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/*
* unweighted.cpp
* Mothur
*
* Created by Sarah Westcott on 2/9/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "unweighted.h"
/**************************************************************************************************/
Unweighted::Unweighted(bool r, vector<string> G) : includeRoot(r), Groups(G) {
try {
int numGroups = Groups.size();
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
for (int i=0; i<numGroups; i++) {
for (int l = 0; l < i; l++) {
vector<string> groups; groups.push_back(Groups[i]); groups.push_back(Groups[l]);
namesOfGroupCombos.push_back(groups);
}
}
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "Unweighted");
exit(1);
}
}
/**************************************************************************************************/
EstOutput Unweighted::getValues(Tree* t, int p) {
try {
processors = p;
return (createProcesses(t));
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "getValues");
exit(1);
}
}
/***********************************************************************/
struct unweightedData {
int start;
int num, count;
MothurOut* m;
EstOutput results;
vector< vector<string> > namesOfGroupCombos;
vector<vector<int> > randomizedTreeNodes;
Tree* t;
CountTable* ct;
bool includeRoot;
vector<string> Treenames;
Utils util;
unweightedData(){}
unweightedData(int st, int en, vector< vector<string> > ngc, Tree* tree, CountTable* count, bool ir) {
m = MothurOut::getInstance();
start = st;
num = en;
namesOfGroupCombos = ngc;
t = tree;
ct = count;
includeRoot = ir;
Treenames = tree->getTreeNames();
results.resize(num);
count = 0;
}
unweightedData(int st, int en, vector< vector<string> > ngc, Tree* tree, CountTable* count, bool ir, vector<vector<int> > randomTreeNodes) {
m = MothurOut::getInstance();
start = st;
num = en;
namesOfGroupCombos = ngc;
randomizedTreeNodes = randomTreeNodes;
t = tree;
ct = count;
includeRoot = ir;
Treenames = tree->getTreeNames();
results.resize(num);
count = 0;
}
};
/**************************************************************************************************/
int findNodeBelonging(MothurOut* m, vector<string>& namesOfGroupCombos, map< string, vector<int> >& groupNodeInfo) {
try {
int nodeBelonging = -1;
for (int g = 0; g < namesOfGroupCombos.size(); g++) {
if (groupNodeInfo[namesOfGroupCombos[g]].size() != 0) { nodeBelonging = groupNodeInfo[namesOfGroupCombos[g]][0]; break; }
}
//sanity check
if (nodeBelonging == -1) {
m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
for (int g = 0; g < namesOfGroupCombos.size()-1; g++) { m->mothurOut(namesOfGroupCombos[g] + "-"); }
m->mothurOut(namesOfGroupCombos[namesOfGroupCombos.size()-1]);
m->mothurOut(", skipping.\n");
}
return nodeBelonging;
}
catch(exception& e) {
m->errorOut(e, "Weighted", "findNodeBelongingToThisComparison");
exit(1);
}
}
/**************************************************************************************************/
void getRoot2(MothurOut* m, Tree* t, int v, vector<string> grouping, set<int>& rootForGrouping) {
try {
//you are a leaf so get your parent
int index = t->tree[v].getParent();
//my parent is a potential root
rootForGrouping.insert(index);
//while you aren't at root
while(t->tree[index].getParent() != -1){
if (m->getControl_pressed()) { return; }
//am I the root for this grouping? if so I want to stop "early"
//does my sibling have descendants from the users groups?
//if so I am not the root
int parent = t->tree[index].getParent();
int lc = t->tree[parent].getLChild();
int rc = t->tree[parent].getRChild();
int sib = lc;
if (lc == index) { sib = rc; }
map<string, int>::iterator itGroup;
int pcountSize = 0;
for (int j = 0; j < grouping.size(); j++) {
map<string, int>::iterator itGroup = t->tree[sib].pcount.find(grouping[j]);
if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
//if yes, I am not the root
if (pcountSize != 0) {
rootForGrouping.clear();
rootForGrouping.insert(parent);
}
index = parent;
}
//get all nodes above the root to add so we don't add their u values above
index = *(rootForGrouping.begin());
while(t->tree[index].getParent() != -1){
int parent = t->tree[index].getParent();
rootForGrouping.insert(parent);
index = parent;
}
return;
}
catch(exception& e) {
m->errorOut(e, "Weighted", "getRoot2");
exit(1);
}
}
/**************************************************************************************************/
void driverUnweighted(unweightedData* params) {
try {
params->count = 0;
for (int h = params->start; h < (params->start+params->num); h++) {
if (params->m->getControl_pressed()) { break; }
double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
double totalBL = 0.00; //all branch lengths
double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
set<int> rootBranches; //if not including root this will hold branches that are "above" the root for this comparison
int nodeBelonging = findNodeBelonging(params->m, params->namesOfGroupCombos[h], params->t->groupNodeInfo);
if (nodeBelonging != -1) {
//fills rootBranches to exclude, if including the root then rootBranches should be empty.
if (!params->includeRoot) { getRoot2(params->m, params->t, nodeBelonging, params->namesOfGroupCombos[h], rootBranches); }
for(int i=0;i<params->t->getNumNodes();i++){
if (params->m->getControl_pressed()) { break; }
//pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
//pcountSize = 2, not unique to one group
//pcountSize = 1, unique to one group
int pcountSize = 0;
for (int j = 0; j < params->namesOfGroupCombos[h].size(); j++) {
map<string, int>::iterator itGroup = params->t->tree[i].pcount.find(params->namesOfGroupCombos[h][j]);
if (itGroup != params->t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
//unique calc
if (pcountSize == 0) { }
else if (!params->util.isEqual(params->t->tree[i].getBranchLength(), -1) && (pcountSize == 1) && (rootBranches.count(i) == 0)) { //you have a unique branch length and you are not the root
UniqueBL += abs(params->t->tree[i].getBranchLength());
}
//total calc
if (pcountSize == 0) { }
else if (!params->util.isEqual(params->t->tree[i].getBranchLength(), -1) && (pcountSize != 0) && (rootBranches.count(i) == 0)) { //you have a branch length and you are not the root
totalBL += abs(params->t->tree[i].getBranchLength());
}
}
UW = (UniqueBL / totalBL);
if (isnan(UW) || isinf(UW)) { UW = 0; }
params->results[params->count] = UW;
}
params->count++;
}
}
catch(exception& e) {
params->m->errorOut(e, "Unweighted", "driverUnweighted");
exit(1);
}
}
/**************************************************************************************************/
EstOutput Unweighted::createProcesses(Tree* t) {
try {
vector<linePair> lines;
int remainingPairs = namesOfGroupCombos.size();
if (remainingPairs < processors) { processors = remainingPairs; }
int startIndex = 0;
for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
int numPairs = remainingPairs; //case for last processor
if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
lines.push_back(linePair(startIndex, numPairs)); //startIndex, numPairs
startIndex = startIndex + numPairs;
remainingPairs = remainingPairs - numPairs;
}
//create array of worker threads
vector<std::thread*> workerThreads;
vector<unweightedData*> data;
vector<string> Treenames; Treenames = t->getTreeNames();
CountTable* ct = t->getCountTable();
//Lauch worker threads
for (int i = 0; i < processors-1; i++) {
CountTable* copyCount = new CountTable();
copyCount->copy(ct);
Tree* copyTree = new Tree(copyCount, Treenames);
copyTree->getCopy(t);
unweightedData* dataBundle = new unweightedData(lines[i+1].start, lines[i+1].end, namesOfGroupCombos, copyTree, copyCount, includeRoot);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(driverUnweighted, dataBundle));
}
CountTable* copyCount = new CountTable();
copyCount->copy(ct);
Tree* copyTree = new Tree(copyCount, Treenames);
copyTree->getCopy(t);
unweightedData* dataBundle = new unweightedData(lines[0].start, lines[0].end, namesOfGroupCombos, t, ct, includeRoot);
driverUnweighted(dataBundle);
EstOutput results = dataBundle->results;
delete copyTree; delete copyCount;
delete dataBundle;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
for (int j = 0; j < data[i]->results.size(); j++) { results.push_back(data[i]->results[j]); }
if (data[i]->count != data[i]->num) { //you didn't complete your tasks
m->mothurOut("[ERROR]: thread " + toString(i+1) + " failed to complete it's tasks, quitting.\n");
m->setControl_pressed(true);
}
delete data[i]->t; delete data[i]->ct; delete data[i]; delete workerThreads[i];
}
return results;
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "createProcesses");
exit(1);
}
}
/**************************************************************************************************/
EstOutput Unweighted::getValues(Tree* t, vector<vector<int> >& randomTreeNodes, int p) {
try {
processors = p;
return (createProcesses(t, randomTreeNodes));
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "getValues");
exit(1);
}
}
/**************************************************************************************************/
void driverRandomCalcs(unweightedData* params) {
try {
params->count = 0;
vector<string> Treenames = params->t->getTreeNames();
Tree* copyTree = new Tree(params->ct, Treenames);
for (int h = params->start; h < (params->start+params->num); h++) {
if (params->m->getControl_pressed()) { break; }
//copy random tree passed in
copyTree->getCopy(params->t);
//swap labels in the groups you want to compare
copyTree->assembleRandomUnifracTree(params->randomizedTreeNodes[h]);
double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
double totalBL = 0.00; //all branch lengths
double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
//find a node that belongs to one of the groups in this combo
set<int> rootBranches; //if not including root this will hold branches that are "above" the root for this comparison
int nodeBelonging = findNodeBelonging(params->m, params->namesOfGroupCombos[h], params->t->groupNodeInfo);
if (nodeBelonging != -1) {
//fills rootBranches to exclude, if including the root then rootBranches should be empty.
if (!params->includeRoot) { getRoot2(params->m, params->t, nodeBelonging, params->namesOfGroupCombos[h], rootBranches); }
for(int i=0;i<copyTree->getNumNodes();i++){
if (params->m->getControl_pressed()) { break; }
//pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
//pcountSize = 2, not unique to one group
//pcountSize = 1, unique to one group
int pcountSize = 0;
for (int j = 0; j < params->namesOfGroupCombos[h].size(); j++) {
map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(params->namesOfGroupCombos[h][j]);
if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
//unique calc
if (pcountSize == 0) { }
else if (!params->util.isEqual(copyTree->tree[i].getBranchLength(), -1) && (pcountSize == 1) && (rootBranches.count(i) == 0)) { //you have a unique branch length and you are not the root
UniqueBL += abs(copyTree->tree[i].getBranchLength());
}
//total calc
if (pcountSize == 0) { }
else if (!params->util.isEqual(copyTree->tree[i].getBranchLength(), -1) && (pcountSize != 0) && (rootBranches.count(i) == 0)) { //you have a branch length and you are not the root
totalBL += abs(copyTree->tree[i].getBranchLength());
}
}
UW = (UniqueBL / totalBL);
if (isnan(UW) || isinf(UW)) { UW = 0; }
params->results[params->count] = UW;
}
params->count++;
}
delete copyTree;
}
catch(exception& e) {
params->m->errorOut(e, "Unweighted", "driverRandomCalcs");
exit(1);
}
}
/**************************************************************************************************/
EstOutput Unweighted::createProcesses(Tree* t, vector<vector<int> >& randomTreeNodes) {
try {
vector<linePair> lines;
int remainingPairs = namesOfGroupCombos.size();
if (remainingPairs < processors) { processors = remainingPairs; }
int startIndex = 0;
for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
int numPairs = remainingPairs; //case for last processor
if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
lines.push_back(linePair(startIndex, numPairs)); //startIndex, numPairs
startIndex = startIndex + numPairs;
remainingPairs = remainingPairs - numPairs;
}
//create array of worker threads
vector<std::thread*> workerThreads;
vector<unweightedData*> data;
vector<string> Treenames; Treenames = t->getTreeNames();
CountTable* ct = t->getCountTable();
//Lauch worker threads
for (int i = 0; i < processors-1; i++) {
CountTable* copyCount = new CountTable();
copyCount->copy(ct);
Tree* copyTree = new Tree(copyCount, Treenames);
copyTree->getCopy(t);
unweightedData* dataBundle = new unweightedData(lines[i+1].start, lines[i+1].end, namesOfGroupCombos, copyTree, copyCount, includeRoot, randomTreeNodes);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(driverRandomCalcs, dataBundle));
}
unweightedData* dataBundle = new unweightedData(lines[0].start, lines[0].end, namesOfGroupCombos, t, ct, includeRoot, randomTreeNodes);
driverRandomCalcs(dataBundle);
EstOutput results = dataBundle->results;
delete dataBundle;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
for (int j = 0; j < data[i]->results.size(); j++) { results.push_back(data[i]->results[j]); }
if (data[i]->count != data[i]->num) { //you didn't complete your tasks
m->mothurOut("[ERROR]: thread " + toString(i+1) + " failed to complete it's tasks, quitting.\n");
m->setControl_pressed(true);
}
delete data[i]->t;
delete data[i]->ct;
delete data[i];
delete workerThreads[i];
}
return results;
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "createProcesses");
exit(1);
}
}
/**************************************************************************************************/
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