for (int i = 0; i < processors; i++) {
int startPos = i * numPairsPerProcessor;
+
if(i == processors - 1){
numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
- lines.push_back(new linePair(startPos, numPairsPerProcessor));
+
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
data = createProcesses(t, namesOfGroupCombos);
-
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ lines.clear();
}
#else
data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
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);
if (m->control_pressed) { exit(0); }
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num);
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
int count = 0;
int total = num;
int twentyPercent = (total * 0.20);
-
+ if (twentyPercent == 0) { twentyPercent = 1; }
+
for (int h = start; h < (start+num); h++) {
if (m->control_pressed) { return results; }
totalBL += abs(t->tree[i].getBranchLength());
}
}
-
+
UW = (UniqueBL / totalBL);
if (isnan(UW) || isinf(UW)) { UW = 0; }
count++;
//report progress
- if((count) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ if((count % twentyPercent) == 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
}
- m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
+ //report progress
+ if((count % twentyPercent) != 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
return results;
}
}
/**************************************************************************************************/
-EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
+EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
try {
- globaldata = GlobalData::getInstance();
+ globaldata = GlobalData::getInstance();
+ processors = p;
+ outputDir = o;
+
- vector<string> groups;
- double UniqueBL; //a branch length is unique if it's chidren are from the same group
- double totalBL; //all branch lengths
- double UW; //Unweighted Value = UniqueBL / totalBL;
- copyTree = new Tree;
-
//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.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++) {
numComp++;
- }
- }
-
- //numComp+1 for AB, AC, BC, ABC
- data.resize(numComp+1,0);
-
- int count = 0;
- for (int a=0; a<numGroups; a++) {
- for (int l = a+1; l < numGroups; l++) {
- UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- totalBL = 0.00; //all branch lengths
- UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
-
- //copy random tree passed in
- copyTree->getCopy(t);
-
- //groups in this combo
- groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
-
- //swap labels in the groups you want to compare
- copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
-
- if (m->control_pressed) { delete copyTree; return data; }
-
- for(int i=0;i<copyTree->getNumNodes();i++){
-
- if (m->control_pressed) { return data; }
-
- //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 < groups.size(); j++) {
- map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
- if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; }
- }
-
- if (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
-
- if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(copyTree->tree[i].getBranchLength());
- }
- }
-
-
- UW = (UniqueBL / totalBL);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- data[count] = UW;
- count++;
- groups.clear();
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[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 < tmap->namesOfGroups.size(); i++) {
groups.push_back(tmap->namesOfGroups[i]);
}
}
+ namesOfGroupCombos.push_back(groups);
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
groups.push_back(globaldata->Groups[i]);
}
+ namesOfGroupCombos.push_back(groups);
}
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ }else{
+ 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, true);
+
+ lines.clear();
+ }
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ #endif
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
- UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- totalBL = 0.00; //all branch lengths
- UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ EstOutput results;
+
+ //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, usingGroups);
+
+ if (m->control_pressed) { exit(0); }
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputDir + toString(getpid()) + ".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("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
+
+ //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();
+ remove(s.c_str());
+ }
+
+ return results;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
+ try {
+
+ EstOutput results; results.resize(num);
+
+ int count = 0;
+ int total = num;
+ int twentyPercent = (total * 0.20);
+
+ Tree* copyTree = new Tree;
+
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { return results; }
//copy random tree passed in
copyTree->getCopy(t);
- //swap labels in all the groups you want to compare
- copyTree->assembleRandomUnifracTree(groups);
+ //swap labels in the groups you want to compare
+ copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
- if (m->control_pressed) { delete copyTree; return data; }
-
- for(int i=0;i<copyTree->getNumNodes();i++){
+ 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;
+
+ for(int i=0;i<t->getNumNodes();i++){
if (m->control_pressed) { return data; }
//pcountSize = 1, unique to one group
int pcountSize = 0;
- for (int j = 0; j < groups.size(); j++) {
- map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
- if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
+ for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
+ map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
+ if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
if (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
- if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(copyTree->tree[i].getBranchLength());
+ if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(t->tree[i].getBranchLength());
}
}
if (isnan(UW) || isinf(UW)) { UW = 0; }
- data[count] = UW;
+ results[count] = UW;
+ count++;
+
}
delete copyTree;
- return data;
-
+ return results;
}
catch(exception& e) {
- m->errorOut(e, "Unweighted", "getValues");
+ m->errorOut(e, "Unweighted", "driver");
exit(1);
}
}
-
/**************************************************************************************************/
projects / mothur.git / blobdiff