/**************************************************************************************************/
-EstOutput Unweighted::getValues(Tree* t) {
+EstOutput Unweighted::getValues(Tree* t, int p, string o) {
try {
-
- //clear out old values
- data.resize(1,0);
- penalty.resize(t->getNumLeaves(), 0);
-
- map<string,double> unique; //group, total of all branch lengths of nodes with that group.
- double shared = 0.0000;
- double UW=0.0000;
-
- //add up the branch lengths for each group.
- for(int i=0;i<t->getNumLeaves();i++){
- if(t->tree[i].pGroups.size() > 0){
- unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+ globaldata = GlobalData::getInstance();
+ processors = p;
+ outputDir = o;
+
+ //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 = 0; l < r; l++) {
+ numComp++;
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ namesOfGroupCombos.push_back(groups);
}
}
- //for each non-leaf node
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ if (numComp != 1) {
+ 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]);
+ }
+ }
+ 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());
+ }else{
+ int numPairs = namesOfGroupCombos.size();
+
+ int numPairsPerProcessor = numPairs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
- //get penalty values
- if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+ if(i == processors - 1){
+ numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
+ }
+
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+ data = createProcesses(t, namesOfGroupCombos);
+ lines.clear();
}
- else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ #endif
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ vector<int> processIDS;
+
+ 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);
+
+ if (m->control_pressed) { exit(0); }
+
+ m->mothurOut("Merging results."); m->mothurOutEndLine();
+
+ //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("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
}
- else{
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+ }
+
+ 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 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());
+ }
+
+ m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ 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) {
+ try {
+
+ EstOutput results; results.resize(num);
+
+ int count = 0;
+ int numLeaves = t->getNumLeaves();
+ int total = num;
+ int twentyPercent = (total * 0.20);
+ if (twentyPercent == 0) { twentyPercent = 1; }
+
+
+ for (int h = start; h < (start+num); h++) {
+ //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;
+ if (m->control_pressed) { return results; }
+
+ 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;
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
+ map<int, int>::iterator itCount;
+
+ for(int i=0;i<t->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 < 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; } }
+ }
+
+ nodePcountSize[i] = pcountSize;
+
+ //cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t';
+ if (pcountSize == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
+
+ //if you are a leaf from a users group add to total
+ if (i < numLeaves) {
+ if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {
+ //cout << "added to total" << endl;
+ totalBL += abs(t->tree[i].getBranchLength());
+ }
+ tempTotals[i] = 0.0; //we don't care about you, or we have already added you
+ }else{ //if you are not a leaf
+ //do both your chidren have have descendants from the users groups?
+ int lc = t->tree[i].getLChild();
+ int rc = t->tree[i].getRChild();
+
+ //if yes, add your childrens tempTotals
+ if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+ totalBL += tempTotals[lc] + tempTotals[rc];
+ //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+ if (t->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = abs(t->tree[i].getBranchLength());
+ }else {
+ tempTotals[i] = 0.0;
+ }
+ }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you
+ }else { //if no, your tempTotal is your childrens temp totals + your branch length
+ if (t->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength());
+ }else {
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc];
+ }
+ }
+ //cout << "temptotal = "<< tempTotals[i] << endl;
+ }
- //not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
- if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
- shared -= 1;
- }
- else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
- shared += t->tree[i].getBranchLength();
}
- else if( t->tree[i].pGroups.size() != 0){
- unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+ //cout << UniqueBL << '\t' << totalBL << endl;
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ results[count] = UW;
+ count++;
+
+ //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(); }
+ }
+
+ //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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "driver");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
+ try {
+ globaldata = GlobalData::getInstance();
+ processors = p;
+ outputDir = o;
+
+
+ //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 = 0; l < r; l++) {
+ numComp++;
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ namesOfGroupCombos.push_back(groups);
}
}
-
- map<string,double>::iterator pos;
- for(pos=unique.begin();pos!=unique.end();pos++){
- if(pos->first!="xxx"){
- UW += unique[pos->first];
+
+ if (numComp != 1) {
+ 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]);
+ }
+ }
+ 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
- UW /= (UW + shared);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- data[0] = UW;
-
return data;
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Unweighted", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ vector<int> processIDS;
+
+ 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("[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, 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 numLeaves = t->getNumLeaves();
+
+ 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 the groups you want to compare
+ copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
+
+ 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;
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
+
+ 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 < namesOfGroupCombos[h].size(); j++) {
+ map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
+ if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
+ }
+
+ nodePcountSize[i] = pcountSize;
+
+ if (pcountSize == 0) { }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+
+ //if you are a leaf from a users group add to total
+ if (i < numLeaves) {
+ if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) {
+ totalBL += abs(copyTree->tree[i].getBranchLength());
+ }
+ tempTotals[i] = 0.0; //we don't care about you, or we have already added you
+ }else{ //if you are not a leaf
+ //do both your chidren have have descendants from the users groups?
+ int lc = copyTree->tree[i].getLChild();
+ int rc = copyTree->tree[i].getRChild();
+
+ //if yes, add your childrens tempTotals
+ if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+ totalBL += tempTotals[lc] + tempTotals[rc];
+
+ if (copyTree->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
+ }else {
+ tempTotals[i] = 0.0;
+ }
+ }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you
+ }else { //if no, your tempTotal is your childrens temp totals + your branch length
+ if (t->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength());
+ }else {
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc];
+ }
+ }
+
+ }
+ }
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ results[count] = UW;
+ count++;
+
+ }
+
+ delete copyTree;
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "driver");
+ exit(1);
+ }
}
+/**************************************************************************************************/
+
-/**************************************************************************************************/
\ No newline at end of file
projects / mothur.git / blobdiff