EstOutput JAbund::getValues(vector<SharedRAbundVector*> shared) {
try {
EstOutput UVest;
UVest.resize(2,0);
data.resize(1,0);
UVest = uv->getUVest(shared);
//UVest[0] is Uest UVest[1] is Vest
data[0] = 1.0-(UVest[0] * UVest[1]) / ((float)(UVest[0] + UVest[1] - (UVest[0] * UVest[1])));
if(data[0] > 1){data[0] = 0; }
if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
return data;
}
catch(exception& e) {
m->errorOut(e, "JAbund", "getValues");
exit(1);
}
}
EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
try {
int process = 1;
vector<int> processIDS;
EstOutput results;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
EstOutput myresults;
myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
if (m->control_pressed) { exit(0); }
//pass numSeqs to parent
ofstream out;
string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
m->openOutputFile(tempFile, out);
out << myresults.size() << endl;
for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
}
}
results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
if (m->control_pressed) { return results; }
//get data created by processes
for (int i=0;i<processIDS.size();i++) {
ifstream in;
string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
m->openInputFile(s, in);
//get scores
if (!in.eof()) {
int num;
in >> num; m->gobble(in);
if (m->control_pressed) { break; }
double w;
for (int j = 0; j < num; j++) {
in >> w;
results.push_back(w);
}
m->gobble(in);
}
in.close();
m->mothurRemove(s);
}
#else
//fill in functions
vector<parsData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
vector<CountTable*> cts;
vector<Tree*> trees;
//Create processor worker threads.
for( int i=1; i<processors; i++ ){
CountTable* copyCount = new CountTable();
copyCount->copy(ct);
Tree* copyTree = new Tree(copyCount);
copyTree->getCopy(t);
cts.push_back(copyCount);
trees.push_back(copyTree);
parsData* temppars = new parsData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount);
pDataArray.push_back(temppars);
processIDS.push_back(i);
hThreadArray[i-1] = CreateThread(NULL, 0, MyParsimonyThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
}
results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); }
delete cts[i];
delete trees[i];
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
return results;
}
EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
try {
EstOutput results;
vector<double> D;
int count = 0;
for (int h = start; h < (start+num); h++) {
if (m->control_pressed) { return results; }
//initialize weighted score
string groupA = namesOfGroupCombos[h][0];
string groupB = namesOfGroupCombos[h][1];
set<int> validBranches;
WScore[groupA+groupB] = 0.0;
D.push_back(0.0000); //initialize a spot in D for each combination
//adding the wieghted sums from group i
for (int j = 0; j < t->groupNodeInfo[groupA].size(); j++) { //the leaf nodes that have seqs from group i
map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupA][j]].pcount.find(groupA);
int numSeqsInGroupI = it->second;
double sum = getLengthToRoot(t, t->groupNodeInfo[groupA][j], groupA, groupB);
double weightedSum = ((numSeqsInGroupI * sum) / (double)ct->getGroupCount(groupA));
D[count] += weightedSum;
}
//adding the wieghted sums from group l
for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l
map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
int numSeqsInGroupL = it->second;
double sum = getLengthToRoot(t, t->groupNodeInfo[groupB][j], groupA, groupB);
double weightedSum = ((numSeqsInGroupL * sum) / (double)ct->getGroupCount(groupB));
D[count] += weightedSum;
}
count++;
}
//calculate u for the group comb
for (int h = start; h < (start+num); h++) {
//report progress
//m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
string groupA = namesOfGroupCombos[h][0];
string groupB = namesOfGroupCombos[h][1];
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
if (m->control_pressed) { return data; }
double u;
//int pcountSize = 0;
//does this node have descendants from groupA
it = t->tree[i].pcount.find(groupA);
//if it does u = # of its descendants with a certain group / total number in tree with a certain group
if (it != t->tree[i].pcount.end()) {
u = (double) t->tree[i].pcount[groupA] / (double) ct->getGroupCount(groupA);
}else { u = 0.00; }
//does this node have descendants from group l
it = t->tree[i].pcount.find(groupB);
//if it does subtract their percentage from u
if (it != t->tree[i].pcount.end()) {
u -= (double) t->tree[i].pcount[groupB] / (double) ct->getGroupCount(groupB);
}
if (includeRoot) {
if (t->tree[i].getBranchLength() != -1) {
u = abs(u * t->tree[i].getBranchLength());
WScore[(groupA+groupB)] += u;
}
}else {
//if this is not the root then add it
if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) {
if (t->tree[i].getBranchLength() != -1) {
u = abs(u * t->tree[i].getBranchLength());
WScore[(groupA+groupB)] += u;
}
}
}
}
}
/********************************************************/
//calculate weighted score for the group combination
double UN;
count = 0;
for (int h = start; h < (start+num); h++) {
UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
if (isnan(UN) || isinf(UN)) { UN = 0; }
results.push_back(UN);
count++;
}
return results;
}
catch(exception& e) {
m->errorOut(e, "Weighted", "driver");
exit(1);
}
}
EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
try {
int process = 1;
vector<int> processIDS;
bool recalc = false;
EstOutput results;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
pid_t pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
EstOutput myresults;
myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
if (m->control_pressed) { exit(0); }
//pass numSeqs to parent
ofstream out;
string tempFile = outputDir + m->mothurGetpid(process) + ".unweighted.results.temp";
m->openOutputFile(tempFile, out);
out << myresults.size() << endl;
for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the number of processes you requested, reducing number to " + toString(process) + "\n"); processors = process;
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
//wait to die
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
m->control_pressed = false;
for (int i=0;i<processIDS.size();i++) {
m->mothurRemove(outputDir + (toString(processIDS[i]) + ".unweighted.results.temp"));
}
recalc = true;
break;
}
}
if (recalc) {
//test line, also set recalc to true.
//for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; wait(&temp); } m->control_pressed = false; for (int i=0;i<processIDS.size();i++) {m->mothurRemove(outputDir + (toString(processIDS[i]) + ".unweighted.results.temp"));}processors=3; m->mothurOut("[ERROR]: unable to spawn the number of processes you requested, reducing number to " + toString(processors) + "\n");
//if the users enters no groups then give them the score of all groups
int numGroups = m->getNumGroups();
//calculate number of comparsions
int numComp = 0;
vector< vector<string> > namesOfGroupCombos;
for (int r=0; r<numGroups; r++) {
for (int l = 0; l < r; l++) {
numComp++;
vector<string> groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
namesOfGroupCombos.push_back(groups);
}
}
if (numComp != 1) {
vector<string> groups;
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
if ((ct->getNamesOfGroups())[i] != "xxx") {
groups.push_back((ct->getNamesOfGroups())[i]);
}
}
namesOfGroupCombos.push_back(groups);
}else {
for (int i = 0; i < m->getNumGroups(); i++) {
groups.push_back((m->getGroups())[i]);
}
namesOfGroupCombos.push_back(groups);
}
}
lines.clear();
int remainingPairs = namesOfGroupCombos.size();
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;
}
results.clear();
processIDS.resize(0);
process = 1;
//loop through and create all the processes you want
while (process != processors) {
pid_t pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
EstOutput myresults;
myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
if (m->control_pressed) { exit(0); }
//pass numSeqs to parent
ofstream out;
string tempFile = outputDir + m->mothurGetpid(process) + ".unweighted.results.temp";
m->openOutputFile(tempFile, out);
out << myresults.size() << endl;
for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
}
}
}
results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
int temp = processIDS[i];
wait(&temp);
}
if (m->control_pressed) { return results; }
//get data created by processes
for (int i=0;i<(processors-1);i++) {
ifstream in;
string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
m->openInputFile(s, in);
//get quantiles
if (!in.eof()) {
int num;
in >> num; m->gobble(in);
if (m->control_pressed) { break; }
double w;
for (int j = 0; j < num; j++) {
in >> w;
results.push_back(w);
}
m->gobble(in);
}
in.close();
m->mothurRemove(s);
}
#else
//fill in functions
vector<unweightedData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
vector<CountTable*> cts;
vector<Tree*> trees;
//Create processor worker threads.
for( int i=1; i<processors; i++ ){
CountTable* copyCount = new CountTable();
copyCount->copy(ct);
Tree* copyTree = new Tree(copyCount);
copyTree->getCopy(t);
cts.push_back(copyCount);
trees.push_back(copyTree);
unweightedData* tempweighted = new unweightedData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount, includeRoot);
pDataArray.push_back(tempweighted);
processIDS.push_back(i);
hThreadArray[i-1] = CreateThread(NULL, 0, MyUnWeightedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
}
results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); }
delete cts[i];
delete trees[i];
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
return results;
}