/**************************************************************************************************/
-EstOutput Unweighted::getValues(Tree* t) {
+EstOutput Unweighted::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 = m->getNumGroups();
- //clear out old values
- data.resize(1,0);
- penalty.resize(t->getNumLeaves(), 0);
+ //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((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
- map<string,double> unique; //group, total of all branch lengths of nodes with that group.
- double shared = 0.0000;
- double UW=0.0000;
+ if (numComp != 1) {
+ vector<string> groups;
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
+ if ((ct->getNamesOfGroups())[i] != "xxx") {
+ groups.push_back((ct->getNamesOfGroups())[i]);
+ }
+ }
+ namesOfGroupCombos.push_back(groups);
+ }else {
+ for (int i = 0; i < m->getNumGroups(); i++) {
+ groups.push_back((m->getGroups())[i]);
+ }
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
+ }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;
+ }
- //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();
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+ data = createProcesses(t, namesOfGroupCombos, ct);
+ lines.clear();
}
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
+ #endif
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ 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, ct);
+
+ 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);
+ }
+ }
+
+ 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<(processors-1);i++) {
+ int temp = processIDS[i];
+ wait(&temp);
}
- //for each non-leaf node
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ if (m->control_pressed) { return results; }
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ //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 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()]);
+ //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);
}
- 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);
+ in.close();
+ m->mothurRemove(s);
+ }
+
+ //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, CountTable* ct) {
+ try {
+
+
+ EstOutput results; results.resize(num);
+
+ 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; }
+
+ 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;
+
+ //find a node that belongs to one of the groups in this combo
+ int nodeBelonging = -1;
+ for (int g = 0; g < namesOfGroupCombos[h].size(); g++) {
+ if (t->groupNodeInfo[namesOfGroupCombos[h][g]].size() != 0) { nodeBelonging = t->groupNodeInfo[namesOfGroupCombos[h][g]][0]; break; }
}
- else{
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+
+ //sanity check
+ if (nodeBelonging == -1) {
+ m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
+ for (int g = 0; g < namesOfGroupCombos[h].size()-1; g++) { m->mothurOut(namesOfGroupCombos[h][g] + "-"); }
+ m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
+ m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
+ }else{
+ //cout << "trying to get root" << endl;
+ //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
+ getRoot(t, nodeBelonging, namesOfGroupCombos[h]);
+ //cout << "here" << endl;
+ for(int i=0;i<t->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+ //cout << i << endl;
+ //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; } }
+ }
+
+
+ //unique calc
+ if (pcountSize == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root
+ UniqueBL += abs(t->tree[i].getBranchLength());
+ }
+
+ //total calc
+ if (pcountSize == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root
+ totalBL += abs(t->tree[i].getBranchLength());
+ }
+ }
+ //cout << UniqueBL << '\t' << totalBL << endl;
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ results[count] = UW;
}
+ count++;
- //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();
+ //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 {
+ processors = p;
+ outputDir = o;
+
+ CountTable* ct = t->getCountTable();
+
+ //if the users enters no groups then give them the score of all groups
+ int numGroups = m->getNumGroups();
+
+ //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((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
+ namesOfGroupCombos.push_back(groups);
}
}
-
- map<string,double>::iterator pos;
- for(pos=unique.begin();pos!=unique.end();pos++){
- if((pos->first!="xxx") && (inUsersGroups(pos->first))){
- UW += unique[pos->first];
+
+ if (numComp != 1) {
+ vector<string> groups;
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
+ if ((ct->getNamesOfGroups())[i] != "xxx") {
+ groups.push_back((ct->getNamesOfGroups())[i]);
+ }
+ }
+ namesOfGroupCombos.push_back(groups);
+ }else {
+ for (int i = 0; i < m->getNumGroups(); i++) {
+ groups.push_back((m->getGroups())[i]);
+ }
+ namesOfGroupCombos.push_back(groups);
}
}
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
+ }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, ct);
+
+ lines.clear();
+ }
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
+ #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, CountTable* ct) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ 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, ct);
+
+ 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, ct);
+
+ //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();
+ m->mothurRemove(s);
+ }
+
+ return results;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "createProcesses");
exit(1);
}
-
}
-
/**************************************************************************************************/
-bool Unweighted::inUsersGroups(string groupname) {
- try {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (groupname == globaldata->Groups[i]) { return true; }
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups, CountTable* ct) {
+ try {
+
+ EstOutput results; results.resize(num);
+
+ int count = 0;
+
+ Tree* copyTree = new Tree(ct);
+
+ 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;
+ //find a node that belongs to one of the groups in this combo
+ int nodeBelonging = -1;
+ for (int g = 0; g < namesOfGroupCombos[h].size(); g++) {
+ if (copyTree->groupNodeInfo[namesOfGroupCombos[h][g]].size() != 0) { nodeBelonging = copyTree->groupNodeInfo[namesOfGroupCombos[h][g]][0]; break; }
+ }
+
+ //sanity check
+ if (nodeBelonging == -1) {
+ m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
+ for (int g = 0; g < namesOfGroupCombos[h].size()-1; g++) { m->mothurOut(namesOfGroupCombos[h][g] + "-"); }
+ m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
+ m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
+ }else{
+
+ //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
+ getRoot(copyTree, nodeBelonging, namesOfGroupCombos[h]);
+
+ 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; } }
+ }
+
+ //unique calc
+ if (pcountSize == 0) { }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root
+ UniqueBL += abs(copyTree->tree[i].getBranchLength());
+ }
+
+ //total calc
+ if (pcountSize == 0) { }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root
+ totalBL += abs(copyTree->tree[i].getBranchLength());
+ }
+
+ }
+ //cout << UniqueBL << '\t' << totalBL << endl;
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ results[count] = UW;
+ }
+ count++;
+
}
- return false;
+
+ delete copyTree;
+
+ return results;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Unweighted", "driver");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Unweighted class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) {
+ try {
+ //you are a leaf so get your parent
+ int index = t->tree[v].getParent();
+
+ if (includeRoot) {
+ rootForGrouping[grouping].clear();
+ }else {
+
+ //my parent is a potential root
+ rootForGrouping[grouping].insert(index);
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+ //cout << index << endl;
+ if (m->control_pressed) { return 0; }
+
+ //am I the root for this grouping? if so I want to stop "early"
+ //does my sibling have descendants from the users groups?
+ //if so I am not the root
+ int parent = t->tree[index].getParent();
+ int lc = t->tree[parent].getLChild();
+ int rc = t->tree[parent].getRChild();
+
+ int sib = lc;
+ if (lc == index) { sib = rc; }
+
+ map<string, int>::iterator itGroup;
+ int pcountSize = 0;
+ for (int j = 0; j < grouping.size(); j++) {
+ map<string, int>::iterator itGroup = t->tree[sib].pcount.find(grouping[j]);
+ if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
+ }
+
+ //if yes, I am not the root
+ if (pcountSize != 0) {
+ rootForGrouping[grouping].clear();
+ rootForGrouping[grouping].insert(parent);
+ }
+
+ index = parent;
+ }
+
+ //get all nodes above the root to add so we don't add their u values above
+ index = *(rootForGrouping[grouping].begin());
+ while(t->tree[index].getParent() != -1){
+ int parent = t->tree[index].getParent();
+ rootForGrouping[grouping].insert(parent);
+ //cout << parent << " in root" << endl;
+ index = parent;
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "getRoot");
exit(1);
}
-}
\ No newline at end of file
+}
+/**************************************************************************************************/
+
+
projects / mothur.git / blobdiff