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/*
* parsimony.cpp
* Mothur
*
* Created by Sarah Westcott on 1/26/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "parsimony.h"
/**************************************************************************************************/
Parsimony::Parsimony(vector<string> G) : 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, "Parsimony", "Parsimony");
exit(1);
}
}
/**************************************************************************************************/
EstOutput Parsimony::getValues(Tree* t, int p, string o) {
try {
processors = p; outputDir = o;
CountTable* ct = t->getCountTable();
Treenames = t->getTreeNames();
return (createProcesses(t, ct));
}
catch(exception& e) {
m->errorOut(e, "Parsimony", "getValues");
exit(1);
}
}
/**************************************************************************************************/
void driverPars(parsData* params) {
try {
Tree copyTree(params->ct, params->Treenames);
int count = 0;
for (int h = params->start; h < (params->start+params->num); h++) {
if (params->m->getControl_pressed()) { break; }
int score = 0;
//groups in this combo
vector<string> groups = params->namesOfGroupCombos[h];
//copy users tree so that you can redo pgroups
copyTree.getCopy(params->t);
//create pgroups that reflect the groups the user want to use
for(int i=copyTree.getNumLeaves();i<copyTree.getNumNodes();i++){
copyTree.tree[i].pGroups = (copyTree.mergeUserGroups(i, groups));
}
for(int i=copyTree.getNumLeaves();i<copyTree.getNumNodes();i++){
if (params->m->getControl_pressed()) { break; }
int lc = copyTree.tree[i].getLChild();
int rc = copyTree.tree[i].getRChild();
int iSize = copyTree.tree[i].pGroups.size();
int rcSize = copyTree.tree[rc].pGroups.size();
int lcSize = copyTree.tree[lc].pGroups.size();
//if isize are 0 then that branch is to be ignored
if (iSize == 0) { }
else if ((rcSize == 0) || (lcSize == 0)) { }
//if you have more groups than either of your kids then theres been a change.
else if(iSize > rcSize || iSize > lcSize){
score++;
}
}
params->results[count] = score;
count++;
}
}
catch(exception& e) {
params->m->errorOut(e, "Parsimony", "driver");
exit(1);
}
}
/**************************************************************************************************/
EstOutput Parsimony::createProcesses(Tree* t, CountTable* ct) {
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<parsData*> data;
//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);
parsData* dataBundle = new parsData(lines[i+1].start, lines[i+1].end, namesOfGroupCombos, copyTree, copyCount);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(driverPars, dataBundle));
}
parsData* dataBundle = new parsData(lines[0].start, lines[0].end, namesOfGroupCombos, t, ct);
driverPars(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]); }
delete data[i]->t;
delete data[i]->ct;
delete data[i];
delete workerThreads[i];
}
return results;
}
catch(exception& e) {
m->errorOut(e, "Parsimony", "createProcesses");
exit(1);
}
}
/**************************************************************************************************/
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