/**************************************************************************************************/
-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;
+
+ CountTable* ct = t->getCountTable();
+
+ numGroups = m->getNumGroups();
- 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;
+ //WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
+ vector<string> groups; groups.push_back((m->getGroups())[i]); groups.push_back((m->getGroups())[l]);
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
+
+ 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, ct);
+
+ lines.clear();
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Weighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
+ try {
+ vector<int> processIDS;
+ EstOutput results;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 1;
+
+ //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);
+
+ //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();
- vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+ 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);
+ }
+
+ 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);
- D.push_back(0.0000); //initialize a spot in D for each combination
+ 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);
+ }
+#else
+
+ //fill in functions
+ vector<weightedData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<CountTable*> cts;
+ vector<Tree*> trees;
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ CountTable* copyCount = new CountTable();
+ copyCount->copy(ct);
+ Tree* copyTree = new Tree(copyCount);
+ copyTree->getCopy(t);
+
+ cts.push_back(copyCount);
+ trees.push_back(copyTree);
+
+ weightedData* tempweighted = new weightedData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount, includeRoot);
+ pDataArray.push_back(tempweighted);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyWeightedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); }
+ delete cts[i];
+ delete trees[i];
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Weighted", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
+ 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;
- /********************************************************/
- //calculate a D value for each group combo
- for(int v=0;v<t->getNumLeaves();v++){
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groupA][j], groupA, groupB);
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)ct->getGroupCount(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;
- if (m->control_pressed) { return data; }
-
- 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 += abs(t->tree[index].getBranchLength());
- }
- index = t->tree[index].getParent();
- }
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groupB][j], groupA, groupB);
+ double weightedSum = ((numSeqsInGroupL * sum) / (double)ct->getGroupCount(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();
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
+ 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) ct->getGroupCount(groupA);
+ }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) ct->getGroupCount(groupB);
+ }
+
+ if (includeRoot) {
+ if (t->tree[i].getBranchLength() != -1) {
+ u = abs(u * t->tree[i].getBranchLength());
+ WScore[(groupA+groupB)] += u;
}
-
- //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 (inUsersGroups(t->tree[v].getGroup(), groups)) {
- int numSeqsInGroupI, numSeqsInGroupL;
-
- map<string, int>::iterator it;
- it = t->tree[v].pcount.find(groups[0]);
- if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
- numSeqsInGroupI = it->second;
- }else{ numSeqsInGroupI = 0; }
-
- it = t->tree[v].pcount.find(groups[1]);
- if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
- numSeqsInGroupL = it->second;
- }else{ numSeqsInGroupL = 0; }
-
- double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
-
- //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-
- D[count] += weightedSum;
+ }else {
+ //if this is not the root then add it
+ if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) {
+ if (t->tree[i].getBranchLength() != -1) {
+ u = abs(u * t->tree[i].getBranchLength());
+ WScore[(groupA+groupB)] += u;
}
}
}
- /*********************************************************/
- count++;
}
+
}
- data.clear(); //clear out old values
-
- 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++) {
-
- if (m->control_pressed) { return data; }
-
- //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]];
- }
-
- u = abs(u * t->tree[i].getBranchLength());
-
- //save groupcombs u value
- WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
- /*********************************************************/
- }
- }
- }
-
- //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]);
-
- if (isnan(UN) || isinf(UN)) { UN = 0; }
- data.push_back(UN);
- 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; }
+ results.push_back(UN);
+ count++;
}
- return data;
+
+ return results;
}
catch(exception& e) {
- m->errorOut(e, "Weighted", "getValues");
+ m->errorOut(e, "Weighted", "driver");
exit(1);
}
}
-
/**************************************************************************************************/
EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
try {
- globaldata = GlobalData::getInstance();
data.clear(); //clear out old values
+
+ CountTable* ct = t->getCountTable();
+
+ 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;
vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
-
- /********************************************************/
- //calculate a D value for the group combo
- for(int v=0;v<t->getNumLeaves();v++){
- if (m->control_pressed) { return data; }
+
+ //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;
- int index = v;
- double sum = 0.0000;
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groups[0]][j], groups[0], groups[1]);
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)ct->getGroupCount(groups[0]));
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
-
- //if you have a BL
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
- }
- index = t->tree[index].getParent();
- }
-
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
- }
-
- if (inUsersGroups(t->tree[v].getGroup(), groups)) {
- int numSeqsInGroupI, numSeqsInGroupL;
-
- map<string, int>::iterator it;
- it = t->tree[v].pcount.find(groups[0]);
- if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
- numSeqsInGroupI = it->second;
- }else{ numSeqsInGroupI = 0; }
-
- it = t->tree[v].pcount.find(groups[1]);
- if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
- numSeqsInGroupL = it->second;
- }else{ numSeqsInGroupL = 0; }
-
- double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
-
- //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-
- D += weightedSum;
- }
+ 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)ct->getGroupCount(groups[1]));
+
+ D += weightedSum;
+ }
+
//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];
+ u = (double) t->tree[i].pcount[groupA] / (double) ct->getGroupCount(groupA);
}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];
+ u -= (double) t->tree[i].pcount[groupB] / (double) ct->getGroupCount(groupB);
}
-
- u = abs(u * t->tree[i].getBranchLength());
-
- //save groupcombs u value
- WScore[(groupA+groupB)] += u;
- }
-
+
+ if (includeRoot) {
+ if (t->tree[i].getBranchLength() != -1) {
+ u = abs(u * t->tree[i].getBranchLength());
+ WScore[(groupA+groupB)] += u;
+ }
+ }else{
+ //if this is not the root then add it
+ if (rootForGrouping[groups].count(i) == 0) {
+ if (t->tree[i].getBranchLength() != -1) {
+ u = abs(u * t->tree[i].getBranchLength());
+ WScore[(groupA+groupB)] += u;
+ }
+ }
+ }
+ }
/********************************************************/
-
+
//calculate weighted score for the group combination
double UN;
UN = (WScore[(groupA+groupB)] / D);
exit(1);
}
}
+/**************************************************************************************************/
+double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) {
+ try {
+
+ double sum = 0.0;
+ int index = v;
+
+ //you are a leaf
+ if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); }
+ double tempTotal = 0.0;
+ index = t->tree[index].getParent();
+
+ vector<string> grouping; grouping.push_back(groupA); grouping.push_back(groupB);
+
+ rootForGrouping[grouping].insert(index);
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
-
-
-
-
-
-
+ if (m->control_pressed) { return sum; }
+
+ int parent = t->tree[index].getParent();
+
+ if (includeRoot) { //add everyone
+ if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); }
+ }else {
+
+ //am I the root for this grouping? if so I want to stop "early"
+ //does my sibling have descendants from the users groups?
+ 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;
+ itGroup = t->tree[sib].pcount.find(groupA);
+ if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; }
+ itGroup = t->tree[sib].pcount.find(groupB);
+ if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; }
+
+ //if yes, I am not the root so add me
+ if (pcountSize != 0) {
+ if (t->tree[index].getBranchLength() != -1) {
+ sum += abs(t->tree[index].getBranchLength()) + tempTotal;
+ tempTotal = 0.0;
+ }else {
+ sum += tempTotal;
+ tempTotal = 0.0;
+ }
+ rootForGrouping[grouping].clear();
+ rootForGrouping[grouping].insert(parent);
+ }else { //if no, I may be the root so add my br to tempTotal until I am proven innocent
+ if (t->tree[index].getBranchLength() != -1) {
+ tempTotal += abs(t->tree[index].getBranchLength());
+ }
+ }
+ }
+
+ 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);
+ index = parent;
+ }
+ return sum;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Weighted", "getBranchLengthSums");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff