EstOutput Parsimony::getValues(Tree* t, int p, string o) {
try {
- globaldata = GlobalData::getInstance();
processors = p;
outputDir = o;
+ CountTable* ct = t->getCountTable();
//if the users enters no groups then give them the score of all groups
- int numGroups = globaldata->Groups.size();
+ vector<string> mGroups = m->getGroups();
+ int numGroups = mGroups.size();
//calculate number of comparsions
int numComp = 0;
vector< vector<string> > namesOfGroupCombos;
for (int r=0; r<numGroups; r++) {
- for (int l = r+1; l < numGroups; l++) {
+ for (int l = 0; l < r; l++) {
numComp++;
- vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
//cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
namesOfGroupCombos.push_back(groups);
}
vector<string> groups;
if (numGroups == 0) {
//get score for all users groups
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- if (tmap->namesOfGroups[i] != "xxx") {
- groups.push_back(tmap->namesOfGroups[i]);
+ vector<string> tGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < tGroups.size(); i++) {
+ if (tGroups[i] != "xxx") {
+ groups.push_back(tGroups[i]);
//cout << tmap->namesOfGroups[i] << endl;
}
}
namesOfGroupCombos.push_back(groups);
}else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- groups.push_back(globaldata->Groups[i]);
+ for (int i = 0; i < mGroups.size(); i++) {
+ groups.push_back(mGroups[i]);
//cout << globaldata->Groups[i] << endl;
}
namesOfGroupCombos.push_back(groups);
}
}
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
- }else{
- lines.clear();
- int numPairs = namesOfGroupCombos.size();
-
- int numPairsPerProcessor = numPairs / processors;
-
- for (int i = 0; i < processors; i++) {
- int startPos = i * numPairsPerProcessor;
-
- if(i == processors - 1){
- numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
- }
-
- lines.push_back(linePair(startPos, numPairsPerProcessor));
- }
-
- data = createProcesses(t, namesOfGroupCombos);
- }
- #else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
- #endif
+
+ lines.clear();
+ int numPairs = namesOfGroupCombos.size();
+ int numPairsPerProcessor = numPairs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
+ if(i == processors - 1){ numPairsPerProcessor = numPairs - i * numPairsPerProcessor; }
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+
+ data = createProcesses(t, namesOfGroupCombos, ct);
return data;
}
/**************************************************************************************************/
-EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 1;
+ 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();
process++;
}else if (pid == 0){
EstOutput myresults;
- myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+ myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
if (m->control_pressed) { exit(0); }
}
}
- results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
+ 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++) {
m->gobble(in);
}
in.close();
- remove(s.c_str());
+ 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];
}
- return results;
#endif
+ return results;
}
catch(exception& e) {
m->errorOut(e, "Parsimony", "createProcesses");
}
}
/**************************************************************************************************/
-EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
+EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
try {
EstOutput results; results.resize(num);
- Tree* copyTree = new Tree();
+ Tree* copyTree = new Tree(ct);
int count = 0;
for (int h = start; h < (start+num); h++) {
projects / mothur.git / blobdiff