#include "parsimony.h"
/**************************************************************************************************/
-EstOutput Parsimony::getValues(Tree* t) {
+
+EstOutput Parsimony::getValues(Tree* t, int p, string o) {
try {
- data.resize(1,0);
+ processors = p;
+ outputDir = o;
+ CountTable* ct = t->getCountTable();
+
+ //if the users enters no groups then give them the score of all groups
+ 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 = 0; l < r; l++) {
+ numComp++;
+ 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);
+ }
+ }
+
+ //numComp+1 for AB, AC, BC, ABC
+ if (numComp != 1) {
+ vector<string> groups;
+ if (numGroups == 0) {
+ //get score for all users groups
+ 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 < mGroups.size(); i++) {
+ groups.push_back(mGroups[i]);
+ //cout << globaldata->Groups[i] << endl;
+ }
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
+
+ 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;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Parsimony", "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();
- int score = 0;
+ 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; }
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
- int lc = t->tree[i].getLChild();
- int rc = t->tree[i].getRChild();
+ //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);
- if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
- score++;
+ //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;
- data[0] = score;
+ //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]);
+ }
- return data;
+ 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;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Parsimony", "createProcesses");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+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(ct);
+ int count = 0;
+
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { delete copyTree; return results; }
+
+ int score = 0;
+
+ //groups in this combo
+ vector<string> groups = namesOfGroupCombos[h];
+
+ //copy users tree so that you can redo pgroups
+ copyTree->getCopy(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 (m->control_pressed) { return data; }
+
+ 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++;
+ }
+ }
+
+ results[count] = score;
+ count++;
+ }
+
+ delete copyTree;
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Parsimony", "driver");
exit(1);
}
-
}
+
/**************************************************************************************************/
+
projects / mothur.git / blobdiff