/**************************************************************************************************/
-EstOutput Unweighted::getValues(Tree* t) {
+EstOutput Unweighted::getValues(Tree* t, 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();
- //clear out old values
- data.resize(1,0);
+ //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++;
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
- float UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- float totalBL = 0.00; //all branch lengths
- float UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ 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;
+ if(i == processors - 1){
+ numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numPairsPerProcessor));
+ }
+
+ data = createProcesses(t, namesOfGroupCombos);
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ }
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ #endif
- map<string, int>::iterator it; //iterator to traverse pgroups
- map<string, int> copyLCpcount;
- map<string, int> copyRCpcount;
- map<string, int> copyIpcount;
-
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ 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;
+ int num = 0;
+ vector<int> processIDS;
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ EstOutput results;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
- /**********************************************************************/
- //This section adds in all lengths that are non leaf
+ 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("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ 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);
- //copy left childs pGroups and remove groups that the user doesn't want
- copyIpcount = t->tree[i].pcount;
- for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyIpcount.erase(it->first); }
+ //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 total = num;
+ int twentyPercent = (total * 0.20);
- //copy left childs pGroups and remove groups that the user doesn't want
- copyLCpcount = t->tree[lc].pcount;
- for (it = copyLCpcount.begin(); it != copyLCpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyLCpcount.erase(it->first); }
+ for (int h = start; h < (start+num); h++) {
+
+ 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;
+
+ 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; } }
+ }
+
+ if (pcountSize == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
+
+ if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(t->tree[i].getBranchLength());
+ }
}
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ results[count] = UW;
+ count++;
- //copy right childs pGroups and remove groups that the user doesn't want
- copyRCpcount = t->tree[rc].pcount;
- for (it = copyRCpcount.begin(); it != copyRCpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyRCpcount.erase(it->first); }
+ //report progress
+ if((count) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ }
+
+ m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "driver");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
+ try {
+ globaldata = GlobalData::getInstance();
+
+ 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;
+ 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; }
- //if i's children are from the same group and i has a BL then add i's length to unique
- //if copyRCpcount.size() = 0 && copyLCpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
- if ((copyRCpcount.size() == 0) && (copyLCpcount.size() == 0)) { }
- else {
- if ((copyRCpcount == copyLCpcount) && (t->tree[i].getBranchLength() != -1)) { UniqueBL += t->tree[i].getBranchLength(); }
- //if either childs groups = 0 then all of there groups were not valid making the parent unique
- else if (((copyRCpcount.size() == 0) || (copyLCpcount.size() == 0)) && (t->tree[i].getBranchLength() != -1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ data[count] = UW;
+ count++;
+ groups.clear();
}
-
- //add i's BL to total if it is from the groups the user wants
- if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ }
+
+
+ if (numComp != 1) {
+ 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]);
+ }
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups.push_back(globaldata->Groups[i]);
+ }
}
+
+ 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);
+
+ //swap labels in all the groups you want to compare
+ copyTree->assembleRandomUnifracTree(groups);
- /**********************************************************************/
- //This section adds in all lengths that are leaf
+ if (m->control_pressed) { delete copyTree; return data; }
+
+ for(int i=0;i<copyTree->getNumNodes();i++){
- //if i's chidren are leaves
- if (t->tree[rc].getRChild() == -1) {
- //if rc is a valid group and rc has a BL
- if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ 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 > 1) { break; } }
}
- }
-
- if (t->tree[lc].getLChild() == -1) {
- //if lc is a valid group and lc has a BL
- if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+
+ 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);
+ UW = (UniqueBL / totalBL);
- if (isnan(UW) || isinf(UW)) { UW = 0; }
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
- data[0] = UW;
+ data[count] = UW;
+ }
+
+ delete copyTree;
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";
- exit(1);
- }
-
}
+/**************************************************************************************************/
+
+
projects / mothur.git / blobdiff