/**************************************************************************************************/
-EstOutput Weighted::getValues(Tree* t) {
+EstOutput Weighted::getValues(Tree* t, int p, string o) {
try {
globaldata = GlobalData::getInstance();
+
+ data.clear(); //clear out old values
int numGroups;
vector<double> D;
+ processors = p;
+ outputDir = o;
numGroups = globaldata->Groups.size();
+ if (m->control_pressed) { return data; }
+
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
- int count = 0;
+ vector< vector<string> > namesOfGroupCombos;
for (int i=0; i<numGroups; i++) {
- for (int l = i+1; l < numGroups; l++) {
+ for (int l = 0; l < i; l++) {
//initialize weighted scores
- WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
-
- D.push_back(0.0000); //initialize a spot in D for each combination
-
- /********************************************************/
- //calculate a D value for each group combo
- for(int v=0;v<t->getNumLeaves();v++){
- int index = v;
- double sum = 0.0000;
-
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
-
- //if you have a BL
- if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
- }
- index = t->tree[index].getParent();
- }
-
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
- }
-
- //is this sum from a sequence which is in one of the users groups
- if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
- //is this sum from a sequence which is in this groupCombo
- if ((t->tree[v].getGroup() == globaldata->Groups[i]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D[count] += sum;
- }
+ //WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
+ vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+ 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(linePair(startPos, numPairsPerProcessor));
}
- /*********************************************************/
- count++;
+
+ data = createProcesses(t, namesOfGroupCombos);
+
+ lines.clear();
}
- }
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ #endif
- data.clear(); //clear out old values
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Weighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ 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){
- for(int i=0;i<t->getNumNodes();i++){
- //calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
- for (int b=0; b<numGroups; b++) {
- for (int l = b+1; l < numGroups; l++) {
- //calculate a u value for each combo
- double u;
- //does this node have descendants from group b-1
- it = t->tree[i].pcount.find(globaldata->Groups[b]);
- //if it does u = # of its descendants with a certain group / total number in tree with a certain group
- if (it != t->tree[i].pcount.end()) {
- u = (double) t->tree[i].pcount[globaldata->Groups[b]] / (double) tmap->seqsPerGroup[globaldata->Groups[b]];
- }else { u = 0.00; }
-
- //does this node have descendants from group l
- it = t->tree[i].pcount.find(globaldata->Groups[l]);
- //if it does subtract their percentage from u
- if (it != t->tree[i].pcount.end()) {
- u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
+ EstOutput Myresults;
+ Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+
+ m->mothurOut("Merging results."); m->mothurOutEndLine();
+
+ //pass numSeqs to parent
+ ofstream out;
+
+ string tempFile = outputDir + toString(getpid()) + ".weighted.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);
+
+ //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]) + ".weighted.results.temp";
+ m->openInputFile(s, in);
+
+ //get quantiles
+ while (!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, "Weighted", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
+ try {
+ EstOutput results;
+ vector<double> D;
+
+ int count = 0;
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { return results; }
+
+ //initialize weighted score
+ string groupA = namesOfGroupCombos[h][0];
+ string groupB = namesOfGroupCombos[h][1];
+
+ set<int> validBranches;
+ WScore[groupA+groupB] = 0.0;
+ D.push_back(0.0000); //initialize a spot in D for each combination
+
+ //adding the wieghted sums from group i
+ for (int j = 0; j < t->groupNodeInfo[groupA].size(); j++) { //the leaf nodes that have seqs from group i
+ map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupA][j]].pcount.find(groupA);
+ int numSeqsInGroupI = it->second;
+
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groupA][j], groupA, groupB);
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groupA]);
+
+ D[count] += weightedSum;
+ }
+
+ //adding the wieghted sums from group l
+ for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l
+ map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
+ int numSeqsInGroupL = it->second;
+
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groupB][j], groupA, groupB);
+ double weightedSum = ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groupB]);
+
+ D[count] += weightedSum;
+ }
+ count++;
+ }
+
+ //calculate u for the group comb
+
+ for (int h = start; h < (start+num); h++) {
+ //report progress
+ m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
+
+ int numLeaves = t->getNumLeaves();
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
+
+ string groupA = namesOfGroupCombos[h][0];
+ string groupB = namesOfGroupCombos[h][1];
+
+ //calculate u for the group comb
+ for(int i=0;i<t->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
+ double u;
+ int pcountSize = 0;
+ //does this node have descendants from groupA
+ it = t->tree[i].pcount.find(groupA);
+ //if it does u = # of its descendants with a certain group / total number in tree with a certain group
+ if (it != t->tree[i].pcount.end()) {
+ u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
+ pcountSize++;
+ }else { u = 0.00; }
+
+
+ //does this node have descendants from group l
+ it = t->tree[i].pcount.find(groupB);
+ //if it does subtract their percentage from u
+ if (it != t->tree[i].pcount.end()) {
+ u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
+ pcountSize++;
+ }
+
+ u = abs(u * t->tree[i].getBranchLength());
+
+ nodePcountSize[i] = pcountSize;
+
+ //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;
+ WScore[(groupA+groupB)] += u;
}
-
- u = abs(u) * 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();
- //save groupcombs u value
- WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
- /*********************************************************/
+ //if yes, add your childrens tempTotals
+ if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+ WScore[(groupA+groupB)] += tempTotals[lc] + tempTotals[rc];
+ //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+ if (t->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = u;
+ }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
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc] + u;
+ }
+ //cout << "temptotal = "<< tempTotals[i] << endl;
}
}
}
-
- //calculate weighted score for each group combination
+
+ /********************************************************/
+ //calculate weighted score for the group combination
double UN;
count = 0;
- for (int i=0; i<numGroups; i++) {
- for (int l = i+1; l < numGroups; l++) {
- UN = (WScore[globaldata->Groups[i]+globaldata->Groups[l]] / D[count]);
+ for (int h = start; h < (start+num); h++) {
+ UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
- if (isnan(UN) || isinf(UN)) { UN = 0; }
- data.push_back(UN);
- count++;
- }
+ if (isnan(UN) || isinf(UN)) { UN = 0; }
+ results.push_back(UN);
+ count++;
}
- return data;
+
+ return results;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Weighted", "driver");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
-
/**************************************************************************************************/
EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
try {
data.clear(); //clear out old values
+ if (m->control_pressed) { return data; }
+
//initialize weighted score
WScore[(groupA+groupB)] = 0.0;
- float D = 0.0;
+ double D = 0.0;
+ set<int> validBranches;
-
- /********************************************************/
- //calculate a D value for the group combo
- for(int v=0;v<t->getNumLeaves();v++){
- int index = v;
- double sum = 0.0000;
-
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
-
- //if you have a BL
- if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
- }
- index = t->tree[index].getParent();
- }
-
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
- }
-
- if ((t->tree[v].getGroup() == groupA) || (t->tree[v].getGroup() == groupB)) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D += sum;
- }
+ vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
+
+ //adding the wieghted sums from group i
+ for (int j = 0; j < t->groupNodeInfo[groups[0]].size(); j++) { //the leaf nodes that have seqs from group i
+ map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[0]][j]].pcount.find(groups[0]);
+ int numSeqsInGroupI = it->second;
+
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groups[0]][j], groups[0], groups[1]);
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]);
+
+ D += weightedSum;
}
- /********************************************************/
+
+ //adding the wieghted sums from group l
+ for (int j = 0; j < t->groupNodeInfo[groups[1]].size(); j++) { //the leaf nodes that have seqs from group l
+ map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[1]][j]].pcount.find(groups[1]);
+ int numSeqsInGroupL = it->second;
+
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groups[1]][j], groups[0], groups[1]);
+ double weightedSum = ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+
+ D += weightedSum;
+ }
+
+ int numLeaves = t->getNumLeaves();
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
double u;
+ int pcountSize = 0;
//does this node have descendants from groupA
it = t->tree[i].pcount.find(groupA);
//if it does u = # of its descendants with a certain group / total number in tree with a certain group
if (it != t->tree[i].pcount.end()) {
u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
+ pcountSize++;
}else { u = 0.00; }
//if it does subtract their percentage from u
if (it != t->tree[i].pcount.end()) {
u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
+ pcountSize++;
}
- u = abs(u) * t->tree[i].getBranchLength();
-
- //save groupcombs u value
- WScore[(groupA+groupB)] += u;
+ u = abs(u * t->tree[i].getBranchLength());
+
+ nodePcountSize[i] = pcountSize;
+
+ //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;
+ WScore[(groupA+groupB)] += u;
+ }
+ 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)) {
+ WScore[(groupA+groupB)] += tempTotals[lc] + tempTotals[rc];
+ //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+ if (t->tree[i].getBranchLength() != -1) {
+ tempTotals[i] = u;
+ }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
+ tempTotals[i] = tempTotals[lc] + tempTotals[rc] + u;
+ }
+ //cout << "temptotal = "<< tempTotals[i] << endl;
+ }
}
/********************************************************/
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Weighted", "getValues");
exit(1);
}
-
}
+/**************************************************************************************************/
+double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) {
+ try {
+
+ double sum = 0.0;
+ map<int, double> tempTotals; //maps node to total Branch Length
+ map<int, int> nodePcountSize; //maps node to pcountSize
+ map<int, int>::iterator itCount;
+ int index = v;
+
+ //you are a leaf
+ if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); }
+ tempTotals[index] = 0.0;
+ index = t->tree[index].getParent();
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+ if (m->control_pressed) { return sum; }
+
+ int pcountSize = 0;
+ map<string, int>::iterator itGroup = t->tree[index].pcount.find(groupA);
+ if (itGroup != t->tree[index].pcount.end()) { pcountSize++; }
+ itGroup = t->tree[index].pcount.find(groupB);
+ if (itGroup != t->tree[index].pcount.end()) { pcountSize++; }
+
+ nodePcountSize[index] = pcountSize;
+
+ //do both your chidren have have descendants from the users groups?
+ int lc = t->tree[index].getLChild();
+ int rc = t->tree[index].getRChild();
+
+ itCount = nodePcountSize.find(lc);
+ if (itCount == nodePcountSize.end()) {
+ int LpcountSize = 0;
+ itGroup = t->tree[lc].pcount.find(groupA);
+ if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
+ itGroup = t->tree[lc].pcount.find(groupB);
+ if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
+ nodePcountSize[lc] = LpcountSize;
+ }
+
+ itCount = nodePcountSize.find(rc);
+ if (itCount == nodePcountSize.end()) {
+ int RpcountSize = 0;
+ itGroup = t->tree[rc].pcount.find(groupA);
+ if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
+ itGroup = t->tree[rc].pcount.find(groupB);
+ if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
+ nodePcountSize[rc] = RpcountSize;
+ }
+
+ //if yes, add your childrens tempTotals
+ if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+ sum += tempTotals[lc] + tempTotals[rc];
+ //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
+ if (t->tree[index].getBranchLength() != -1) {
+ tempTotals[index] = abs(t->tree[index].getBranchLength());
+ }else {
+ tempTotals[index] = 0.0;
+ }
+ }else { //if no, your tempTotal is your childrens temp totals + your branch length
+ tempTotals[index] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[index].getBranchLength());
+ }
+ //cout << "temptotal = "<< tempTotals[i] << endl;
+
+ index = t->tree[index].getParent();
+ }
-
-
+ return sum;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Weighted", "getBranchLengthSums");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff