to j
......@@ -1029,8 +1001,9 @@ vector<double> BioGeoTree::calculate_reverse_stochmap(Node & node,bool time)
#endif
for (unsigned int i = 0; i < dists->size(); i++) {
if (accumulate(dists->at(i).begin(), dists->at(i).end(), 0) > 0) {
VectorNodeObject<vector<int> >* exdist =
((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist =
//((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), dists->at(i));
if (cou == 0) {
LHOODS[i] = Bs.at(i) * (tsegs->at(0).distconds->at(i) );
......@@ -1060,8 +1033,9 @@ vector<double> BioGeoTree::calculate_reverse_stochmap(Node & node,bool time)
#endif
for (unsigned int i = 0; i < dists->size(); i++) {
if (accumulate(dists->at(i).begin(), dists->at(i).end(), 0) > 0) {
VectorNodeObject<vector<int> >* exdist =
((VectorNodeObject<vector<int> >*) node.getObject(en));
//VectorNodeObject<vector<int> >* exdist =
//((VectorNodeObject<vector<int> >*) node.getObject(en));
vector<vector<int> > * exdist = node.getExclDistVector();
int cou = count(exdist->begin(), exdist->end(), dists->at(i));
if (cou == 0) {
LHOODS[i] = Bs.at(i) * (alphs[i]);
......@@ -1088,8 +1062,8 @@ BioGeoTree::~BioGeoTree(){
delete tsegs->at(j).distconds;
delete tsegs->at(j).ancdistconds;
}
delete tree->getNode(i)->getObject(seg);
delete tree->getNode(i)->getObject(en);
//delete tree->getNode(i)->getObject(en);
tree->getNode(i)->deleteExclDistVector();
if(rev == true && tree->getNode(i)->isInternal()){
tree->getNode(i)->deleteDoubleVector(revB);
}
......@@ -1099,5 +1073,6 @@ BioGeoTree::~BioGeoTree(){
//delete tree->getRoot()->getObject(andc);
tree->getRoot()->deleteDoubleVector(dc);
tree->getRoot()->deleteDoubleVector(andc);
tree->getRoot()->deleteDoubleVector(revB);
}
BioGeoTree.h
View file @ 21f826b2
......@@ -35,7 +35,6 @@ class BioGeoTree{
private:
Tree * tree;
vector<double> periods;
string seg;
string age;
string dc;
string en;
......@@ -61,13 +60,6 @@ private:
map<int,map<double, mat > > stored_ER_matrices;
//end mapping bits
//scaling for larger trees
double scale;
double totalscale;
double limit;
bool run_with_scale;
void scale_node(VectorNodeObject<double> * conds);
/*
* benchmark variables
*/
......@@ -131,12 +123,6 @@ public:
vector<double> calculate_reverse_stochmap_TEST(Node & node,bool time);
//get the scale
double get_scale();
//this should be in the form of the get_scale so (log(scale)*totalscale);
void set_scale(double sc, double tsc);
void set_run_with_scale(bool );
/*
for timing things
*/
......
node.cpp
View file @ 21f826b2
......@@ -274,11 +274,8 @@ void Node::deleteDoubleVector(string name){
}
void Node::assocSegVector(vector<BranchSegment> & obj){
void Node::initSegVector(){
segs = new vector<BranchSegment> ();
for (unsigned int i=0;i<obj.size();i++){
segs->push_back(obj[i]);
}
}
vector<BranchSegment> * Node::getSegVector(){
......@@ -286,9 +283,19 @@ vector<BranchSegment> * Node::getSegVector(){
}
void Node::deleteSegVector(){
if (segs->size() > 0 ){
delete segs;
}
delete segs;
}
void Node::initExclDistVector(){
excluded_dists = new vector<vector<int > > ();
}
vector<vector< int> > * Node::getExclDistVector(){
return excluded_dists;
}
void Node::deleteExclDistVector(){
delete excluded_dists;
}
/*
......
node.h
View file @ 21f826b2
......@@ -30,6 +30,7 @@ private:
map<string, vector<double> > assocDV;
string comment;
vector<BranchSegment> * segs;
vector< vector<int> > * excluded_dists;
public:
Node();
......@@ -65,9 +66,12 @@ public:
void assocDoubleVector(string name, vector<double> & obj);
vector<double> * getDoubleVector(string name);
void deleteDoubleVector(string name);
void assocSegVector(vector<BranchSegment> & obj);
void initSegVector();
vector<BranchSegment> * getSegVector();
void deleteSegVector();
void initExclDistVector();
vector<vector< int> > * getExclDistVector();
void deleteExclDistVector();
NodeObject * getObject(string name);
};
......
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